qtltools →
1.2+dfsg-2+b3 →
armhf → 2020-06-10 06:43:58
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| qtltools 1.2+dfsg-2+b3 (armhf) Wed, 10 Jun 2020 04:26:24 +0000 |
+==============================================================================+
Package: qtltools
Version: 1.2+dfsg-2+b3
Source Version: 1.2+dfsg-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-132a2465-a48a-47f1-82e2-d17eb79673d9' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| 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 [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.5 MB in 25s (976 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'qtltools' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/qtltools.git
Please use:
git clone https://salsa.debian.org/med-team/qtltools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 13.7 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main qtltools 1.2+dfsg-2 (dsc) [2171 B]
Get:2 http://172.17.0.1/private bullseye-staging/main qtltools 1.2+dfsg-2 (tar) [105 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main qtltools 1.2+dfsg-2 (diff) [13.6 MB]
Fetched 13.7 MB in 1s (11.6 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/qtltools-QosTS0/qtltools-1.2+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/qtltools-QosTS0' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-IZYf90/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-IZYf90/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-IZYf90/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-IZYf90/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-IZYf90/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-IZYf90/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-IZYf90/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-IZYf90/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2836 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 37 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-IZYf90/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (23.2 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12234 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 12~), libblas-dev, libboost-iostreams-dev, libboost-program-options-dev, libbz2-dev, libeigen3-dev, libgsl-dev, libhts-dev, r-mathlib, zlib1g-dev
Filtered Build-Depends: debhelper (>= 12~), libblas-dev, libboost-iostreams-dev, libboost-program-options-dev, libbz2-dev, libeigen3-dev, libgsl-dev, libhts-dev, r-mathlib, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-qtltools-dummy' in '/<<BUILDDIR>>/resolver-IZYf90/apt_archive/sbuild-build-depends-qtltools-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-qtltools-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-IZYf90/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-IZYf90/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-IZYf90/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-IZYf90/apt_archive ./ Sources [551 B]
Get:5 copy:/<<BUILDDIR>>/resolver-IZYf90/apt_archive ./ Packages [635 B]
Fetched 2519 B in 1s (3110 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install qtltools build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils bzip2 debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base icu-devtools intltool-debian libarchive-zip-perl libblas-dev
libblas3 libboost-iostreams-dev libboost-iostreams1.71-dev
libboost-iostreams1.71.0 libboost-program-options-dev
libboost-program-options1.71-dev libboost-program-options1.71.0
libboost-regex1.71-dev libboost-regex1.71.0 libboost1.71-dev libbrotli1
libbsd0 libbz2-1.0 libbz2-dev libcroco3 libcurl3-gnutls libdebhelper-perl
libdeflate0 libeigen3-dev libelf1 libfile-stripnondeterminism-perl
libglib2.0-0 libgsl-dev libgsl25 libgslcblas0 libgssapi-krb5-2 libhts-dev
libhts3 libicu-dev libicu67 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libsigsegv2 libssh2-1 libssl1.1
libsub-override-perl libtinfo5 libtool libuchardet0 libxml2 m4 man-db
pkg-config po-debconf r-mathlib sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation bzip2-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev
groff liblapack-doc libboost1.71-doc libboost-atomic1.71-dev
libboost-chrono1.71-dev libboost-container1.71-dev libboost-context1.71-dev
libboost-contract1.71-dev libboost-coroutine1.71-dev
libboost-date-time1.71-dev libboost-exception1.71-dev libboost-fiber1.71-dev
libboost-filesystem1.71-dev libboost-graph1.71-dev
libboost-graph-parallel1.71-dev libboost-locale1.71-dev libboost-log1.71-dev
libboost-math1.71-dev libboost-mpi1.71-dev libboost-mpi-python1.71-dev
libboost-numpy1.71-dev libboost-python1.71-dev libboost-random1.71-dev
libboost-serialization1.71-dev libboost-stacktrace1.71-dev
libboost-system1.71-dev libboost-test1.71-dev libboost-thread1.71-dev
libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev
libboost1.71-tools-dev libmpfrc++-dev libntl-dev libeigen3-doc gsl-ref-psdoc
| gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user icu-doc
liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc
apparmor less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl
libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix
libltdl-dev libmail-sendmail-perl r-base-core r-base-dev
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base icu-devtools intltool-debian libarchive-zip-perl libblas-dev
libblas3 libboost-iostreams-dev libboost-iostreams1.71-dev
libboost-iostreams1.71.0 libboost-program-options-dev
libboost-program-options1.71-dev libboost-program-options1.71.0
libboost-regex1.71-dev libboost-regex1.71.0 libboost1.71-dev libbrotli1
libbsd0 libbz2-dev libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0
libeigen3-dev libelf1 libfile-stripnondeterminism-perl libglib2.0-0
libgsl-dev libgsl25 libgslcblas0 libgssapi-krb5-2 libhts-dev libhts3
libicu-dev libicu67 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5
librtmp1 libsigsegv2 libssh2-1 libssl1.1 libsub-override-perl libtinfo5
libtool libuchardet0 libxml2 m4 man-db pkg-config po-debconf r-mathlib
sbuild-build-depends-qtltools-dummy sensible-utils zlib1g-dev
The following packages will be upgraded:
bzip2 libbz2-1.0
2 upgraded, 73 newly installed, 0 to remove and 35 not upgraded.
