bedops →
2.4.39+dfsg1-2 →
armhf → 2021-03-01 06:13:15
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| bedops 2.4.39+dfsg1-2 (armhf) Mon, 01 Mar 2021 05:41:15 +0000 |
+==============================================================================+
Package: bedops
Version: 2.4.39+dfsg1-2
Source Version: 2.4.39+dfsg1-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bullseye-staging-armhf-sbuild-d086f3c6-04a9-416f-8ce7-b5d9d5fa5c3a' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/bedops-U8U9IV/resolver-FmaEYl' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [12.2 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.2 MB]
Fetched 25.4 MB in 14s (1815 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'bedops' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/bedops.git
Please use:
git clone https://salsa.debian.org/med-team/bedops.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 13.5 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main bedops 2.4.39+dfsg1-2 (dsc) [2185 B]
Get:2 http://172.17.0.1/private bullseye-staging/main bedops 2.4.39+dfsg1-2 (tar) [13.4 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main bedops 2.4.39+dfsg1-2 (diff) [11.1 kB]
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Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bedops-U8U9IV/bedops-2.4.39+dfsg1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bedops-U8U9IV' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), help2man, libbz2-dev, libjansson-dev, python3-distutils, zlib1g-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 12), help2man, libbz2-dev, libjansson-dev, python3-distutils, zlib1g-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
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Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
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Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libbz2-dev
libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
libicu67 libjansson-dev libjansson4 libmagic-mgc libmagic1 libmpdec3
libpipeline1 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib
libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
media-types po-debconf python3 python3-distutils python3-lib2to3
python3-minimal python3.9 python3.9-minimal sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv python3.9-venv
python3.9-doc binfmt-support
Recommended packages:
curl | wget | lynx bzip2-doc libarchive-cpio-perl ca-certificates
libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libbz2-dev
libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
libicu67 libjansson-dev libjansson4 libmagic-mgc libmagic1 libmpdec3
libpipeline1 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib
libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
media-types po-debconf python3 python3-distutils python3-lib2to3
python3-minimal python3.9 python3.9-minimal sbuild-build-depends-main-dummy
sensible-utils zlib1g-dev
0 upgraded, 49 newly installed, 0 to remove and 44 not upgraded.
Need to get 23.0 MB of archives.
After this operation, 86.1 MB of additional disk space will be used.
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Get:2 http://172.17.0.1/private bullseye-staging/main armhf bsdextrautils armhf 2.36.1-7 [137 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.4-1 [1307 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-minimal armhf 3.9.1-4+rpi1 [790 kB]
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Get:9 http://172.17.0.1/private bullseye-staging/main armhf python3.9-minimal armhf 3.9.1-4+rpi1 [1625 kB]
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Get:17 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.14 [14.8 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3.3 [189 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.11.0-1 [15.3 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.183-1 [161 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13+20210201-1 [164 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-6 [8289 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3.3 [1011 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf help2man armhf 1.48.1 [190 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-4 [28.0 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libjansson4 armhf 2.13.1-1.1 [36.2 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libjansson-dev armhf 2.13.1-1.1 [37.0 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.9.1-2 [77.2 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.9.1-2 [143 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
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Setting up python3.9 (3.9.1-4+rpi1) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up po-debconf (1.0.21+nmu1) ...
Setting up python3 (3.9.1-1) ...
Setting up man-db (2.9.4-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up python3-lib2to3 (3.9.1-2) ...
Setting up python3-distutils (3.9.1-2) ...
Setting up debhelper (13.3.3) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-9+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.35.1-7+rpi1 dpkg-dev_1.20.7.1+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-9+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.9-1+rpi1
Package versions: adduser_3.118 apt_2.1.18 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1-2 binutils_2.35.1-7+rpi1 binutils-arm-linux-gnueabihf_2.35.1-7+rpi1 binutils-common_2.35.1-7+rpi1 bsdextrautils_2.36.1-7 bsdutils_1:2.36.1-6 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.74 debhelper_13.3.3 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.11.0-1 diffutils_1:3.7-5 dirmngr_2.2.20-1 dpkg_1.20.7.1+rpi1 dpkg-dev_1.20.7.1+rpi1 dwz_0.13+20210201-1 e2fsprogs_1.45.7-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-6+rpi1 gcc-9-base_9.3.0-20+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-2 help2man_1.48.1 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10 libapt-pkg6.0_2.1.18 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.1-7+rpi1 libblkid1_2.36.1-6 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.31-9+rpi1 libc-dev-bin_2.31-9+rpi1 libc6_2.31-9+rpi1 libc6-dev_2.31-9+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.45.7-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-7+rpi1 libctf0_2.35.1-7+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.256 libdebhelper-perl_13.3.3 libdpkg-perl_1.20.7.1+rpi1 libelf1_0.183-1 libexpat1_2.2.10-1 libext2fs2_1.45.7-1 libfakeroot_1.25.3-1.1 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.11.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.0-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-4 libhogweed6_3.6-2 libicu67_67.1-6 libidn2-0_2.3.0-5 libisl23_0.23-1 libjansson-dev_2.13.1-1.1 libjansson4_2.13.1-1.1 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 libksba8_1.5.0-3 libldap-2.4-2_2.4.57+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-1+rpi1 liblzma5_5.2.5-1.0 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-6 libmpc3_1.2.0-1 libmpdec3_2.5.1-1+rpi1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-2 libnettle8_3.6-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.22-1 libpam-modules_1.4.0-2 libpam-modules-bin_1.4.0-2 libpam-runtime_1.4.0-2 libpam0g_1.4.0-2 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-2 libpipeline1_1.5.3-1 libpython3-stdlib_3.9.1-1 libpython3.9-minimal_3.9.1-4+rpi1 libpython3.9-stdlib_3.9.1-4+rpi1 libreadline8_8.1-1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-2+b1 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.36.1-6 libsqlite3-0_3.34.1-1 libss2_1.45.7-1 libssl1.1_1.1.1i-3 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.2-5+rpi1 libtasn1-6_4.16.0-2 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.2-5+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-6 libxml2_2.9.10+dfsg-6.3 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-1 linux-libc-dev_5.10.9-1+rpi1 login_1:4.8.1-1 logsave_1.45.7-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4 man-db_2.9.4-1 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.36.1-6 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-2 perl-base_5.32.1-2 perl-modules-5.32_5.32.1-2 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 python3_3.9.1-1 python3-distutils_3.9.1-2 python3-lib2to3_3.9.1-2 python3-minimal_3.9.1-1 python3.9_3.9.1-4+rpi1 python3.9-minimal_3.9.1-4+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 sysvinit-utils_2.96-5 tar_1.32+dfsg-1+rpi1 tzdata_2021a-1 util-linux_2.36.1-6 xz-utils_5.2.5-1.0 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: bedops
Binary: bedops, bedops-doc
Architecture: any all
Version: 2.4.39+dfsg1-2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Olivier Sallou <osallou@debian.org>
Homepage: https://github.com/bedops/bedops
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/bedops
Vcs-Git: https://salsa.debian.org/med-team/bedops.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 12), help2man, libbz2-dev, libjansson-dev, python3-distutils, zlib1g-dev
Build-Depends-Indep: sphinx-common, libjs-mathjax, python3-sphinx
Package-List:
bedops deb science optional arch=any
bedops-doc deb doc optional arch=all
Checksums-Sha1:
4d9474ee3486ac33679866b87651884b45d0ab91 13440720 bedops_2.4.39+dfsg1.orig.tar.xz
37fa86e7d27c344eee083190d132240709a5cd63 11072 bedops_2.4.39+dfsg1-2.debian.tar.xz
Checksums-Sha256:
550fe1473e93f406b577b9cdf097fb919e32349741e03a2741563ef45946e788 13440720 bedops_2.4.39+dfsg1.orig.tar.xz
1501befb37a66ff2295884995200251bf88d9207df806147313bada8fa792872 11072 bedops_2.4.39+dfsg1-2.debian.tar.xz
Files:
a3df3c35bd857999eb0e5b68c4f8f078 13440720 bedops_2.4.39+dfsg1.orig.tar.xz
0136d1fbffd563982a994c0228d28641 11072 bedops_2.4.39+dfsg1-2.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.u8H3eaYj/trustedkeys.kbx': General error
gpgv: Signature made Fri Feb 19 13:34:11 2021 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./bedops_2.4.39+dfsg1-2.dsc
dpkg-source: info: extracting bedops in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking bedops_2.4.39+dfsg1.orig.tar.xz
dpkg-source: info: unpacking bedops_2.4.39+dfsg1-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying tests_use_installed_binaries.patch
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying use_debian_libs
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying parallel.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/build/buildd
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-d086f3c6-04a9-416f-8ce7-b5d9d5fa5c3a
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c141533
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package bedops
dpkg-buildpackage: info: source version 2.4.39+dfsg1-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
make -j4 clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make clean -f system.mk/Makefile.linux
make[3]: Entering directory '/<<PKGBUILDDIR>>'
rm -rf bin
rm -rf bin
rm -rf bin
make -C applications/bed/bedmap/src -f Makefile clean
make -C applications/bed/sort-bed/src -f Makefile clean
rm -rf modules
make -C applications/bed/bedops/src -f Makefile clean
make -C applications/bed/closestfeats/src -f Makefile clean
make[4]: Entering directory '/<<PKGBUILDDIR>>/applications/bed/sort-bed/src'
make[4]: Entering directory '/<<PKGBUILDDIR>>/applications/bed/bedmap/src'
rm -rf objects_typical
make[4]: Entering directory '/<<PKGBUILDDIR>>/applications/bed/bedops/src'
rm -rf objects_typical
rm -rf ../bin
make[4]: Entering directory '/<<PKGBUILDDIR>>/applications/bed/closestfeats/src'
rm -rf objects-typical
rm -rf objects_typical
rm -rf ../bin
make[4]: Leaving directory '/<<PKGBUILDDIR>>/applications/bed/bedmap/src'
make -C applications/bed/bedextract/src -f Makefile clean
rm -rf ../bin
rm -rf ../bin
make[4]: Leaving directory '/<<PKGBUILDDIR>>/applications/bed/bedops/src'
make -C applications/bed/starch/src -f Makefile clean
make[4]: Leaving directory '/<<PKGBUILDDIR>>/applications/bed/sort-bed/src'
make -C applications/bed/conversion/src -f Makefile clean
make[4]: Entering directory '/<<PKGBUILDDIR>>/applications/bed/bedextract/src'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/applications/bed/closestfeats/src'
rm -rf objects_typical
rm -rf ../bin
make[4]: Entering directory '/<<PKGBUILDDIR>>/applications/bed/starch/src'
make[4]: Entering directory '/<<PKGBUILDDIR>>/applications/bed/conversion/src'
rm -rf ../bin
rm -rf ../lib
rm -f ../lib/libstarch_debug.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/applications/bed/bedextract/src'
rm -rf objects
rm -f ../lib/libstarch_gprof.a
rm -rf *.so *~
rm -rf objects
make[4]: Leaving directory '/<<PKGBUILDDIR>>/applications/bed/conversion/src'
rm -rf ../bin
make[4]: Leaving directory '/<<PKGBUILDDIR>>/applications/bed/starch/src'
rm -rf third-party/bzip2-1.0.6
rm -f third-party/bzip2
rm -rf third-party/jansson-2.6
rm -f third-party/jansson
rm -rf third-party/zlib-1.2.7
rm -f third-party/zlib
rm -rf bin
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -rf docs/_build/
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
dh_auto_build -a
make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make -f system.mk/Makefile.linux
make[2]: Entering directory '/<<PKGBUILDDIR>>'
#bzcat | tar -x -C third-party
#cd third-party/jansson-2.6 && ./configure --prefix=/<<PKGBUILDDIR>>/third-party/jansson-2.6 && make && make install && cd /<<PKGBUILDDIR>> && rm -f jansson && ln -sf jansson-2.6 third-party/jansson
#bzcat | tar -x -C third-party
#cd third-party/bzip2-1.0.6 && make libbz2.a && cd /<<PKGBUILDDIR>> && rm -f bzip2 && ln -sf bzip2-1.0.6 third-party/bzip2
#bzcat | tar -x -C third-party
#cd third-party/zlib-1.2.7 && ./configure --static && make && cd /<<PKGBUILDDIR>> && rm -f zlib && ln -sf zlib-1.2.7 third-party/zlib
make build -f /<<PKGBUILDDIR>>/system.mk/Makefile.linux
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make -C applications/bed/bedmap/src -f Makefile build
make -C applications/bed/sort-bed/src -f Makefile build
make -C applications/bed/bedops/src -f Makefile build
make -C applications/bed/closestfeats/src -f Makefile build
make[4]: Entering directory '/<<PKGBUILDDIR>>/applications/bed/sort-bed/src'
make[4]: Entering directory '/<<PKGBUILDDIR>>/applications/bed/bedmap/src'
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers
make[4]: Entering directory '/<<PKGBUILDDIR>>/applications/bed/bedops/src'
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers
make[4]: Entering directory '/<<PKGBUILDDIR>>/applications/bed/closestfeats/src'
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchConstants.c -o objects-typical/starchConstants.o -iquote../../../../interfaces/general-headers
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects-typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchHelpers.c -o objects-typical/starchHelpers.o -iquote../../../../interfaces/general-headers
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow]
2171 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow]
2908 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow]
3434 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow]
4202 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~^~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’:
../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncat(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow]
2171 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow]
2171 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow]
2908 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow]
2908 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow]