Need to get 53.1 MB of archives.
After this operation, 303 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-IZYf90/apt_archive ./ sbuild-build-depends-qtltools-dummy 0.invalid.0 [916 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.2-1 [318 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.2-1 [1269 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf bzip2 armhf 1.0.8-3 [46.9 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libbz2-1.0 armhf 1.0.8-3 [44.0 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-1 [775 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.1 [187 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.8.1-1 [25.2 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.8.1-1 [14.9 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.3-1 [1159 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-2 [8286 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5+b1 [593 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.1 [1012 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf icu-devtools armhf 67.1-2 [170 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-2 [108 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-2 [113 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libboost1.71-dev armhf 1.71.0-6+b1 [9099 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libboost-regex1.71.0 armhf 1.71.0-6+b1 [435 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libicu-dev armhf 67.1-2 [9216 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libboost-regex1.71-dev armhf 1.71.0-6+b1 [571 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams1.71.0 armhf 1.71.0-6+b1 [256 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams1.71-dev armhf 1.71.0-6+b1 [271 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams-dev armhf 1.71.0.3+b1 [4388 B]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libboost-program-options1.71.0 armhf 1.71.0-6+b1 [341 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libboost-program-options1.71-dev armhf 1.71.0-6+b1 [396 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libboost-program-options-dev armhf 1.71.0.3+b1 [4412 B]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6.1 [255 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-3 [28.0 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-7+rpi1+b1 [61.8 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-7+rpi1+b1 [112 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1g-1 [1272 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-7+rpi1+b1 [318 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-7+rpi1+b1 [136 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.41.0-2 [61.2 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.68.0-1 [284 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.6-1 [47.4 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libeigen3-dev all 3.3.7-2 [850 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libgslcblas0 armhf 2.6+dfsg-2 [79.5 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libgsl25 armhf 2.6+dfsg-2 [753 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libgsl-dev armhf 2.6+dfsg-2 [950 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.10.2-3 [319 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.10.2-3 [4796 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf r-mathlib armhf 4.0.0-3+b1 [2006 kB]
debconf: delaying package configuration, since apt-utils is not installed
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Processing triggers for libc-bin (2.30-8+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.34-8+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-12+rpi1 gcc-9_9.3.0-12+rpi1 libc6-dev_2.30-8+rpi1 libstdc++-9-dev_9.3.0-12+rpi1 libstdc++6_10.1.0-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.1.4 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8+rpi1 binutils-arm-linux-gnueabihf_2.34-8+rpi1 binutils-common_2.34-8+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.35.1-5 build-essential_12.8 bzip2_1.0.8-3 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-12+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.8.1-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.1-5 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-12+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-1+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1 gcc-8-base_8.4.0-3+rpi1 gcc-9_9.3.0-12+rpi1 gcc-9-base_9.3.0-12+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 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_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 icu-devtools_67.1-2 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg6.0_2.1.4 libarchive-zip-perl_1.68-1 libasan5_9.3.0-12+rpi1 libassuan0_2.5.3-7 libatomic1_10.1.0-1+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-8+rpi1 libblas-dev_3.9.0-2 libblas3_3.9.0-2 libblkid1_2.35.1-5 libboost-iostreams-dev_1.71.0.3+b1 libboost-iostreams1.71-dev_1.71.0-6+b1 libboost-iostreams1.71.0_1.71.0-6+b1 libboost-program-options-dev_1.71.0.3+b1 libboost-program-options1.71-dev_1.71.0-6+b1 libboost-program-options1.71.0_1.71.0-6+b1 libboost-regex1.71-dev_1.71.0-6+b1 libboost-regex1.71.0_1.71.0-6+b1 libboost1.71-dev_1.71.0-6+b1 libbrotli1_1.0.7-6.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-3 libbz2-dev_1.0.8-3 libc-bin_2.30-8+rpi1 libc-dev-bin_2.30-8+rpi1 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sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.35.1-5 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun Dec 29 16:18:48 2019 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./qtltools_1.2+dfsg-2.dsc
dpkg-source: info: extracting qtltools in /<<BUILDDIR>>/qtltools-1.2+dfsg
dpkg-source: info: unpacking qtltools_1.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking qtltools_1.2+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying Makefile_config.patch
dpkg-source: info: applying Spelling_error.patch
dpkg-source: info: applying reproducible_build.patch
Check disc space
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Sufficient free space for build
Hack binNMU version
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Created changelog entry for binNMU version 1.2+dfsg-2+b3
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-132a2465-a48a-47f1-82e2-d17eb79673d9
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package qtltools
dpkg-buildpackage: info: source version 1.2+dfsg-2+b3
dpkg-buildpackage: info: source distribution bullseye-staging
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 '/<<BUILDDIR>>/qtltools-1.2+dfsg'
rm -f debian/upstream.example/examples.tar.xz
dh_auto_clean
make -j4 clean
make[2]: Entering directory '/<<BUILDDIR>>/qtltools-1.2+dfsg'
rm -f obj/*.o bin/QTLtools
make[2]: Leaving directory '/<<BUILDDIR>>/qtltools-1.2+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/qtltools-1.2+dfsg'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/qtltools-1.2+dfsg'
mkdir -p /<<BUILDDIR>>/qtltools-1.2+dfsg/obj/
mkdir -p /<<BUILDDIR>>/qtltools-1.2+dfsg/bin/
dh_auto_build
make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<BUILDDIR>>/qtltools-1.2+dfsg'
g++ -std=c++0x -o obj/QTLtools.o -c src/QTLtools.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/data.o -c src/common/data.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/ase_main.o -c src/mode_ase/ase_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/ase_read_genotypes.o -c src/mode_ase/ase_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
src/mode_ase/ase_read_genotypes.cpp: In member function 'void ase_data::readGenotypes(std::string, std::string)':
src/mode_ase/ase_read_genotypes.cpp:42:27: warning: this statement may fall through [-Wimplicit-fallthrough=]
42 | case not_bgzf: vrb.error("Not compressed with bgzip");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_ase/ase_read_genotypes.cpp:43:3: note: here
43 | case idx_load_failed: vrb.error("Impossible to load index file");
| ^~~~
src/mode_ase/ase_read_genotypes.cpp:43:34: warning: this statement may fall through [-Wimplicit-fallthrough=]
43 | case idx_load_failed: vrb.error("Impossible to load index file");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_ase/ase_read_genotypes.cpp:44:3: note: here
44 | case file_type_error: vrb.error("Unrecognized file format");
| ^~~~
src/mode_ase/ase_read_genotypes.cpp:44:34: warning: this statement may fall through [-Wimplicit-fallthrough=]
44 | case file_type_error: vrb.error("Unrecognized file format");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_ase/ase_read_genotypes.cpp:45:3: note: here
45 | default: vrb.error("Unknown error when opening");
| ^~~~~~~
g++ -std=c++0x -o obj/ase_read_sequences.o -c src/mode_ase/ase_read_sequences.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/bamstat_main.o -c src/mode_bamstat/bamstat_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/bamstat_read_annotations.o -c src/mode_bamstat/bamstat_read_annotations.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/bamstat_read_bam.o -c src/mode_bamstat/bamstat_read_bam.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
src/mode_ase/ase_read_sequences.cpp: In member function 'void ase_data::readSequences(std::string, std::string)':
src/mode_ase/ase_read_sequences.cpp:83:18: warning: ignoring return value of 'int bcf_hdr_write(htsFile*, bcf_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
83 | bcf_hdr_write(bcf_fd, bcf_hdr);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
g++ -std=c++0x -o obj/bamstat_write_output.o -c src/mode_bamstat/bamstat_write_output.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/cis_chunking.o -c src/mode_cis/cis_chunking.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/cis_collapse_phenotypes.o -c src/mode_cis/cis_collapse_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/cis_conditionnal_pass.o -c src/mode_cis/cis_conditionnal_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
In file included from src/mode_cis/cis_conditionnal_pass.cpp:16:
src/mode_cis/cis_data.h: In member function 'double cis_data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/mode_cis/cis_data.h:149:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
149 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/mode_cis/cis_data.h:150:2: note: here
150 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/mode_cis/cis_data.h:150:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
150 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/mode_cis/cis_data.h:151:2: note: here
151 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
g++ -std=c++0x -o obj/cis_initilization.o -c src/mode_cis/cis_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
In file included from /usr/include/c++/9/vector:72,
from lib/OTools/otools.h:20,
from src/mode_cis/../common/data.h:19,
from src/mode_cis/cis_data.h:32,
from src/mode_cis/cis_conditionnal_pass.cpp:16:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from lib/OTools/otools.h:20,
from src/mode_cis/../common/data.h:19,
from src/mode_cis/cis_data.h:32,
from src/mode_cis/cis_collapse_phenotypes.cpp:16:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void cis_data::runConditionalPass(std::string)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
g++ -std=c++0x -o obj/cis_learn_beta.o -c src/mode_cis/cis_learn_beta.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/cis_learn_dof.o -c src/mode_cis/cis_learn_dof.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/cis_main.o -c src/mode_cis/cis_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/cis_management.o -c src/mode_cis/cis_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/cis_nominal_pass.o -c src/mode_cis/cis_nominal_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/cis_permutation_pass.o -c src/mode_cis/cis_permutation_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/cis_read_covariates.o -c src/mode_cis/cis_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
In file included from src/mode_cis/cis_nominal_pass.cpp:16:
src/mode_cis/cis_data.h: In member function 'double cis_data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/mode_cis/cis_data.h:149:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
149 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/mode_cis/cis_data.h:150:2: note: here