2171 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow]
3434 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow]
3434 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow]
2908 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow]
4202 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow]
4202 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow]
3434 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow]
4202 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncat(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~^~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~^~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~^~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’:
../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’:
../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’:
../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncat(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncat(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncat(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncat(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncat(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncat(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects-typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_JSONMetadataExists(FILE**, const char*)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1096:20: warning: comparison is always true due to limited range of data type [-Wtype-limits]
1096 | } while (currC != EOF);
| ^
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1097:63: warning: comparison is always false due to limited range of data type [-Wtype-limits]
1097 | if ((nReadBytes == STARCH_LEGACY_METADATA_SIZE) || (currC == EOF)) {
| ^
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1313:24: warning: comparison is always true due to limited range of data type [-Wtype-limits]
1313 | } while (currC != EOF);
| ^
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~^~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~^~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here
2228 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here
2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here
2256 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here
1684 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here
1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~^~~~~~~~~~~~~
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~^~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~^~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~^~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~^~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~^~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~^~~~~~~~~~~
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects-typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘void starch::UNSTARCH_printMetadataSignature(const unsigned char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:2276:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2276 | static_cast<const size_t>( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:2278:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2278 | static_cast<const size_t>( mdSha1BufferLength ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:2640:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2640 | static_cast<const size_t>( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:2642:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2642 | static_cast<const size_t>( STARCH2_MD_FOOTER_SHA1_LENGTH ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here
2228 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here
2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here
2256 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here
2228 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here
2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here
2256 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here
2228 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here
2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here
2256 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here
1684 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here
1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~^~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here
1684 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here
1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~^~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here
1684 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here
1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~^~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here
2559 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects-typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here
2559 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here
2559 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here
2559 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects-typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security SortDetails.cpp -o objects-typical/SortDetails.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers
mkdir -p ../bin && g++ -o ../bin/closest-features-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 ClosestFeature.cpp
mkdir -p ../bin && g++ -o ../bin/bedops-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 Bedops.cpp
mkdir -p ../bin && g++ -o ../bin/bedmap-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 Bedmap.cpp
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from SortDetails.cpp:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘ChromBedData* initializeChromBedData(char*, double*)’ at SortDetails.cpp:250:12:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SortDetails.cpp: In function ‘ChromBedData* initializeChromBedData(char*, double*)’:
SortDetails.cpp:249:25: note: length computed here
249 | chromBufLen = strlen(chromBuf); // we know >= 1
| ~~~~~~^~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from SortDetails.cpp:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void lexSortBedData(BedData*)’ at SortDetails.cpp:1343:20:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SortDetails.cpp: In function ‘void lexSortBedData(BedData*)’:
SortDetails.cpp:1342:33: note: length computed here
1342 | chromBufLen = strlen(beds->chroms[i]->chromName); // we know >= 1
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security Sort.cpp -o objects-typical/Sort.o -iquote../../../../interfaces/general-headers
mkdir -p objects-typical && g++ -c -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security CheckSort.cpp -o objects-typical/CheckSort.o -iquote../../../../interfaces/general-headers
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::listJSONMetadata(FILE*, FILE*)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1226:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1226 | static_cast<const CompressionType>( getArchiveType() ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1230:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1230 | static_cast<const Boolean>( getArchiveHeaderFlag() ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1231:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1231 | static_cast<const Boolean>( getArchiveShowNewlineFlag() ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractAllData(const string&, FILE*)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:2003:51: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2003 | static_cast<const Boolean>( getArchiveHeaderFlag() )) != 0 ) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/data/starch/starchApi.hpp:2014:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2014 | static_cast<const Boolean>( getArchiveHeaderFlag() )) != 0 ) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp: In instantiation of ‘Bed::bed_check_iterator<BedType*, Sz> Bed::bed_check_iterator<BedType*, Sz>::operator++(int) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]’:
CheckSort.cpp:51:28: required from here
../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:268:12: warning: implicitly-declared ‘Bed::bed_check_iterator<Bed::BasicCoords<true, true>*, 16>::bed_check_iterator(const Bed::bed_check_iterator<Bed::BasicCoords<true, true>*, 16>&)’ is deprecated [-Wdeprecated-copy]
268 | auto __tmp = *this;
| ^~~~~
../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:308:10: note: because ‘Bed::bed_check_iterator<Bed::BasicCoords<true, true>*, 16>’ has user-provided ‘bool Bed::bed_check_iterator<BedType*, Sz>::operator=(const Bed::bed_check_iterator<BedType*, Sz>&) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]’
308 | bool operator=(const bed_check_iterator& b);
| ^~~~~~~~
../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:295:14: warning: implicitly-declared ‘Bed::bed_check_iterator<Bed::BasicCoords<true, true>*, 16>::bed_check_iterator(const Bed::bed_check_iterator<Bed::BasicCoords<true, true>*, 16>&)’ is deprecated [-Wdeprecated-copy]
295 | return __tmp;
| ^~~~~
../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:308:10: note: because ‘Bed::bed_check_iterator<Bed::BasicCoords<true, true>*, 16>’ has user-provided ‘bool Bed::bed_check_iterator<BedType*, Sz>::operator=(const Bed::bed_check_iterator<BedType*, Sz>&) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]’
308 | bool operator=(const bed_check_iterator& b);
| ^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here
541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here
551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1);
| ~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here
556 | std::strncpy(_recFilename, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::Starch::zReadLine()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here
1913 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1521:82:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1712:86:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1758:40:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1769:45:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1576:86:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1620:40:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1628:45:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentRemainder(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here
899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27,
from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here
541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27,
from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here
551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1);
| ~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27,
from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here
556 | std::strncpy(_recFilename, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27,
from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::Starch::zReadLine()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here
1913 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27,
from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1521:82:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27,
from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1712:86:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27,
from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1758:40:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27,
from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1769:45:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27,
from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1576:86:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27,
from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1620:40:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27,
from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1628:45:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27,
from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentRemainder(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here
899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27,
from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27,
from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27,
from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from Bedops.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here
541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from Bedops.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here
551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1);
| ~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from Bedops.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here
556 | std::strncpy(_recFilename, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from Bedops.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘const char* starch::Starch::getCurrentChromosome()’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27,
from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘Bed::bed_check_iterator<BedType*, Sz>::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory<BedType, SZ>&, const string&, bool) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::bed_check_iterator<BedType*, Sz>::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory<BedType, SZ>&, const string&, bool) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from Bedops.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::Starch::zReadLine()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here
1913 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from Bedops.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1769:45:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from Bedops.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1628:45:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from Bedops.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentRemainder(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here
899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from Bedops.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from Bedops.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from Bedops.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedCompare.hpp:27,
from ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:32,
from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:41,
from CheckSort.cpp:28:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘Bed::bed_check_iterator<BedType*, Sz> Bed::bed_check_iterator<BedType*, Sz>::operator++(int) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36,
inlined from ‘int checkSort(const char**, unsigned int)’ at CheckSort.cpp:51:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from CheckSort.cpp:28:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function ‘int checkSort(const char**, unsigned int)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
mkdir -p ../bin && cp update-sort-bed-slurm.py ../bin/update-sort-bed-slurm-typical
mkdir -p ../bin && cp update-sort-bed-starch-slurm.py ../bin/update-sort-bed-starch-slurm-typical
mkdir -p ../bin && cp update-sort-bed-migrate-candidates.py ../bin/update-sort-bed-migrate-candidates-typical
mkdir -p ../bin && g++ -o ../bin/sort-bed-typical -s -Wall -Wextra -pedantic -ansi -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now objects-typical/starchConstants.o objects-typical/starchFileHelpers.o objects-typical/starchHelpers.o objects-typical/starchMetadataHelpers.o objects-typical/unstarchHelpers.o objects-typical/starchSha1Digest.o objects-typical/starchBase64Coding.o objects-typical/SortDetails.o objects-typical/Sort.o objects-typical/CheckSort.o -ljansson -lz -lbz2