150 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/mode_cis/cis_data.h:150:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
150 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/mode_cis/cis_data.h:151:2: note: here
151 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from src/mode_cis/cis_permutation_pass.cpp:16:
src/mode_cis/cis_data.h: In member function 'double cis_data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/mode_cis/cis_data.h:149:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
149 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/mode_cis/cis_data.h:150:2: note: here
150 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/mode_cis/cis_data.h:150:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
150 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/mode_cis/cis_data.h:151:2: note: here
151 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
g++ -std=c++0x -o obj/cis_read_genotypes.o -c src/mode_cis/cis_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/cis_read_phenotypes.o -c src/mode_cis/cis_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/cis_read_thresholds.o -c src/mode_cis/cis_read_thresholds.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/correct_main.o -c src/mode_correct/correct_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/correct_management.o -c src/mode_correct/correct_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/correct_processing.o -c src/mode_correct/correct_processing.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/correct_read_covariates.o -c src/mode_correct/correct_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/extract_main.o -c src/mode_extract/extract_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
src/mode_correct/correct_read_covariates.cpp: In member function 'void correct_data::readQTLCovariates(std::string, std::string)':
src/mode_correct/correct_read_covariates.cpp:107:59: warning: unused variable 'nsl' [-Wunused-variable]
107 | int ngt, ngt_arr = 0, nds, nds_arr = 0, * gt_arr = NULL, nsl, nsl_arr = 0, * sl_arr = NULL;
| ^~~
src/mode_correct/correct_read_covariates.cpp:107:64: warning: unused variable 'nsl_arr' [-Wunused-variable]
107 | int ngt, ngt_arr = 0, nds, nds_arr = 0, * gt_arr = NULL, nsl, nsl_arr = 0, * sl_arr = NULL;
| ^~~~~~~
src/mode_correct/correct_read_covariates.cpp:107:79: warning: unused variable 'sl_arr' [-Wunused-variable]
107 | int ngt, ngt_arr = 0, nds, nds_arr = 0, * gt_arr = NULL, nsl, nsl_arr = 0, * sl_arr = NULL;
| ^~~~~~
src/mode_correct/correct_processing.cpp: In member function 'void correct_data::processVCF(std::string, std::string)':
src/mode_correct/correct_processing.cpp:124:15: warning: ignoring return value of 'int bcf_hdr_write(htsFile*, bcf_hdr_t*)', declared with attribute warn_unused_result [-Wunused-result]
124 | bcf_hdr_write(fp, hdr_new);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~
g++ -std=c++0x -o obj/extract_managment.o -c src/mode_extract/extract_managment.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/extract_read_data.o -c src/mode_extract/extract_read_data.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/extract_write.o -c src/mode_extract/extract_write.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/fdensity_main.o -c src/mode_fdensity/fdensity_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/fdensity_process.o -c src/mode_fdensity/fdensity_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/fdensity_read_annotation.o -c src/mode_fdensity/fdensity_read_annotation.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
src/mode_extract/extract_read_data.cpp: In member function 'void extract_data::readVCF(std::string)':
src/mode_extract/extract_read_data.cpp:101:27: warning: this statement may fall through [-Wimplicit-fallthrough=]
101 | case not_bgzf: vrb.error("File not compressed with bgzip!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_extract/extract_read_data.cpp:102:3: note: here
102 | case idx_load_failed: vrb.error("Impossible to load index file!");
| ^~~~
src/mode_extract/extract_read_data.cpp:102:34: warning: this statement may fall through [-Wimplicit-fallthrough=]
102 | case idx_load_failed: vrb.error("Impossible to load index file!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_extract/extract_read_data.cpp:103:3: note: here
103 | case file_type_error: vrb.error("File format not detected by htslib!");
| ^~~~
src/mode_extract/extract_read_data.cpp:103:34: warning: this statement may fall through [-Wimplicit-fallthrough=]
103 | case file_type_error: vrb.error("File format not detected by htslib!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_extract/extract_read_data.cpp:104:3: note: here
104 | default : vrb.error("Unknown error!");
| ^~~~~~~
g++ -std=c++0x -o obj/fdensity_read_qtl.o -c src/mode_fdensity/fdensity_read_qtl.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/fenrich_main.o -c src/mode_fenrich/fenrich_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/fenrich_management.o -c src/mode_fenrich/fenrich_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/fenrich_process.o -c src/mode_fenrich/fenrich_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/fenrich_read_annotation.o -c src/mode_fenrich/fenrich_read_annotation.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/fenrich_read_qtl.o -c src/mode_fenrich/fenrich_read_qtl.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/fenrich_read_tss.o -c src/mode_fenrich/fenrich_read_tss.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/genrich_binning_process.o -c src/mode_genrich/genrich_binning_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/genrich_main.o -c src/mode_genrich/genrich_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/genrich_process.o -c src/mode_genrich/genrich_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/genrich_read_auxillliary_data.o -c src/mode_genrich/genrich_read_auxillliary_data.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/genrich_read_phenotypes.o -c src/mode_genrich/genrich_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/genrich_read_reference_genotypes.o -c src/mode_genrich/genrich_read_reference_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/genrich_routines.o -c src/mode_genrich/genrich_routines.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