rm -rf objects-typical
make[4]: Leaving directory '/<<PKGBUILDDIR>>/applications/bed/sort-bed/src'
make -C applications/bed/bedextract/src -f Makefile build
make[4]: Entering directory '/<<PKGBUILDDIR>>/applications/bed/bedextract/src'
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/measurement/NaN.cpp -o objects_typical/NaN.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchConstants.c -o objects_typical/starchConstants.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects_typical/starchFileHelpers.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchHelpers.c -o objects_typical/starchHelpers.o -iquote../../../../interfaces/general-headers
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow]
2171 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow]
2908 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow]
3434 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow]
4202 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~^~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’:
../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncat(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncat(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects_typical/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~^~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~^~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here
2228 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here
2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here
2256 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here
1684 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here
1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~^~~~~~~~~~~~~
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects_typical/unstarchHelpers.o -iquote../../../../interfaces/general-headers
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here
2559 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects_typical/starchSha1Digest.o -iquote../../../../interfaces/general-headers
mkdir -p objects_typical && g++ -c -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers
mkdir -p ../bin && g++ -o ../bin/bedextract-typical -s -Wall -pedantic -O3 -std=c++11 -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security objects_typical/NaN.o objects_typical/starchConstants.o objects_typical/starchFileHelpers.o objects_typical/starchHelpers.o objects_typical/starchMetadataHelpers.o objects_typical/unstarchHelpers.o objects_typical/starchSha1Digest.o objects_typical/starchBase64Coding.o -iquote../../../../interfaces/general-headers -Wl,-z,relro -Wl,-z,now -ljansson -lz -lbz2 ExtractRows.cpp
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ExtractRows.cpp:27:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here
541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ExtractRows.cpp:27:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here
551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1);
| ~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ExtractRows.cpp:27:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here
556 | std::strncpy(_recFilename, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ExtractRows.cpp:27:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::Starch::zReadLine()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here
1913 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ExtractRows.cpp:27:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1521:82:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ExtractRows.cpp:27:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1712:86:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ExtractRows.cpp:27:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1758:40:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ExtractRows.cpp:27:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1769:45:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ExtractRows.cpp:27:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1576:86:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ExtractRows.cpp:27:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1620:40:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ExtractRows.cpp:27:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1628:45:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ExtractRows.cpp:27:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentRemainder(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here
899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ExtractRows.cpp:27:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ExtractRows.cpp:27:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ExtractRows.cpp:27:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1507:22:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/c++/10/map:60,
from ExtractRows.cpp:33:
/usr/include/c++/10/bits/stl_tree.h: In member function ‘void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = Bed::BasicCoords<true, true>; _Val = std::pair<const Bed::BasicCoords<true, true>, long long int>; _KeyOfValue = std::_Select1st<std::pair<const Bed::BasicCoords<true, true>, long long int> >; _Compare = Bed::extract_details::CompBed<Bed::BasicCoords<true, true> >; _Alloc = std::allocator<std::pair<const Bed::BasicCoords<true, true>, long long int> >]’:
/usr/include/c++/10/bits/stl_tree.h:2524:5: note: parameter passing for argument of type ‘std::_Rb_tree<Bed::BasicCoords<true, true>, std::pair<const Bed::BasicCoords<true, true>, long long int>, std::_Select1st<std::pair<const Bed::BasicCoords<true, true>, long long int> >, Bed::extract_details::CompBed<Bed::BasicCoords<true, true> >, std::allocator<std::pair<const Bed::BasicCoords<true, true>, long long int> > >::const_iterator’ changed in GCC 7.1
2524 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h:2524:5: note: parameter passing for argument of type ‘std::_Rb_tree<Bed::BasicCoords<true, true>, std::pair<const Bed::BasicCoords<true, true>, long long int>, std::_Select1st<std::pair<const Bed::BasicCoords<true, true>, long long int> >, Bed::extract_details::CompBed<Bed::BasicCoords<true, true> >, std::allocator<std::pair<const Bed::BasicCoords<true, true>, long long int> > >::const_iterator’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_tree.h: In function ‘std::pair<bool, long long int> Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = __gnu_cxx::__normal_iterator<Bed::BasicCoords<true, true>**, std::vector<Bed::BasicCoords<true, true>*> >; Op = {anonymous}::Cache<Bed::BasicCoords<true, true> >]’:
/usr/include/c++/10/bits/stl_tree.h:1245:14: note: parameter passing for argument of type ‘std::_Rb_tree<Bed::BasicCoords<true, true>, std::pair<const Bed::BasicCoords<true, true>, long long int>, std::_Select1st<std::pair<const Bed::BasicCoords<true, true>, long long int> >, Bed::extract_details::CompBed<Bed::BasicCoords<true, true> >, std::allocator<std::pair<const Bed::BasicCoords<true, true>, long long int> > >::const_iterator’ changed in GCC 7.1
1245 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h: In function ‘std::pair<bool, long long int> Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = __gnu_cxx::__normal_iterator<Bed::BasicCoords<true, true>**, std::vector<Bed::BasicCoords<true, true>*> >; Op = Visitors::BedHelpers::Println]’:
/usr/include/c++/10/bits/stl_tree.h:1245:14: note: parameter passing for argument of type ‘std::_Rb_tree<Bed::BasicCoords<true, true>, std::pair<const Bed::BasicCoords<true, true>, long long int>, std::_Select1st<std::pair<const Bed::BasicCoords<true, true>, long long int> >, Bed::extract_details::CompBed<Bed::BasicCoords<true, true> >, std::allocator<std::pair<const Bed::BasicCoords<true, true>, long long int> > >::const_iterator’ changed in GCC 7.1
1245 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ExtractRows.cpp:27:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘Bed::bed_check_iterator<BedType*, Sz>::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory<BedType, SZ>&, const string&, bool) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::bed_check_iterator<BedType*, Sz>::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory<BedType, SZ>&, const string&, bool) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/c++/10/map:60,
from ExtractRows.cpp:33:
/usr/include/c++/10/bits/stl_tree.h:1245:14: note: parameter passing for argument of type ‘std::_Rb_tree<Bed::BasicCoords<true, true>, std::pair<const Bed::BasicCoords<true, true>, long long int>, std::_Select1st<std::pair<const Bed::BasicCoords<true, true>, long long int> >, Bed::extract_details::CompBed<Bed::BasicCoords<true, true> >, std::allocator<std::pair<const Bed::BasicCoords<true, true>, long long int> > >::const_iterator’ changed in GCC 7.1
1245 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘Bed::bed_check_iterator<BedType*, Sz>::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory<BedType, SZ>&, const string&, bool) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:136:36:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::bed_check_iterator<BedType*, Sz>::bed_check_iterator(std::istream&, const string&, Ext::PooledMemory<BedType, SZ>&, const string&, bool) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 512]’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ExtractRows.cpp:27:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘Bed::bed_check_iterator<BedType*, Sz> Bed::bed_check_iterator<BedType*, Sz>::operator++(int) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 16]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36,
inlined from ‘std::pair<bool, long long int> Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = Bed::bed_check_iterator<Bed::BasicCoords<true, true>*, 16>; Op = Visitors::BedHelpers::Println]’ at ../../../../interfaces/general-headers/algorithm/bed/FindBedRange.hpp:102:64:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:44,
from ExtractRows.cpp:43:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function ‘std::pair<bool, long long int> Bed::find_bed_range(FILE*, TargetIter, TargetIter, Op) [with TargetIter = Bed::bed_check_iterator<Bed::BasicCoords<true, true>*, 16>; Op = Visitors::BedHelpers::Println]’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/c++/10/map:60,
from ExtractRows.cpp:33:
/usr/include/c++/10/bits/stl_tree.h:1245:14: note: parameter passing for argument of type ‘std::_Rb_tree<Bed::BasicCoords<true, true>, std::pair<const Bed::BasicCoords<true, true>, long long int>, std::_Select1st<std::pair<const Bed::BasicCoords<true, true>, long long int> >, Bed::extract_details::CompBed<Bed::BasicCoords<true, true> >, std::allocator<std::pair<const Bed::BasicCoords<true, true>, long long int> > >::const_iterator’ changed in GCC 7.1
1245 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘Bed::bed_check_iterator<BedType*, Sz> Bed::bed_check_iterator<BedType*, Sz>::operator++(int) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/BedCheckIterator.hpp:292:36,
inlined from ‘FeatDist::BedReader<IterType>::BedType* FeatDist::BedReader<IterType>::ReadLine() [with IterType = Bed::bed_check_iterator<Bed::BasicCoords<true, true>*, 512>]’ at BedReader.hpp:78:19:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘FeatDist::BedReader<IterType>::BedType* FeatDist::BedReader<IterType>::ReadLine() [with IterType = Bed::bed_check_iterator<Bed::BasicCoords<true, true>*, 512>]’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘Bed::allocate_iterator_starch_bed<BedType*, SZ>::allocate_iterator_starch_bed(Ext::FPWrap<ErrorType>&, Ext::PooledMemory<BedType, SZ>&, const string&) [with ErrorType = Ext::Exception<Ext::Exception<std::exception, 0>, 0>; BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:117:36:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In constructor ‘Bed::allocate_iterator_starch_bed<BedType*, SZ>::allocate_iterator_starch_bed(Ext::FPWrap<ErrorType>&, Ext::PooledMemory<BedType, SZ>&, const string&) [with ErrorType = Ext::Exception<Ext::Exception<std::exception, 0>, 0>; BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 512]’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ClosestFeature.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘Bed::allocate_iterator_starch_bed<BedType*, SZ> Bed::allocate_iterator_starch_bed<BedType*, SZ>::operator++(int) [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:207:36,
inlined from ‘FeatDist::BedReader<IterType>::BedType* FeatDist::BedReader<IterType>::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, true>*, 512>]’ at BedReader.hpp:78:19:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from ClosestFeature.cpp:38:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘FeatDist::BedReader<IterType>::BedType* FeatDist::BedReader<IterType>::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, true>*, 512>]’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
rm -rf objects_typical
make[4]: Leaving directory '/<<PKGBUILDDIR>>/applications/bed/bedextract/src'
make -C applications/bed/starch/src -f Makefile build
make[4]: Entering directory '/<<PKGBUILDDIR>>/applications/bed/starch/src'
mkdir -p objects
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchConstants.c -o objects/starchConstants.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p objects
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/unstarchHelpers.c -o objects/unstarchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../..
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘void starch::UNSTARCH_printMetadataSignature(const unsigned char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:2276:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2276 | static_cast<const size_t>( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:2278:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2278 | static_cast<const size_t>( mdSha1BufferLength ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:2640:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2640 | static_cast<const size_t>( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c:2642:33: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2642 | static_cast<const size_t>( STARCH2_MD_FOOTER_SHA1_LENGTH ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1651:83: note: length computed here
1651 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1678:75: note: length computed here
1678 | strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_createInverseTransformTokens(const unsigned char*, char, char*, char*)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:1667:75: note: length computed here
1667 | strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘int starch::UNSTARCH_extractDataWithGzip(FILE**, FILE*, const char*, const Metadata*, uint64_t, starch::Boolean)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:200:32: note: length computed here
200 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/unstarchHelpers.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’ at ../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/unstarchHelpers.c: In function ‘char* starch::UNSTARCH_observedSignatureForChromosome(FILE**, const Metadata*, uint64_t, const char*, starch::CompressionType)’:
../../../../interfaces/src/data/starch/unstarchHelpers.c:2559:40: note: length computed here
2559 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mkdir -p objects
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchHelpers.c -o objects/starchHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../..