src/mode_genrich/genrich_read_reference_genotypes.cpp: In member function 'void genrich_data::readReferenceGenotypes(std::string)':
src/mode_genrich/genrich_read_reference_genotypes.cpp:26:27: warning: this statement may fall through [-Wimplicit-fallthrough=]
26 | case not_bgzf: vrb.error("File not compressed with bgzip!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_genrich/genrich_read_reference_genotypes.cpp:27:3: note: here
27 | case idx_load_failed: vrb.error("Impossible to load index file!");
| ^~~~
src/mode_genrich/genrich_read_reference_genotypes.cpp:27:34: warning: this statement may fall through [-Wimplicit-fallthrough=]
27 | case idx_load_failed: vrb.error("Impossible to load index file!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_genrich/genrich_read_reference_genotypes.cpp:28:3: note: here
28 | case file_type_error: vrb.error("File format not detected by htslib!");
| ^~~~
src/mode_genrich/genrich_read_reference_genotypes.cpp:28:34: warning: this statement may fall through [-Wimplicit-fallthrough=]
28 | case file_type_error: vrb.error("File format not detected by htslib!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_genrich/genrich_read_reference_genotypes.cpp:29:3: note: here
29 | default : vrb.error("Unknown error!");
| ^~~~~~~
g++ -std=c++0x -o obj/gwas_analysis_pass.o -c src/mode_gwas/gwas_analysis_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/gwas_initilization.o -c src/mode_gwas/gwas_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/gwas_main.o -c src/mode_gwas/gwas_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/gwas_managment.o -c src/mode_gwas/gwas_managment.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
src/mode_gwas/gwas_analysis_pass.cpp: In member function 'void gwas_data::runGwasPassOnVCF(std::string, std::string)':
src/mode_gwas/gwas_analysis_pass.cpp:28:21: warning: ignoring return value of 'int bcf_hdr_set_samples(bcf_hdr_t*, const char*, int)', declared with attribute warn_unused_result [-Wunused-result]
28 | bcf_hdr_set_samples(hdr, concat_id.c_str(), 0);
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from src/mode_gwas/gwas_analysis_pass.cpp:16:
src/mode_gwas/gwas_data.h: In member function 'double gwas_data::fastCorrelation(std::vector<float>&, float*)':
src/mode_gwas/gwas_data.h:93:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
93 | case 3: sum0 += P[i+2] * G[i+2];
| ~~~~~^~~~~~~~~~~~~~~~~~
src/mode_gwas/gwas_data.h:94:2: note: here
94 | case 2: sum0 += P[i+1] * G[i+1];
| ^~~~
src/mode_gwas/gwas_data.h:94:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
94 | case 2: sum0 += P[i+1] * G[i+1];
| ~~~~~^~~~~~~~~~~~~~~~~~
src/mode_gwas/gwas_data.h:95:2: note: here
95 | case 1: sum0 += P[i+0] * G[i+0];
| ^~~~
src/mode_gwas/gwas_data.h: In member function 'double gwas_data::fastCorrelation(std::vector<float>&, std::vector<float>&)':
src/mode_gwas/gwas_data.h:117:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
117 | case 3: sum0 += P[i+2] * G[i+2];
src/mode_gwas/gwas_data.h:118:2: note: here
118 | case 2: sum0 += P[i+1] * G[i+1];
| ^~~~
src/mode_gwas/gwas_data.h:118:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
118 | case 2: sum0 += P[i+1] * G[i+1];
src/mode_gwas/gwas_data.h:119:2: note: here
119 | case 1: sum0 += P[i+0] * G[i+0];
| ^~~~
g++ -std=c++0x -o obj/gwas_read_covariates.o -c src/mode_gwas/gwas_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/gwas_read_phenotypes.o -c src/mode_gwas/gwas_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/match_main.o -c src/mode_match/match_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/match_managment.o -c src/mode_match/match_managment.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/match_process.o -c src/mode_match/match_process.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/match_read_genotypes.o -c src/mode_match/match_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/match_read_sequences.o -c src/mode_match/match_read_sequences.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/pca_main.o -c src/mode_pca/pca_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
src/mode_match/match_read_genotypes.cpp: In member function 'void match_data::readGenotypes(std::string, std::string)':
src/mode_match/match_read_genotypes.cpp:40:27: warning: this statement may fall through [-Wimplicit-fallthrough=]
40 | case not_bgzf: vrb.error("Not compressed with bgzip");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_match/match_read_genotypes.cpp:41:3: note: here
41 | case idx_load_failed: vrb.error("Impossible to load index file");
| ^~~~
src/mode_match/match_read_genotypes.cpp:41:34: warning: this statement may fall through [-Wimplicit-fallthrough=]
41 | case idx_load_failed: vrb.error("Impossible to load index file");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_match/match_read_genotypes.cpp:42:3: note: here
42 | case file_type_error: vrb.error("Unrecognized file format");
| ^~~~
src/mode_match/match_read_genotypes.cpp:42:34: warning: this statement may fall through [-Wimplicit-fallthrough=]
42 | case file_type_error: vrb.error("Unrecognized file format");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_match/match_read_genotypes.cpp:43:3: note: here
43 | default: vrb.error("Unknown error when opening");
| ^~~~~~~
g++ -std=c++0x -o obj/pca_management.o -c src/mode_pca/pca_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/pca_pca.o -c src/mode_pca/pca_pca.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/pca_read_data.o -c src/mode_pca/pca_read_data.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/quan_main.o -c src/mode_quan/quan_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
src/mode_pca/pca_read_data.cpp: In member function 'void pca_data::readDataVCF(std::string)':
src/mode_pca/pca_read_data.cpp:47:37: warning: this statement may fall through [-Wimplicit-fallthrough=]
47 | case not_bgzf: vrb.error("File not compressed with bgzip!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_pca/pca_read_data.cpp:48:13: note: here