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2171:88: warning: left shift count >= width of type [-Wshift-count-overflow]
2171 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:2908:68: warning: left shift count >= width of type [-Wshift-count-overflow]
2908 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:3434:88: warning: left shift count >= width of type [-Wshift-count-overflow]
3434 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../../../../interfaces/src/data/starch/starchHelpers.c:4202:68: warning: left shift count >= width of type [-Wshift-count-overflow]
4202 | bzBytesWritten = static_cast<size_t>( bzBytesWrittenHi32 ) << 32 | bzBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:359:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:359:87: note: length computed here
359 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:383:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:383:48: note: length computed here
383 | strncpy(*chr, s, strlen(s) + 1);
| ~~~~~~^~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:485:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokens(const char*, char, char**, int64_t*, int64_t*, char**, starch::BedLineType*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:485:77: note: length computed here
485 | strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:560:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_createTransformTokensForHeaderlessInput(const char*, char, char**, int64_t*, int64_t*, char**)’:
../../../../interfaces/src/data/starch/starchHelpers.c:560:83: note: length computed here
560 | strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:923:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:923:97: note: length computed here
923 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncat(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:964:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:964:98: note: length computed here
964 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:1411:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH_transformHeaderlessInput(starch::Metadata**, const FILE*, starch::CompressionType, const char*, starch::Boolean, const char*)’:
../../../../interfaces/src/data/starch/starchHelpers.c:1411:97: note: length computed here
1411 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2416:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2416:97: note: length computed here
2416 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncat(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:2464:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:34: warning: ‘char* __builtin___strncat_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderedBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:2464:98: note: length computed here
2464 | strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
rm -rf objects_typical
make[4]: Leaving directory '/<<PKGBUILDDIR>>/applications/bed/closestfeats/src'
make -C applications/bed/conversion/src -f Makefile build
make[4]: Entering directory '/<<PKGBUILDDIR>>/applications/bed/conversion/src'
mkdir -p ../bin && gcc -Wall -Wextra -pedantic -std=c99 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -iquote"/<<PKGBUILDDIR>>/applications/bed/conversion/src" -iquote"../../../../interfaces/general-headers" -Wl,-z,relro -Wl,-z,now convert2bed.c -o ../bin/convert2bed-typical -lpthread
convert2bed.c: In function ‘c2b_process_intermediate_bytes_by_lines’:
convert2bed.c:6315:103: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 3 has type ‘long unsigned int’ [-Wformat=]
6315 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| unsigned int long unsigned int
| %lu
convert2bed.c:6315:109: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 4 has type ‘long unsigned int’ [-Wformat=]
6315 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| unsigned int long unsigned int
| %lu
convert2bed.c:6315:115: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘long unsigned int’ [-Wformat=]
6315 | fprintf(stderr, "Error: Could not find newline in intermediate buffer; check input [%zu | %zu | %zu]\n", (unsigned long) src_bytes_read, (unsigned long) remainder_length, (unsigned long) src_buffer_capacity);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| unsigned int long unsigned int
| %lu
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’ at ../../../../interfaces/src/data/starch/starchHelpers.c:3695:28:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchHelpers.c: In function ‘int starch::STARCH2_transformHeaderlessBEDInput(const FILE*, starch::Metadata**, starch::CompressionType, const char*, const char*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
../../../../interfaces/src/data/starch/starchHelpers.c:3695:97: note: length computed here
3695 | strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
| ~~~~~~^~~~~~~~~~~~
mkdir -p objects
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchMetadataHelpers.c -o objects/starchMetadataHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../..
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_JSONMetadataExists(FILE**, const char*)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1096:20: warning: comparison is always true due to limited range of data type [-Wtype-limits]
1096 | } while (currC != EOF);
| ^
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1097:63: warning: comparison is always false due to limited range of data type [-Wtype-limits]
1097 | if ((nReadBytes == STARCH_LEGACY_METADATA_SIZE) || (currC == EOF)) {
| ^
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1313:24: warning: comparison is always true due to limited range of data type [-Wtype-limits]
1313 | } while (currC != EOF);
| ^
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:20:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:311:47: note: length computed here
311 | strncpy(iter->filename, fn, strlen(fn) + 1);
| ~~~~~~^~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_updateMetadataForChromosome(starch::Metadata**, char*, char*, uint64_t, Bed::LineCountType, Bed::BaseCountType, Bed::BaseCountType, starch::Boolean, starch::Boolean, char*, Bed::LineLengthType)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:330:59: note: length computed here
330 | strncpy(iter->signature, signature, strlen(signature) + 1);
| ~~~~~~^~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2228:57: note: length computed here
2228 | strncpy(recTokBuf, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2244:65: note: length computed here
2244 | strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
| ~~~~~~^~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:32:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readLegacyMetadata(const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, uint64_t*, starch::Boolean*, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:2256:59: note: length computed here
2256 | strncpy(recFilename, token, strlen(token) + 1);
| ~~~~~~^~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1684:50: note: length computed here
1684 | strncpy(*note, streamNote, strlen(streamNote) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:30:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’ at ../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/src/data/starch/starchMetadataHelpers.c: In function ‘int starch::STARCH_readJSONMetadata(json_t**, FILE**, const char*, starch::Metadata**, starch::CompressionType*, starch::ArchiveVersion**, char**, char**, uint64_t*, starch::Boolean*, starch::Boolean, starch::Boolean)’:
../../../../interfaces/src/data/starch/starchMetadataHelpers.c:1667:52: note: length computed here
1667 | strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
| ~~~~~~^~~~~~~~~~~~~
mkdir -p objects
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchFileHelpers.c -o objects/starchFileHelpers.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p objects
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchSha1Digest.c -o objects/starchSha1Digest.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p objects
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c ../../../../interfaces/src/data/starch/starchBase64Coding.c -o objects/starchBase64Coding.o -iquote../../../../interfaces/general-headers -iquote../../../..
mkdir -p ../bin
cp starchcluster_gnuParallel.tcsh ../bin/starchcluster_gnuParallel-typical
mkdir -p ../bin
cp starchcluster_sge.tcsh ../bin/starchcluster_sge-typical
mkdir -p ../bin
cp starchcluster_slurm.tcsh ../bin/starchcluster_slurm-typical
mkdir -p ../bin
cp starch-diff.py ../bin/starch-diff-typical
mkdir -p ../lib
ar rcs ../lib/libstarch.a objects/starchConstants.o objects/unstarchHelpers.o objects/starchHelpers.o objects/starchMetadataHelpers.o objects/starchFileHelpers.o objects/starchSha1Digest.o objects/starchBase64Coding.o
mkdir -p ../bin
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c starch.c -o objects/starch.o -iquote../../../../interfaces/general-headers -iquote../../../..
starch.c: In function ‘int main(int, char**)’:
starch.c:106:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
106 | static_cast<const CompressionType>( type ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:121:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
121 | static_cast<const CompressionType>( type ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:123:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
123 | static_cast<const Boolean>( kStarchFinalizeTransformTrue ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:146:40: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
146 | static_cast<const CompressionType>( type ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:161:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
161 | static_cast<const CompressionType>( type ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:163:50: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
163 | static_cast<const Boolean>( kStarchFinalizeTransformTrue ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:191:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
191 | static_cast<const CompressionType>( type ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:194:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
194 | static_cast<const Boolean>( bedGeneratePerChrSignatureFlag ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:195:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
195 | static_cast<const Boolean>( bedHeaderFlag ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:196:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
196 | static_cast<const Boolean>( bedReportProgressFlag ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starch.c:197:36: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
197 | static_cast<const LineCountType>( bedReportProgressN )) != STARCH_EXIT_SUCCESS)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security objects/starch.o -o ../bin/starch-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now
mkdir -p ../bin
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c unstarch.c -o objects/unstarch.o -iquote../../../../interfaces/general-headers -iquote../../../..
unstarch.c: In function ‘int main(int, char**)’:
unstarch.c:401:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
401 | static_cast<const unsigned long long>( metadataOffset ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:402:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
402 | static_cast<const Boolean>( headerFlag )) != 0) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:422:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
422 | static_cast<const unsigned long long>( metadataOffset ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:423:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
423 | static_cast<const Boolean>( headerFlag )) != 0) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:452:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
452 | static_cast<const unsigned long long>( sizeof(starchRevision2HeaderBytes) ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:453:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
453 | static_cast<const Boolean>( headerFlag )) != 0) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:473:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
473 | static_cast<const unsigned long long>( sizeof(starchRevision2HeaderBytes) ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:474:58: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
474 | static_cast<const Boolean>( headerFlag )) != 0) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:567:39: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
567 | UNSTARCH_printCompressionType(static_cast<const CompressionType>( type ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:798:78: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
798 | static_cast<const unsigned long long>( sizeof(starchRevision2HeaderBytes) ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:809:82: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
809 | static_cast<const unsigned long long>( sizeof(starchRevision2HeaderBytes) ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c: In function ‘void starch::UNSTARCH_printMetadataSha1Signature(unsigned char*)’:
unstarch.c:1334:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1334 | static_cast<const size_t>( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
unstarch.c:1336:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1336 | static_cast<const size_t>( sha1BufferLength ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rm -rf objects
make[4]: Leaving directory '/<<PKGBUILDDIR>>/applications/bed/conversion/src'
mkdir -p ../bin
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c starchcat.c -o objects/starchcat.o -iquote../../../../interfaces/general-headers -iquote../../../..
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security objects/unstarch.o -o ../bin/unstarch-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now
In file included from /usr/include/c++/10/cassert:44,
from starchcat.c:33:
starchcat.c: In function ‘int main(int, char**)’:
starchcat.c:136:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
136 | assert( STARCHCAT_allocMetadataRecords ( &mdRecords, static_cast<const unsigned int>( numRecords ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:137:75: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
137 | assert( STARCHCAT_allocMetadataJSONObjects ( &metadataJSONs, static_cast<const unsigned int>( numRecords ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:138:87: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
138 | assert( STARCHCAT_buildMetadataRecords ( &metadataJSONs, &mdRecords, static_cast<const unsigned int>( firstArgc ), static_cast<const int>( argc ), const_cast<const char **>( argv ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:138:133: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
138 | assert( STARCHCAT_buildMetadataRecords ( &metadataJSONs, &mdRecords, static_cast<const unsigned int>( firstArgc ), static_cast<const int>( argc ), const_cast<const char **>( argv ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:139:75: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
139 | assert( STARCHCAT_checkMetadataJSONVersions ( &metadataJSONs, static_cast<const unsigned int>( numRecords ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:140:145: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
140 | assert( STARCHCAT_buildUniqueChromosomeList ( &chromosomes, &numChromosomes, reinterpret_cast<const MetadataRecord *>( mdRecords ), static_cast<const unsigned int>( numRecords ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:141:69: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
141 | assert( STARCHCAT_allocChromosomeSummary ( &summary, static_cast<const unsigned int>( numChromosomes ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:142:124: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
142 | assert( STARCHCAT_buildChromosomeSummary ( &summary, reinterpret_cast<const MetadataRecord *>( mdRecords ), static_cast<const unsigned int>( numRecords ), const_cast<const char **>( chromosomes ), static_cast<const unsigned int>( numChromosomes ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:142:213: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
142 | assert( STARCHCAT_buildChromosomeSummary ( &summary, reinterpret_cast<const MetadataRecord *>( mdRecords ), static_cast<const unsigned int>( numRecords ), const_cast<const char **>( chromosomes ), static_cast<const unsigned int>( numChromosomes ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:143:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
143 | assert( STARCHCAT_allocChromosomeSummaries ( &summaries, static_cast<const unsigned int>( numChromosomes ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:144:127: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
144 | assert( STARCHCAT_buildChromosomeSummaries ( &summaries, reinterpret_cast<const ChromosomeSummary *>( summary ), static_cast<const unsigned int>( numChromosomes ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:164:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
164 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:178:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
178 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:223:60: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
223 | assert( STARCHCAT_freeMetadataRecords( &mdRecords, static_cast<const unsigned int>( numRecords ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:233:68: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
233 | assert (STARCHCAT_freeMetadataJSONObjects( &metadataJSONs, static_cast<const unsigned int>( numRecords ) ) );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function ‘int starch::STARCHCAT2_rewriteInputRecordToOutput(starch::Metadata**, const char*, starch::CompressionType, const char*, const MetadataRecord*, size_t*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
starchcat.c:1338:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1338 | UNSTARCH_reverseTransformCoordinates( static_cast<const LineCountType>( t_lineIdx ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:1806:71: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
1806 | UNSTARCH_reverseTransformCoordinates( static_cast<const LineCountType>( t_lineIdx ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:2131:78: warning: left shift count >= width of type [-Wshift-count-overflow]
2131 | bzOutBytesWritten = static_cast<size_t>( bzOutBytesWrittenHi32 ) << 32 | bzOutBytesWrittenLo32;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
starchcat.c: In function ‘int starch::STARCHCAT_rewriteInputRecordToOutput(starch::Metadata**, const char*, starch::CompressionType, const char*, const MetadataRecord*)’:
starchcat.c:2450:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2450 | static_cast<const uint64_t>( inRec->mdOffset ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:2451:25: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2451 | static_cast<const Boolean>( inRec->hFlag )) != 0 ) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:2471:28: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2471 | static_cast<const uint64_t>( inRec->mdOffset ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:2472:28: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2472 | static_cast<const Boolean>( inRec->hFlag )) != 0 ) {
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:2509:23: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2509 | static_cast<const CompressionType>( outType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:2511:23: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
2511 | static_cast<const Boolean>( kStarchFinalizeTransformFalse ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function ‘int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)’:
starchcat.c:3152:54: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
3152 | if (STARCHCAT2_setupBzip2InputStream(static_cast<const size_t>( inRecIdx ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:3316:69: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
3316 | static_cast<const size_t>( summary->numRecords ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:3455:77: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
3455 | static_cast<const Boolean>( flushZStreamFlag ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mkdir -p ../bin
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c starchstrip.c -o objects/starchstrip.o -iquote../../../../interfaces/general-headers -iquote../../../..
starchcat.c: In function ‘int starch::STARCHCAT_mergeInputRecordsToOutput(starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*)’:
starchcat.c:4265:43: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4265 | static_cast<const CompressionType>( outType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:4267:43: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4267 | static_cast<const Boolean>( kStarchFinalizeTransformFalse ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/cassert:44,
from starchcat.c:33:
starchcat.c: In function ‘int starch::STARCHCAT_mergeChromosomeStreams(const ChromosomeSummaries*, starch::CompressionType, const char*)’:
starchcat.c:4402:60: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4402 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:4420:63: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4420 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:4447:57: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4447 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:4479:39: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4479 | static_cast<const Boolean>( hFlag ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function ‘int starch::STARCHCAT_freeChromosomeSummaries(starch::ChromosomeSummaries**)’:
starchcat.c:4541:62: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
4541 | STARCHCAT_freeChromosomeSummary( &((*chrSums)->summary), static_cast<const unsigned int>( (*chrSums)->numChromosomes ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/cassert:44,
from starchcat.c:33:
starchcat.c: In function ‘int starch::STARCHCAT2_mergeChromosomeStreams(const ChromosomeSummaries*, starch::CompressionType, const char*, size_t*, starch::Boolean, starch::Boolean, Bed::LineCountType)’:
starchcat.c:5902:61: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
5902 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:5929:64: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
5929 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:5952:64: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
5952 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:5990:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
5990 | static_cast<const CompressionType>( outputType ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:6025:38: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
6025 | static_cast<const Boolean>( hFlag ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:6053:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
6053 | static_cast<const size_t>( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c:6055:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
6055 | static_cast<const size_t>( STARCH2_MD_FOOTER_SHA1_LENGTH ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function ‘int starch::STARCHCAT2_fillExtractionBufferFromBzip2Stream(starch::Boolean*, char*, char*, size_t*, BZFILE**, size_t*, char*, size_t*, starch::TransformState*)’:
starchcat.c:6719:55: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
6719 | UNSTARCH_reverseTransformCoordinates( static_cast<const LineCountType>( *t_lineIdxPtr ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function ‘int starch::STARCHCAT2_fillExtractionBufferFromGzipStream(starch::Boolean*, FILE**, char*, char*, size_t*, z_stream*, size_t*, char**, size_t*, starch::TransformState*)’:
starchcat.c:7060:59: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
7060 | UNSTARCH_reverseTransformCoordinates( static_cast<const LineCountType>( *t_lineIdxPtr ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchstrip.c: In function ‘void starch::STARCHSTRIP_write_updated_metadata(FILE*)’:
starchstrip.c:124:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
124 | static_cast<const size_t>( STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH ),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchstrip.c:126:13: warning: type qualifiers ignored on cast result type [-Wignored-qualifiers]
126 | static_cast<const size_t>( STARCH2_MD_FOOTER_SHA1_LENGTH ));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security objects/starchstrip.o -o ../bin/starchstrip-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from Bedops.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘Bed::allocate_iterator_starch_bed<BedType*, SZ>& Bed::allocate_iterator_starch_bed<BedType*, SZ>::operator++() [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function ‘Bed::allocate_iterator_starch_bed<BedType*, SZ>& Bed::allocate_iterator_starch_bed<BedType*, SZ>::operator++() [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 512]’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from starchcat.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCHCAT_buildMetadataRecords(json_t***, starch::MetadataRecord**, unsigned int, int, const char**)’ at starchcat.c:5368:20:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function ‘int starch::STARCHCAT_buildMetadataRecords(json_t***, starch::MetadataRecord**, unsigned int, int, const char**)’:
starchcat.c:5368:53: note: length computed here
5368 | strncpy(cTime, creationTimestamp, strlen(creationTimestamp) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from Bedops.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘Bed::allocate_iterator_starch_bed<BedType*, SZ>& Bed::allocate_iterator_starch_bed<BedType*, SZ>::operator++() [with BedType = Bed::BasicCoords<true, false>; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In function ‘Bed::allocate_iterator_starch_bed<BedType*, SZ>& Bed::allocate_iterator_starch_bed<BedType*, SZ>::operator++() [with BedType = Bed::BasicCoords<true, false>; unsigned int SZ = 512]’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from starchcat.c:31:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)’ at starchcat.c:3123:16:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
starchcat.c: In function ‘int starch::STARCHCAT2_mergeInputRecordsToOutput(const char*, starch::Metadata**, const char*, starch::CompressionType, const ChromosomeSummary*, size_t*)’:
starchcat.c:3123:78: note: length computed here
3123 | strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1);
| ~~~~~~^~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -s -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security objects/starchcat.o -o ../bin/starchcat-typical ../lib/libstarch.a -ljansson -lz -lbz2 -Wl,-z,relro -Wl,-z,now
rm -rf objects
make[4]: Leaving directory '/<<PKGBUILDDIR>>/applications/bed/starch/src'
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from Bedops.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘Bed::allocate_iterator_starch_bed<BedType*, SZ>& Bed::allocate_iterator_starch_bed<BedType*, SZ>::operator++() [with BedType = Bed::BasicCoords<true, true>; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36,
inlined from ‘BedOperations::BedPadReader<IterType>::BedType* BedOperations::BedPadReader<IterType>::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, true>*, 512>]’ at BedPadReader.hpp:140:11:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘BedOperations::BedPadReader<IterType>::BedType* BedOperations::BedPadReader<IterType>::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, true>*, 512>]’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from Bedops.cpp:26:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘Bed::allocate_iterator_starch_bed<BedType*, SZ>& Bed::allocate_iterator_starch_bed<BedType*, SZ>::operator++() [with BedType = Bed::BasicCoords<true, false>; unsigned int SZ = 512]’ at ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:189:36,
inlined from ‘BedOperations::BedPadReader<IterType>::BedType* BedOperations::BedPadReader<IterType>::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, false>*, 512>]’ at BedPadReader.hpp:140:11:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:42,
from Bedops.cpp:41:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘BedOperations::BedPadReader<IterType>::BedType* BedOperations::BedPadReader<IterType>::ReadLine() [with IterType = Bed::allocate_iterator_starch_bed<Bed::BasicCoords<true, false>*, 512>]’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
rm -rf objects_typical
make[4]: Leaving directory '/<<PKGBUILDDIR>>/applications/bed/bedops/src'
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:28,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
/usr/include/c++/10/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:49:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, unsigned int, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39,
from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:541:76: note: length computed here
541 | std::strncpy(_recTokBuf, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:49:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39,
from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:551:89: note: length computed here
551 | std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1);
| ~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:49:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39,
from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In static member function ‘static bool starch::Starch::hasStarchRevision1LegacyHeader(FILE*)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:556:78: note: length computed here
556 | std::strncpy(_recFilename, _token, strlen(_token) + 1);
| ~~~~~~^~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39,
from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘const char* starch::Starch::getCurrentChromosome()’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39,
from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘void starch::Starch::iterateArchiveMdIter()’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘int starch::Starch::zReadLine()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:24:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39,
from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::zReadLine()’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:1913:118: note: length computed here
1913 | strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )) + 1);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentRemainder(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:24,
inlined from ‘int starch::Starch::extractLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1810:36:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39,
from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘int starch::Starch::extractLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:899:61: note: length computed here
899 | strncpy(currentRemainder, _remainder, strlen(_remainder) + 1);
| ~~~~~~^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘const char* starch::Starch::getCurrentChromosome()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:718:130,
inlined from ‘bool starch::Starch::isEOF()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:729:80,
inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1452:22:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39,
from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:31,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
In function ‘char* strncpy(char*, const char*, size_t)’,
inlined from ‘void starch::Starch::setCurrentChromosome(char*)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:24,
inlined from ‘void starch::Starch::iterateArchiveMdIter()’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:874:37,
inlined from ‘bool starch::Starch::extractBEDLine(std::string&)’ at ../../../../interfaces/general-headers/data/starch/starchApi.hpp:1472:37:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:39,
from ../../../../interfaces/general-headers/algorithm/../../src/algorithm/sweep/WindowSweepImpl.cpp:27,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:91,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
../../../../interfaces/general-headers/data/starch/starchApi.hpp: In member function ‘bool starch::Starch::extractBEDLine(std::string&)’:
../../../../interfaces/general-headers/data/starch/starchApi.hpp:887:55: note: length computed here