48 | case idx_load_failed: vrb.error("Impossible to load index file!");
| ^~~~
src/mode_pca/pca_read_data.cpp:48:44: warning: this statement may fall through [-Wimplicit-fallthrough=]
48 | case idx_load_failed: vrb.error("Impossible to load index file!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_pca/pca_read_data.cpp:49:13: note: here
49 | case file_type_error: vrb.error("File format not detected by htslib!");
| ^~~~
src/mode_pca/pca_read_data.cpp:49:44: warning: this statement may fall through [-Wimplicit-fallthrough=]
49 | case file_type_error: vrb.error("File format not detected by htslib!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_pca/pca_read_data.cpp:50:13: note: here
50 | default : vrb.error("Unknown error!");
| ^~~~~~~
g++ -std=c++0x -o obj/quan_readBAM.o -c src/mode_quan/quan_readBAM.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/quan_readGTF.o -c src/mode_quan/quan_readGTF.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/quan_writeResults.o -c src/mode_quan/quan_writeResults.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/quan_xxhash.o -c src/mode_quan/quan_xxhash.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
In file included from /usr/include/c++/9/vector:72,
from lib/OTools/otools.h:20,
from src/mode_quan/../common/data.h:19,
from src/mode_quan/quan_data.h:21,
from src/mode_quan/quan_readGTF.cpp:16:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const my_exon&}; _Tp = my_exon; _Alloc = std::allocator<my_exon>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<my_exon>::iterator' {aka '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {my_gene}; _Tp = my_gene; _Alloc = std::allocator<my_gene>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<my_gene>::iterator' {aka '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from lib/OTools/otools.h:29,
from src/mode_quan/../common/data.h:19,
from src/mode_quan/quan_data.h:21,
from src/mode_quan/quan_readGTF.cpp:16:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from lib/OTools/otools.h:20,
from src/mode_quan/../common/data.h:19,
from src/mode_quan/quan_data.h:21,
from src/mode_quan/quan_readBAM.cpp:16:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const my_gene&}; _Tp = my_gene; _Alloc = std::allocator<my_gene>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<my_gene>::iterator' {aka '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
In file included from /usr/include/c++/9/queue:62,
from lib/OTools/otools.h:22,
from src/mode_quan/../common/data.h:19,
from src/mode_quan/quan_data.h:21,
from src/mode_quan/quan_readGTF.cpp:16:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >; _Distance = int; _Tp = my_exon; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from lib/OTools/otools.h:20,
from src/mode_quan/../common/data.h:19,
from src/mode_quan/quan_data.h:21,
from src/mode_quan/quan_readBAM.cpp:16:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<my_gene> quan2_data::getOverlappingGenesQ(my_block&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from lib/OTools/otools.h:29,
from src/mode_quan/../common/data.h:19,
from src/mode_quan/quan_data.h:21,
from src/mode_quan/quan_readGTF.cpp:16:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
In file included from /usr/include/c++/9/queue:62,
from lib/OTools/otools.h:22,
from src/mode_quan/../common/data.h:19,
from src/mode_quan/quan_data.h:21,
from src/mode_quan/quan_readGTF.cpp:16:
/usr/include/c++/9/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
408 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from lib/OTools/otools.h:29,
from src/mode_quan/../common/data.h:19,
from src/mode_quan/quan_data.h:21,
from src/mode_quan/quan_readGTF.cpp:16:
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'void my_gene::assign(my_exon&)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from lib/OTools/otools.h:20,
from src/mode_quan/../common/data.h:19,
from src/mode_quan/quan_data.h:21,
from src/mode_quan/quan_readGTF.cpp:16:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_exon*, std::vector<my_exon> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/queue:62,
from lib/OTools/otools.h:22,
from src/mode_quan/../common/data.h:19,
from src/mode_quan/quan_data.h:21,
from src/mode_quan/quan_readGTF.cpp:16:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >; _Distance = int; _Tp = my_gene; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
In file included from /usr/include/c++/9/algorithm:62,
from lib/OTools/otools.h:29,
from src/mode_quan/../common/data.h:19,
from src/mode_quan/quan_data.h:21,
from src/mode_quan/quan_readGTF.cpp:16:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
In file included from /usr/include/c++/9/queue:62,
from lib/OTools/otools.h:22,
from src/mode_quan/../common/data.h:19,
from src/mode_quan/quan_data.h:21,
from src/mode_quan/quan_readGTF.cpp:16:
/usr/include/c++/9/bits/stl_heap.h:408:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
408 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from lib/OTools/otools.h:29,
from src/mode_quan/../common/data.h:19,
from src/mode_quan/quan_data.h:21,
from src/mode_quan/quan_readGTF.cpp:16:
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
1671 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++0x -o obj/rep_initilization.o -c src/mode_rep/rep_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/rep_main.o -c src/mode_rep/rep_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
In file included from /usr/include/c++/9/vector:72,
from lib/OTools/otools.h:20,
from src/mode_quan/../common/data.h:19,
from src/mode_quan/quan_data.h:21,
from src/mode_quan/quan_readGTF.cpp:16:
/usr/include/c++/9/bits/vector.tcc: In member function 'void quan2_data::readGTF(std::string)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from lib/OTools/otools.h:29,
from src/mode_quan/../common/data.h:19,
from src/mode_quan/quan_data.h:21,
from src/mode_quan/quan_readGTF.cpp:16:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<my_gene*, std::vector<my_gene> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++0x -o obj/rep_management.o -c src/mode_rep/rep_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/rep_nominal_pass.o -c src/mode_rep/rep_nominal_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