887 | strncpy(currentChromosome, _cC, strlen(_cC) + 1);
| ~~~~~~^~~~~
In file included from /usr/include/c++/10/algorithm:62,
from ../../../../interfaces/general-headers/data/bed/BedDistances.hpp:28,
from ../../../../interfaces/general-headers/algorithm/WindowSweep.hpp:27,
from ../../../../interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp:31,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:27,
from Bedmap.cpp:37:
/usr/include/c++/10/bits/stl_algo.h: In function ‘void std::nth_element(_RAIter, _RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >]’:
/usr/include/c++/10/bits/stl_algo.h:4773:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
4773 | nth_element(_RandomAccessIterator __first, _RandomAccessIterator __nth,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:4773:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:4773:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from Bedmap.cpp:35:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ../../../../interfaces/general-headers/algorithm/visitors/NumericalVisitors.hpp:32,
from ../../../../interfaces/general-headers/algorithm/visitors/BedVisitors.hpp:34,
from Bedmap.cpp:37:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::Visitor<Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::Visitor<Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapMapping, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapMapping, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::Visitor<Bed::BasicCoords<true, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::Visitor<Bed::NoPool::BasicCoords<true, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapMapping, Bed::BasicCoords<true, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapMapping, Bed::NoPool::BasicCoords<true, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapReference, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapReference, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapReference, Bed::BasicCoords<true, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapReference, Bed::NoPool::BasicCoords<true, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapBoth, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapBoth, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapBoth, Bed::BasicCoords<true, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapBoth, Bed::NoPool::BasicCoords<true, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapEither, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapEither, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapEither, Bed::BasicCoords<true, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::PercentOverlapEither, Bed::NoPool::BasicCoords<true, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::RangedDist, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::RangedDist, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::RangedDist, Bed::BasicCoords<true, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::RangedDist, Bed::NoPool::BasicCoords<true, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::Overlapping, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::Overlapping, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::Overlapping, Bed::BasicCoords<true, true>, Bed::Bed5<Bed::Bed4<Bed::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp: In member function ‘void Visitors::MedianAbsoluteDeviation<Process, BaseVisitor, ExceptionType>::DoneReference() [with Process = Visitors::BedHelpers::PrintScorePrecision; BaseVisitor = Visitors::BedBaseVisitor<Bed::Overlapping, Bed::NoPool::BasicCoords<true, true>, Bed::NoPool::Bed5<Bed::NoPool::Bed4<Bed::NoPool::BasicCoords<true, true>, true>, double, true> >; ExceptionType = Ext::Exception<Ext::Exception<std::exception, 3>, 2>]’:
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:99:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
99 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:102:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
102 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
../../../../interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp:107:25: note: parameter passing for argument of type ‘std::vector<double, std::allocator<double> >::iterator’ changed in GCC 7.1
107 | std::nth_element(vec.begin(), n, vec.end());
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
rm -rf objects_typical
make[4]: Leaving directory '/<<PKGBUILDDIR>>/applications/bed/bedmap/src'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
make -j4 install DESTDIR=/<<BUILDDIR>>/bedops-2.4.39\+dfsg1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p bin
cp applications/bed/conversion/src/wrappers/bam2bed applications/bed/conversion/src/wrappers/bam2bed_gnuParallel applications/bed/conversion/src/wrappers/bam2bed_sge applications/bed/conversion/src/wrappers/bam2bed_slurm applications/bed/conversion/src/wrappers/bam2starch applications/bed/conversion/src/wrappers/bam2starch_gnuParallel applications/bed/conversion/src/wrappers/bam2starch_sge applications/bed/conversion/src/wrappers/bam2starch_slurm applications/bed/conversion/src/wrappers/gff2bed applications/bed/conversion/src/wrappers/gff2starch applications/bed/conversion/src/wrappers/gtf2bed applications/bed/conversion/src/wrappers/gtf2starch applications/bed/conversion/src/wrappers/gvf2bed applications/bed/conversion/src/wrappers/gvf2starch applications/bed/conversion/src/wrappers/psl2bed applications/bed/conversion/src/wrappers/psl2starch applications/bed/conversion/src/wrappers/rmsk2bed applications/bed/conversion/src/wrappers/rmsk2starch applications/bed/conversion/src/wrappers/sam2bed applications/bed/conversion/src/wrappers/sam2starch applications/bed/conversion/src/wrappers/vcf2bed applications/bed/conversion/src/wrappers/vcf2starch applications/bed/conversion/src/wrappers/wig2bed applications/bed/conversion/src/wrappers/wig2starch bin
cp applications/bed/starch/bin/starchcluster_sge-typical bin/starchcluster_sge
cp applications/bed/starch/bin/starchcluster_gnuParallel-typical bin/starchcluster_gnuParallel
cp applications/bed/starch/bin/starchcluster_slurm-typical bin/starchcluster_slurm
cp applications/bed/starch/bin/starch-diff-typical bin/starch-diff
cp applications/bed/sort-bed/bin/sort-bed-typical bin/sort-bed
cp applications/bed/sort-bed/bin/update-sort-bed-slurm-typical bin/update-sort-bed-slurm
cp applications/bed/sort-bed/bin/update-sort-bed-starch-slurm-typical bin/update-sort-bed-starch-slurm
cp applications/bed/sort-bed/bin/update-sort-bed-migrate-candidates-typical bin/update-sort-bed-migrate-candidates
cp applications/bed/bedops/bin/bedops-typical bin/bedops
cp applications/bed/closestfeats/bin/closest-features-typical bin/closest-features
cp applications/bed/bedmap/bin/bedmap-typical bin/bedmap
cp applications/bed/bedextract/bin/bedextract-typical bin/bedextract
cp applications/bed/starch/bin/starch-typical bin/starch
cp applications/bed/starch/bin/unstarch-typical bin/unstarch
cp applications/bed/starch/bin/starchcat-typical bin/starchcat
cp applications/bed/starch/bin/starchstrip-typical bin/starchstrip
cp applications/bed/conversion/bin/convert2bed-typical bin/convert2bed
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_install-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install -a
mv bin/starch bin/bedops-starch
mkdir -p debian/bedops/usr/bin/
cp bin/* debian/bedops/usr/bin/
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
debian/rules override_dh_installman-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd bin && for f in * ; do help2man --no-discard-stderr --version-string="2.4.39+dfsg1" -o $f.1 ./$f; done
help2man: can't get `--help' info from ./bam2bed_gnuParallel
help2man: can't get `--help' info from ./bam2bed_sge
help2man: can't get `--help' info from ./bam2bed_slurm
help2man: can't get `--help' info from ./bam2starch_gnuParallel
help2man: can't get `--help' info from ./bam2starch_sge
help2man: can't get `--help' info from ./bam2starch_slurm
help2man: can't get `--help' info from ./starchcluster_gnuParallel
help2man: can't get `--help' info from ./starchcluster_sge
help2man: can't get `--help' info from ./starchcluster_slurm
dh_installman -a
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
debian/rules override_dh_dwz
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# Work around: dwz: Too few files for multifile optimization
echo "Do not run dh_dwz"
Do not run dh_dwz
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/bedops/usr/bin/bedmap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/bedops/usr/bin/bedops contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/bedops/usr/bin/bedextract contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/bedops/usr/bin/sort-bed contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/bedops/usr/bin/closest-features contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/bedops/usr/bin/bedmap debian/bedops/usr/bin/bedops debian/bedops/usr/bin/starchcat debian/bedops/usr/bin/convert2bed debian/bedops/usr/bin/bedextract debian/bedops/usr/bin/sort-bed debian/bedops/usr/bin/bedops-starch debian/bedops/usr/bin/starchstrip debian/bedops/usr/bin/closest-features debian/bedops/usr/bin/unstarch were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'bedops-dbgsym' in '../bedops-dbgsym_2.4.39+dfsg1-2_armhf.deb'.
dpkg-deb: building package 'bedops' in '../bedops_2.4.39+dfsg1-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> >../bedops_2.4.39+dfsg1-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-03-01T06:13:05Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
bedops_2.4.39+dfsg1-2_armhf.changes:
------------------------------------
Format: 1.8
Date: Fri, 19 Feb 2021 11:50:32 +0200
Source: bedops
Binary: bedops bedops-dbgsym
Architecture: armhf
Version: 2.4.39+dfsg1-2
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Juhani Numminen <juhaninumminen0@gmail.com>
Description:
bedops - high-performance genomic feature operations
Changes:
bedops (2.4.39+dfsg1-2) unstable; urgency=medium
.
* Team upload.
* Add parallel.patch: toplevel Makefile should use our -jN argument.
* Update hardening.patch: our optimization flags now override upstream -O3.
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Files:
58441903c80b3413d9654f6ebaae057f 99072 debug optional bedops-dbgsym_2.4.39+dfsg1-2_armhf.deb
8fb8d3987fa21ad9b306acaef95b75ef 5567 science optional bedops_2.4.39+dfsg1-2_armhf.buildinfo
56c43fa0f54e18fb3e75c56c009e157b 937140 science optional bedops_2.4.39+dfsg1-2_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: bedops
Binary: bedops bedops-dbgsym
Architecture: armhf
Version: 2.4.39+dfsg1-2
Checksums-Md5:
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Checksums-Sha1:
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Checksums-Sha256:
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Mon, 01 Mar 2021 06:13:02 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.69-14),
automake (= 1:1.16.3-2),
autopoint (= 0.21-4),
autotools-dev (= 20180224.1+nmu1),
base-files (= 11+rpi1),
base-passwd (= 3.5.48),
bash (= 5.1-2),
binutils (= 2.35.1-7+rpi1),
binutils-arm-linux-gnueabihf (= 2.35.1-7+rpi1),
binutils-common (= 2.35.1-7+rpi1),
bsdextrautils (= 2.36.1-7),
bsdutils (= 1:2.36.1-6),
build-essential (= 12.9),
bzip2 (= 1.0.8-4),
coreutils (= 8.32-4),
cpp (= 4:10.2.1-1+rpi1),
cpp-10 (= 10.2.1-6+rpi1),
dash (= 0.5.11+git20200708+dd9ef66-5),
debconf (= 1.5.74),
debhelper (= 13.3.3),
debianutils (= 4.11.2),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.11.0-1),
diffutils (= 1:3.7-5),
dpkg (= 1.20.7.1+rpi1),
dpkg-dev (= 1.20.7.1+rpi1),
dwz (= 0.13+20210201-1),
file (= 1:5.39-3),
findutils (= 4.8.0-1),
g++ (= 4:10.2.1-1+rpi1),
g++-10 (= 10.2.1-6+rpi1),
gcc (= 4:10.2.1-1+rpi1),
gcc-10 (= 10.2.1-6+rpi1),
gcc-10-base (= 10.2.1-6+rpi1),
gettext (= 0.21-4),
gettext-base (= 0.21-4),
grep (= 3.6-1),
groff-base (= 1.22.4-6),
gzip (= 1.10-2),
help2man (= 1.48.1),
hostname (= 3.23),
init-system-helpers (= 1.60),
intltool-debian (= 0.35.0+20060710.5),
libacl1 (= 2.2.53-10),
libarchive-zip-perl (= 1.68-1),
libasan6 (= 10.2.1-6+rpi1),
libatomic1 (= 10.2.1-6+rpi1),
libattr1 (= 1:2.4.48-6),