In file included from src/mode_rep/rep_nominal_pass.cpp:16:
src/mode_rep/rep_data.h: In member function 'double rep_data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/mode_rep/rep_data.h:121:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
121 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/mode_rep/rep_data.h:122:2: note: here
122 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/mode_rep/rep_data.h:122:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
122 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/mode_rep/rep_data.h:123:2: note: here
123 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
g++ -std=c++0x -o obj/rep_read_covariates.o -c src/mode_rep/rep_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/rep_read_genotypes.o -c src/mode_rep/rep_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/rep_read_phenotypes.o -c src/mode_rep/rep_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/rep_read_qtls.o -c src/mode_rep/rep_read_qtls.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/rtc_chunking.o -c src/mode_rtc/rtc_chunking.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/rtc_collapse_phenotypes.o -c src/mode_rtc/rtc_collapse_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/rtc_common.o -c src/mode_rtc/rtc_common.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/rtc_gwas_cis.o -c src/mode_rtc/rtc_gwas_cis.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/rtc_gwas_trans.o -c src/mode_rtc/rtc_gwas_trans.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
In file included from src/mode_rtc/rtc_common.cpp:16:
src/mode_rtc/rtc_data.h: In member function 'double rtc_data::getCorrelation(std::vector<float>&, std::vector<float>&, int)':
src/mode_rtc/rtc_data.h:300:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
300 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/mode_rtc/rtc_data.h:301:9: note: here
301 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/mode_rtc/rtc_data.h:301:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
301 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/mode_rtc/rtc_data.h:302:9: note: here
302 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
g++ -std=c++0x -o obj/rtc_initilization.o -c src/mode_rtc/rtc_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
src/mode_rtc/rtc_data.h: In member function 'double rtc_data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/mode_rtc/rtc_data.h:276:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
276 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/mode_rtc/rtc_data.h:277:2: note: here
277 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/mode_rtc/rtc_data.h:277:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
277 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/mode_rtc/rtc_data.h:278:2: note: here
278 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from /usr/include/c++/9/vector:72,
from lib/OTools/otools.h:20,
from src/mode_rtc/../common/data.h:19,
from src/mode_rtc/rtc_data.h:36,
from src/mode_rtc/rtc_collapse_phenotypes.cpp:16:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from lib/OTools/otools.h:20,
from src/mode_rtc/../common/data.h:19,
from src/mode_rtc/rtc_data.h:36,
from src/mode_rtc/rtc_common.cpp:16:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pairsToTestForRTC&}; _Tp = pairsToTestForRTC; _Alloc = std::allocator<pairsToTestForRTC>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pairsToTestForRTC>::iterator' {aka '__gnu_cxx::__normal_iterator<pairsToTestForRTC*, std::vector<pairsToTestForRTC> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from lib/OTools/otools.h:29,
from src/mode_rtc/../common/data.h:19,
from src/mode_rtc/rtc_data.h:36,
from src/mode_rtc/rtc_common.cpp:16:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/queue:62,
from lib/OTools/otools.h:22,
from src/mode_rtc/../common/data.h:19,
from src/mode_rtc/rtc_data.h:36,
from src/mode_rtc/rtc_common.cpp:16:
/usr/include/c++/9/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> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from lib/OTools/otools.h:29,
from src/mode_rtc/../common/data.h:19,
from src/mode_rtc/rtc_data.h:36,
from src/mode_rtc/rtc_common.cpp:16:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++0x -o obj/rtc_main.o -c src/mode_rtc/rtc_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/rtc_management.o -c src/mode_rtc/rtc_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
In file included from src/mode_rtc/rtc_management.cpp:16:
src/mode_rtc/rtc_data.h: In member function 'double rtc_data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/mode_rtc/rtc_data.h:276:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
276 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/mode_rtc/rtc_data.h:277:2: note: here
277 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/mode_rtc/rtc_data.h:277:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
277 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/mode_rtc/rtc_data.h:278:2: note: here
278 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
g++ -std=c++0x -o obj/rtc_mergeQTL_cis.o -c src/mode_rtc/rtc_mergeQTL_cis.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/rtc_mergeQTL_trans.o -c src/mode_rtc/rtc_mergeQTL_trans.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/rtc_read_covariates.o -c src/mode_rtc/rtc_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/rtc_read_genotypes.o -c src/mode_rtc/rtc_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
src/mode_rtc/rtc_read_genotypes.cpp: In member function 'void rtc_data::readGenotypesVCF(std::string)':
src/mode_rtc/rtc_read_genotypes.cpp:81:27: warning: this statement may fall through [-Wimplicit-fallthrough=]
81 | case not_bgzf: vrb.error("File not compressed with bgzip!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_rtc/rtc_read_genotypes.cpp:82:3: note: here
82 | case idx_load_failed: vrb.error("Impossible to load index file!");
| ^~~~
src/mode_rtc/rtc_read_genotypes.cpp:82:34: warning: this statement may fall through [-Wimplicit-fallthrough=]