libaudit-common (= 1:3.0-2),
libaudit1 (= 1:3.0-2),
libbinutils (= 2.35.1-7+rpi1),
libblkid1 (= 2.36.1-6),
libbz2-1.0 (= 1.0.8-4),
libbz2-dev (= 1.0.8-4),
libc-bin (= 2.31-9+rpi1),
libc-dev-bin (= 2.31-9+rpi1),
libc6 (= 2.31-9+rpi1),
libc6-dev (= 2.31-9+rpi1),
libcap-ng0 (= 0.7.9-2.2+b1),
libcc1-0 (= 10.2.1-6+rpi1),
libcom-err2 (= 1.45.7-1),
libcrypt-dev (= 1:4.4.17-1),
libcrypt1 (= 1:4.4.17-1),
libctf-nobfd0 (= 2.35.1-7+rpi1),
libctf0 (= 2.35.1-7+rpi1),
libdb5.3 (= 5.3.28+dfsg1-0.6),
libdebconfclient0 (= 0.256),
libdebhelper-perl (= 13.3.3),
libdpkg-perl (= 1.20.7.1+rpi1),
libelf1 (= 0.183-1),
libexpat1 (= 2.2.10-1),
libffi7 (= 3.3-5),
libfile-stripnondeterminism-perl (= 1.11.0-1),
libgcc-10-dev (= 10.2.1-6+rpi1),
libgcc-s1 (= 10.2.1-6+rpi1),
libgcrypt20 (= 1.8.7-2),
libgdbm-compat4 (= 1.19-2),
libgdbm6 (= 1.19-2),
libgmp10 (= 2:6.2.1+dfsg-1),
libgomp1 (= 10.2.1-6+rpi1),
libgpg-error0 (= 1.38-2),
libgssapi-krb5-2 (= 1.18.3-4),
libicu67 (= 67.1-6),
libisl23 (= 0.23-1),
libjansson-dev (= 2.13.1-1.1),
libjansson4 (= 2.13.1-1.1),
libk5crypto3 (= 1.18.3-4),
libkeyutils1 (= 1.6.1-2),
libkrb5-3 (= 1.18.3-4),
libkrb5support0 (= 1.18.3-4),
liblocale-gettext-perl (= 1.07-4+b1),
liblz4-1 (= 1.9.3-1+rpi1),
liblzma5 (= 5.2.5-1.0),
libmagic-mgc (= 1:5.39-3),
libmagic1 (= 1:5.39-3),
libmount1 (= 2.36.1-6),
libmpc3 (= 1.2.0-1),
libmpdec3 (= 2.5.1-1+rpi1),
libmpfr6 (= 4.1.0-3),
libncursesw6 (= 6.2+20201114-2),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libpam-modules (= 1.4.0-2),
libpam-modules-bin (= 1.4.0-2),
libpam-runtime (= 1.4.0-2),
libpam0g (= 1.4.0-2),
libpcre2-8-0 (= 10.36-2),
libpcre3 (= 2:8.39-13),
libperl5.32 (= 5.32.1-2),
libpipeline1 (= 1.5.3-1),
libpython3-stdlib (= 3.9.1-1),
libpython3.9-minimal (= 3.9.1-4+rpi1),
libpython3.9-stdlib (= 3.9.1-4+rpi1),
libreadline8 (= 8.1-1),
libseccomp2 (= 2.5.1-1+rpi1),
libselinux1 (= 3.1-2+b1),
libsigsegv2 (= 2.13-1),
libsmartcols1 (= 2.36.1-6),
libsqlite3-0 (= 3.34.1-1),
libssl1.1 (= 1.1.1i-3),
libstdc++-10-dev (= 10.2.1-6+rpi1),
libstdc++6 (= 10.2.1-6+rpi1),
libsub-override-perl (= 0.09-2),
libsystemd0 (= 247.2-5+rpi1),
libtinfo6 (= 6.2+20201114-2),
libtirpc-common (= 1.3.1-1),
libtirpc-dev (= 1.3.1-1),
libtirpc3 (= 1.3.1-1),
libtool (= 2.4.6-15),
libubsan1 (= 10.2.1-6+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 247.2-5+rpi1),
libunistring2 (= 0.9.10-4),
libuuid1 (= 2.36.1-6),
libxml2 (= 2.9.10+dfsg-6.3),
libzstd1 (= 1.4.8+dfsg-1),
linux-libc-dev (= 5.10.9-1+rpi1),
login (= 1:4.8.1-1),
lsb-base (= 11.1.0+rpi1),
m4 (= 1.4.18-5),
make (= 4.3-4),
man-db (= 2.9.4-1),
mawk (= 1.3.4.20200120-2),
media-types (= 4.0.0),
ncurses-base (= 6.2+20201114-2),
ncurses-bin (= 6.2+20201114-2),
patch (= 2.7.6-7),
perl (= 5.32.1-2),
perl-base (= 5.32.1-2),
perl-modules-5.32 (= 5.32.1-2),
po-debconf (= 1.0.21+nmu1),
python3 (= 3.9.1-1),
python3-distutils (= 3.9.1-2),
python3-lib2to3 (= 3.9.1-2),
python3-minimal (= 3.9.1-1),
python3.9 (= 3.9.1-4+rpi1),
python3.9-minimal (= 3.9.1-4+rpi1),
readline-common (= 8.1-1),
sed (= 4.7-1),
sensible-utils (= 0.0.14),
sysvinit-utils (= 2.96-5),
tar (= 1.32+dfsg-1+rpi1),
tzdata (= 2021a-1),
util-linux (= 2.36.1-6),
xz-utils (= 5.2.5-1.0),
zlib1g (= 1:1.2.11.dfsg-2),
zlib1g-dev (= 1:1.2.11.dfsg-2)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1613728232"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
bedops-dbgsym_2.4.39+dfsg1-2_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 99072 bytes: control archive=540 bytes.
380 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: bedops-dbgsym
Source: bedops
Version: 2.4.39+dfsg1-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 114
Depends: bedops (= 2.4.39+dfsg1-2)
Section: debug
Priority: optional
Description: debug symbols for bedops
Build-Ids: e4949ce466a2132ad7e0bbf858d622688dea60db
drwxr-xr-x root/root 0 2021-02-19 09:50 ./
drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/
drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/lib/
drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/lib/debug/.build-id/e4/
-rw-r--r-- root/root 106024 2021-02-19 09:50 ./usr/lib/debug/.build-id/e4/949ce466a2132ad7e0bbf858d622688dea60db.debug
drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/
drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-02-19 09:50 ./usr/share/doc/bedops-dbgsym -> bedops
bedops_2.4.39+dfsg1-2_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 937140 bytes: control archive=5376 bytes.
732 bytes, 15 lines control
17229 bytes, 204 lines md5sums
Package: bedops
Version: 2.4.39+dfsg1-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6632
Depends: libbz2-1.0, libc6 (>= 2.28), libgcc-s1 (>= 3.5), libjansson4 (>= 2.3), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), python3, tcsh
Section: science
Priority: optional
Homepage: https://github.com/bedops/bedops
Description: high-performance genomic feature operations
BEDOPS is a suite of tools to address common questions raised in genomic
studies, mostly with regard to overlap and proximity relationships between
data sets.
It aims to be scalable and flexible, facilitating the efficient and accurate
analysis and management of large-scale genomic data.
drwxr-xr-x root/root 0 2021-02-19 09:50 ./
drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/
drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/bin/
-rwxr-xr-x root/root 4711 2021-02-19 09:50 ./usr/bin/bam2bed
-rwxr-xr-x root/root 4501 2021-02-19 09:50 ./usr/bin/bam2bed_gnuParallel
-rwxr-xr-x root/root 5022 2021-02-19 09:50 ./usr/bin/bam2bed_sge
-rwxr-xr-x root/root 5021 2021-02-19 09:50 ./usr/bin/bam2bed_slurm
-rwxr-xr-x root/root 5842 2021-02-19 09:50 ./usr/bin/bam2starch
-rwxr-xr-x root/root 4507 2021-02-19 09:50 ./usr/bin/bam2starch_gnuParallel
-rwxr-xr-x root/root 5076 2021-02-19 09:50 ./usr/bin/bam2starch_sge
-rwxr-xr-x root/root 5014 2021-02-19 09:50 ./usr/bin/bam2starch_slurm
-rwxr-xr-x root/root 169400 2021-02-19 09:50 ./usr/bin/bedextract
-rwxr-xr-x root/root 4924880 2021-02-19 09:50 ./usr/bin/bedmap
-rwxr-xr-x root/root 357816 2021-02-19 09:50 ./usr/bin/bedops
-rwxr-xr-x root/root 75332 2021-02-19 09:50 ./usr/bin/bedops-starch
-rwxr-xr-x root/root 210364 2021-02-19 09:50 ./usr/bin/closest-features
-rwxr-xr-x root/root 104520 2021-02-19 09:50 ./usr/bin/convert2bed
-rwxr-xr-x root/root 3773 2021-02-19 09:50 ./usr/bin/gff2bed
-rwxr-xr-x root/root 4904 2021-02-19 09:50 ./usr/bin/gff2starch
-rwxr-xr-x root/root 3532 2021-02-19 09:50 ./usr/bin/gtf2bed
-rwxr-xr-x root/root 4663 2021-02-19 09:50 ./usr/bin/gtf2starch
-rwxr-xr-x root/root 3773 2021-02-19 09:50 ./usr/bin/gvf2bed
-rwxr-xr-x root/root 4904 2021-02-19 09:50 ./usr/bin/gvf2starch
-rwxr-xr-x root/root 3976 2021-02-19 09:50 ./usr/bin/psl2bed
-rwxr-xr-x root/root 5107 2021-02-19 09:50 ./usr/bin/psl2starch
-rwxr-xr-x root/root 3776 2021-02-19 09:50 ./usr/bin/rmsk2bed
-rwxr-xr-x root/root 4907 2021-02-19 09:50 ./usr/bin/rmsk2starch
-rwxr-xr-x root/root 4711 2021-02-19 09:50 ./usr/bin/sam2bed
-rwxr-xr-x root/root 5842 2021-02-19 09:50 ./usr/bin/sam2starch
-rwxr-xr-x root/root 177588 2021-02-19 09:50 ./usr/bin/sort-bed
-rwxr-xr-x root/root 10163 2021-02-19 09:50 ./usr/bin/starch-diff
-rwxr-xr-x root/root 144948 2021-02-19 09:50 ./usr/bin/starchcat
-rwxr-xr-x root/root 4299 2021-02-19 09:50 ./usr/bin/starchcluster_gnuParallel
-rwxr-xr-x root/root 4810 2021-02-19 09:50 ./usr/bin/starchcluster_sge
-rwxr-xr-x root/root 4716 2021-02-19 09:50 ./usr/bin/starchcluster_slurm
-rwxr-xr-x root/root 79364 2021-02-19 09:50 ./usr/bin/starchstrip
-rwxr-xr-x root/root 107956 2021-02-19 09:50 ./usr/bin/unstarch
-rwxr-xr-x root/root 32686 2021-02-19 09:50 ./usr/bin/update-sort-bed-migrate-candidates
-rwxr-xr-x root/root 20701 2021-02-19 09:50 ./usr/bin/update-sort-bed-slurm
-rwxr-xr-x root/root 22682 2021-02-19 09:50 ./usr/bin/update-sort-bed-starch-slurm
-rwxr-xr-x root/root 4675 2021-02-19 09:50 ./usr/bin/vcf2bed
-rwxr-xr-x root/root 5806 2021-02-19 09:50 ./usr/bin/vcf2starch
-rwxr-xr-x root/root 4598 2021-02-19 09:50 ./usr/bin/wig2bed
-rwxr-xr-x root/root 5729 2021-02-19 09:50 ./usr/bin/wig2starch
drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/
drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/doc/bedops/
-rw-r--r-- root/root 267 2021-02-19 09:50 ./usr/share/doc/bedops/README.Debian
-rw-r--r-- root/root 1506 2021-02-19 09:50 ./usr/share/doc/bedops/changelog.Debian.gz
-rw-r--r-- root/root 1156 2021-02-19 09:50 ./usr/share/doc/bedops/copyright
drwxr-xr-x root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/
-rw-r--r-- root/root 718 2020-04-06 20:55 ./usr/share/doc/bedops/tests/Makefile
drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/doc/bedops/tests/bedops/
-rw-r--r-- root/root 2166 2021-02-19 09:50 ./usr/share/doc/bedops/tests/bedops/Makefile.gz
drwxr-xr-x root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/
-rw-r--r-- root/root 197 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001.expected
-rw-r--r-- root/root 44 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001a.test
-rw-r--r-- root/root 53 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.chop.001b.test
-rw-r--r-- root/root 24 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.chrom.001.expected
-rw-r--r-- root/root 26 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.complement.001.expected
-rw-r--r-- root/root 31 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.difference.001.expected
-rw-r--r-- root/root 23 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.ec.001a.test
-rw-r--r-- root/root 69 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.element-of.001.expected
-rw-r--r-- root/root 91 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001.expected
-rw-r--r-- root/root 52 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001a.test
-rw-r--r-- root/root 104 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.intersection.001b.test
-rw-r--r-- root/root 37 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.merge.001.expected
-rw-r--r-- root/root 111 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.merge.001.test
-rw-r--r-- root/root 368 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.named-pipe.001.expected
-rw-r--r-- root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.not-element-of.001.expected
-rw-r--r-- root/root 148 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001.expected
-rw-r--r-- root/root 39 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001a.test
-rw-r--r-- root/root 56 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001b.test
-rw-r--r-- root/root 40 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.partition.001c.test
-rw-r--r-- root/root 257 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.stdin.001.expected
-rw-r--r-- root/root 130 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.symdiff.001.expected
-rw-r--r-- root/root 134 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.union.001.expected
-rw-r--r-- root/root 126 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/001.union.001.test
-rw-r--r-- root/root 171 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.chop.002.expected
-rw-r--r-- root/root 20 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.chrom.002.expected
-rw-r--r-- root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.complement.002.expected
-rw-r--r-- root/root 2172 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002.expected
-rw-r--r-- root/root 3033 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002a.test
-rw-r--r-- root/root 2941 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.difference.002b.test
-rw-r--r-- root/root 18 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.element-of.002.expected
-rw-r--r-- root/root 13 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.intersection.002.expected
-rw-r--r-- root/root 26 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.intersection.002.test
-rw-r--r-- root/root 11 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.merge.002.expected
-rw-r--r-- root/root 11 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.not-element-of.002.expected
-rw-r--r-- root/root 376 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002.expected
-rw-r--r-- root/root 48 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002a.test
-rw-r--r-- root/root 49 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002b.test
-rw-r--r-- root/root 101 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002c.test
-rw-r--r-- root/root 39 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002d.test
-rw-r--r-- root/root 131 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.partition.002e.test
-rw-r--r-- root/root 118 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.symdiff.002.expected
-rw-r--r-- root/root 56 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/002.union.002.expected
-rw-r--r-- root/root 368 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.chop.003.expected
-rw-r--r-- root/root 24 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.chrom.003.expected
-rw-r--r-- root/root 61 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.complement.003.expected
-rw-r--r-- root/root 3794 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.difference.003.expected
-rw-r--r-- root/root 42 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.element-of.003.expected
-rw-r--r-- root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.intersection.003.expected
-rw-r--r-- root/root 35 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.merge.003.expected
-rw-r--r-- root/root 46 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.merge.003.test
-rw-r--r-- root/root 21 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003.expected
-rw-r--r-- root/root 63 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003a.test
-rw-r--r-- root/root 42 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.not-element-of.003b.test
-rw-r--r-- root/root 153 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.partition.003.expected
-rw-r--r-- root/root 398 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.partition.003.test
-rw-r--r-- root/root 22 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003.expected
-rw-r--r-- root/root 18 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003a.test
-rw-r--r-- root/root 29 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003b.test
-rw-r--r-- root/root 9 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003c.test
-rw-r--r-- root/root 11 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.symdiff.003d.test
-rw-r--r-- root/root 355 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.union.003.expected
-rw-r--r-- root/root 360 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/003.union.003.test
-rw-r--r-- root/root 257 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.chop.004.expected
-rw-r--r-- root/root 24 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.chrom.004.expected
-rw-r--r-- root/root 111 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004.expected
-rw-r--r-- root/root 46 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004a.test
-rw-r--r-- root/root 132 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004b.test
-rw-r--r-- root/root 94 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.complement.004c.test
-rw-r--r-- root/root 30 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004.expected
-rw-r--r-- root/root 30 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004a.test
-rw-r--r-- root/root 31 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.difference.004b.test
-rw-r--r-- root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004.expected
-rw-r--r-- root/root 92 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004a.test
-rw-r--r-- root/root 23 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.element-of.004b.test
-rw-r--r-- root/root 49 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004.expected
-rw-r--r-- root/root 103 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004a.test
-rw-r--r-- root/root 85 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004b.test
-rw-r--r-- root/root 47 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.intersection.004c.test
-rw-r--r-- root/root 72 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.merge.004.expected
-rw-r--r-- root/root 117 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.partition.004.expected
-rw-r--r-- root/root 117 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.partition.004.test
-rw-r--r-- root/root 52 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.symdiff.004.expected
-rw-r--r-- root/root 22 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.union.004.expected
-rw-r--r-- root/root 32 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/004.union.004.test
-rw-r--r-- root/root 385 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.chop.005.expected
-rw-r--r-- root/root 87 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.chop.005.test
-rw-r--r-- root/root 20 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.complement.005.expected
-rw-r--r-- root/root 40 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.complement.005.test
-rw-r--r-- root/root 31 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.difference.005.expected
-rw-r--r-- root/root 93 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.merge.005.expected
-rw-r--r-- root/root 43 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.merge.005.test
-rw-r--r-- root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.symdiff.005.expected
-rw-r--r-- root/root 11 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/005.union.005.expected
-rw-r--r-- root/root 35 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/006.complement.006.expected
-rw-r--r-- root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/006.difference.006.expected
-rw-r--r-- root/root 41 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006.expected
-rw-r--r-- root/root 37 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006a.test
-rw-r--r-- root/root 35 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006b.test
-rw-r--r-- root/root 31 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/006.merge.006c.test
-rw-r--r-- root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/006.union.006.expected
-rw-r--r-- root/root 9 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/007.complement.007.expected
-rw-r--r-- root/root 0 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/007.difference.007.expected
-rw-r--r-- root/root 55 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007.expected
-rw-r--r-- root/root 56 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007a.test
-rw-r--r-- root/root 69 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/007.merge.007b.test
-rw-r--r-- root/root 33 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/007.union.007.expected
-rw-r--r-- root/root 79 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/008.complement.008.expected
-rw-r--r-- root/root 197 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/008.merge.008.expected
-rw-r--r-- root/root 33 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/008.union.008.expected
-rw-r--r-- root/root 175 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/009.complement.009.expected
-rw-r--r-- root/root 52 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/009.merge.009.expected
-rw-r--r-- root/root 33 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/009.union.009.expected
-rw-r--r-- root/root 43 2020-04-06 20:55 ./usr/share/doc/bedops/tests/bedops/data/009.union.009.test
drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/doc/bedops/tests/starch/
-rw-r--r-- root/root 1078 2021-02-19 09:50 ./usr/share/doc/bedops/tests/starch/Makefile.gz
drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/doc/bedops/tests/starch/data/
-rw-r--r-- root/root 1935 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/001.starch_api.bedmap.001.expected
-rw-r--r-- root/root 2813 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/001.starch_api.bedmap.001.test.gz
-rw-r--r-- root/root 772 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr1.001.test
-rw-r--r-- root/root 1166 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr1andChr2.001.expected
-rw-r--r-- root/root 772 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/001.starchcat.disjoint_chrs.chr2.001.test
-rw-r--r-- root/root 764 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/001.unstarch.signature.001.expected
-rw-r--r-- root/root 2851 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/001.unstarch.signature.001.test.gz
-rw-r--r-- root/root 218 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/002.unstarch.signature.001.expected
-rw-r--r-- root/root 2254 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/002.unstarch.signature.001.test.gz
-rw-r--r-- root/root 109 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/README
-rw-r--r-- root/root 426 2020-04-06 20:55 ./usr/share/doc/bedops/tests/starch/data/hg38.bed
-rw-r--r-- root/root 1516 2021-02-19 09:50 ./usr/share/doc/bedops/tests/starch/generate_random_intervals.sh
drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/man/
drwxr-xr-x root/root 0 2021-02-19 09:50 ./usr/share/man/man1/
-rw-r--r-- root/root 348 2021-02-19 09:50 ./usr/share/man/man1/bam2bed.1.gz
-rw-r--r-- root/root 356 2021-02-19 09:50 ./usr/share/man/man1/bam2starch.1.gz
-rw-r--r-- root/root 850 2021-02-19 09:50 ./usr/share/man/man1/bedextract.1.gz
-rw-r--r-- root/root 2563 2021-02-19 09:50 ./usr/share/man/man1/bedmap.1.gz
-rw-r--r-- root/root 1045 2021-02-19 09:50 ./usr/share/man/man1/bedops-starch.1.gz
-rw-r--r-- root/root 1394 2021-02-19 09:50 ./usr/share/man/man1/bedops.1.gz
-rw-r--r-- root/root 1279 2021-02-19 09:50 ./usr/share/man/man1/closest-features.1.gz
-rw-r--r-- root/root 1225 2021-02-19 09:50 ./usr/share/man/man1/convert2bed.1.gz
-rw-r--r-- root/root 348 2021-02-19 09:50 ./usr/share/man/man1/gff2bed.1.gz
-rw-r--r-- root/root 356 2021-02-19 09:50 ./usr/share/man/man1/gff2starch.1.gz
-rw-r--r-- root/root 348 2021-02-19 09:50 ./usr/share/man/man1/gtf2bed.1.gz
-rw-r--r-- root/root 356 2021-02-19 09:50 ./usr/share/man/man1/gtf2starch.1.gz
-rw-r--r-- root/root 349 2021-02-19 09:50 ./usr/share/man/man1/gvf2bed.1.gz
-rw-r--r-- root/root 357 2021-02-19 09:50 ./usr/share/man/man1/gvf2starch.1.gz
-rw-r--r-- root/root 348 2021-02-19 09:50 ./usr/share/man/man1/psl2bed.1.gz
-rw-r--r-- root/root 356 2021-02-19 09:50 ./usr/share/man/man1/psl2starch.1.gz
-rw-r--r-- root/root 351 2021-02-19 09:50 ./usr/share/man/man1/rmsk2bed.1.gz
-rw-r--r-- root/root 358 2021-02-19 09:50 ./usr/share/man/man1/rmsk2starch.1.gz
-rw-r--r-- root/root 348 2021-02-19 09:50 ./usr/share/man/man1/sam2bed.1.gz
-rw-r--r-- root/root 356 2021-02-19 09:50 ./usr/share/man/man1/sam2starch.1.gz
-rw-r--r-- root/root 742 2021-02-19 09:50 ./usr/share/man/man1/sort-bed.1.gz
-rw-r--r-- root/root 722 2021-02-19 09:50 ./usr/share/man/man1/starch-diff.1.gz
-rw-r--r-- root/root 989 2021-02-19 09:50 ./usr/share/man/man1/starchcat.1.gz
-rw-r--r-- root/root 1111 2021-02-19 09:50 ./usr/share/man/man1/starchstrip.1.gz
-rw-r--r-- root/root 1544 2021-02-19 09:50 ./usr/share/man/man1/unstarch.1.gz
-rw-r--r-- root/root 1765 2021-02-19 09:50 ./usr/share/man/man1/update-sort-bed-migrate-candidates.1.gz
-rw-r--r-- root/root 1331 2021-02-19 09:50 ./usr/share/man/man1/update-sort-bed-slurm.1.gz
-rw-r--r-- root/root 1384 2021-02-19 09:50 ./usr/share/man/man1/update-sort-bed-starch-slurm.1.gz
-rw-r--r-- root/root 349 2021-02-19 09:50 ./usr/share/man/man1/vcf2bed.1.gz
-rw-r--r-- root/root 357 2021-02-19 09:50 ./usr/share/man/man1/vcf2starch.1.gz
-rw-r--r-- root/root 349 2021-02-19 09:50 ./usr/share/man/man1/wig2bed.1.gz
-rw-r--r-- root/root 357 2021-02-19 09:50 ./usr/share/man/man1/wig2starch.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 43176
Build-Time: 1589
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 285
Job: bedops_2.4.39+dfsg1-2
Machine Architecture: armhf
Package: bedops
Package-Time: 1910
Source-Version: 2.4.39+dfsg1-2
Space: 43176
Status: successful
Version: 2.4.39+dfsg1-2
--------------------------------------------------------------------------------
Finished at 2021-03-01T06:13:05Z
Build needed 00:31:50, 43176k disk space