82 | case idx_load_failed: vrb.error("Impossible to load index file!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_rtc/rtc_read_genotypes.cpp:83:3: note: here
83 | case file_type_error: vrb.error("File format not detected by htslib!");
| ^~~~
src/mode_rtc/rtc_read_genotypes.cpp:83:34: warning: this statement may fall through [-Wimplicit-fallthrough=]
83 | case file_type_error: vrb.error("File format not detected by htslib!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_rtc/rtc_read_genotypes.cpp:84:3: note: here
84 | default : vrb.error("Unknown error!");
| ^~~~~~~
src/mode_rtc/rtc_read_genotypes.cpp: In member function 'int rtc_data::readGenotypesVCFStats(std::string, std::string&, std::vector<std::__cxx11::basic_string<char> >&)':
src/mode_rtc/rtc_read_genotypes.cpp:263:37: warning: this statement may fall through [-Wimplicit-fallthrough=]
263 | case not_bgzf: vrb.error("File not compressed with bgzip!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_rtc/rtc_read_genotypes.cpp:264:13: note: here
264 | case idx_load_failed: vrb.error("Impossible to load index file!");
| ^~~~
src/mode_rtc/rtc_read_genotypes.cpp:264:44: warning: this statement may fall through [-Wimplicit-fallthrough=]
264 | case idx_load_failed: vrb.error("Impossible to load index file!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_rtc/rtc_read_genotypes.cpp:265:13: note: here
265 | case file_type_error: vrb.error("File format not detected by htslib!");
| ^~~~
src/mode_rtc/rtc_read_genotypes.cpp:265:44: warning: this statement may fall through [-Wimplicit-fallthrough=]
265 | case file_type_error: vrb.error("File format not detected by htslib!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_rtc/rtc_read_genotypes.cpp:266:13: note: here
266 | default : vrb.error("Unknown error!");
| ^~~~~~~
src/mode_rtc/rtc_read_genotypes.cpp: In member function 'void rtc_data::scanGenotypesVCF(std::string)':
src/mode_rtc/rtc_read_genotypes.cpp:330:37: warning: this statement may fall through [-Wimplicit-fallthrough=]
330 | case not_bgzf: vrb.error("File not compressed with bgzip!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_rtc/rtc_read_genotypes.cpp:331:13: note: here
331 | case idx_load_failed: vrb.error("Impossible to load index file!");
| ^~~~
src/mode_rtc/rtc_read_genotypes.cpp:331:44: warning: this statement may fall through [-Wimplicit-fallthrough=]
331 | case idx_load_failed: vrb.error("Impossible to load index file!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_rtc/rtc_read_genotypes.cpp:332:13: note: here
332 | case file_type_error: vrb.error("File format not detected by htslib!");
| ^~~~
src/mode_rtc/rtc_read_genotypes.cpp:332:44: warning: this statement may fall through [-Wimplicit-fallthrough=]
332 | case file_type_error: vrb.error("File format not detected by htslib!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_rtc/rtc_read_genotypes.cpp:333:13: note: here
333 | default : vrb.error("Unknown error!");
| ^~~~~~~
g++ -std=c++0x -o obj/rtc_read_get_hotspots.o -c src/mode_rtc/rtc_read_get_hotspots.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/rtc_read_phenotypes.o -c src/mode_rtc/rtc_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/rtc_sampling.o -c src/mode_rtc/rtc_sampling.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/trans_adjust.o -c src/mode_trans/trans_adjust.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
In file included from src/mode_rtc/rtc_sampling.cpp:16:
src/mode_rtc/rtc_data.h: In member function 'double rtc_data::getCorrelation(std::vector<float>&, std::vector<float>&, int)':
src/mode_rtc/rtc_data.h:300:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
300 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/mode_rtc/rtc_data.h:301:9: note: here
301 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/mode_rtc/rtc_data.h:301:22: warning: this statement may fall through [-Wimplicit-fallthrough=]
301 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/mode_rtc/rtc_data.h:302:9: note: here
302 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
src/mode_rtc/rtc_data.h: In member function 'double rtc_data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/mode_rtc/rtc_data.h:276:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
276 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/mode_rtc/rtc_data.h:277:2: note: here
277 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/mode_rtc/rtc_data.h:277:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
277 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/mode_rtc/rtc_data.h:278:2: note: here
278 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from /usr/include/c++/9/set:60,
from lib/OTools/otools.h:25,
from src/mode_rtc/../common/data.h:19,
from src/mode_rtc/rtc_data.h:36,
from src/mode_rtc/rtc_sampling.cpp:16:
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from lib/OTools/otools.h:29,
from src/mode_rtc/../common/data.h:19,
from src/mode_rtc/rtc_data.h:36,
from src/mode_rtc/rtc_sampling.cpp:16:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/queue:62,
from lib/OTools/otools.h:22,
from src/mode_rtc/../common/data.h:19,
from src/mode_rtc/rtc_data.h:36,
from src/mode_rtc/rtc_sampling.cpp:16:
/usr/include/c++/9/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> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from lib/OTools/otools.h:29,
from src/mode_rtc/../common/data.h:19,
from src/mode_rtc/rtc_data.h:36,
from src/mode_rtc/rtc_sampling.cpp:16:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from lib/OTools/otools.h:20,
from src/mode_trans/../common/data.h:19,
from src/mode_trans/trans_data.h:26,
from src/mode_trans/trans_adjust.cpp:16:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from lib/OTools/otools.h:26,
from src/mode_rtc/../common/data.h:19,
from src/mode_rtc/rtc_data.h:36,
from src/mode_rtc/rtc_sampling.cpp:16:
/usr/include/c++/9/bits/stl_map.h: In member function 'rtc_sample_results rtc_data::sampleRTC(std::vector<int>&, std::vector<float>&, int, double, int)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/algorithm:62,
from lib/OTools/otools.h:29,
from src/mode_rtc/../common/data.h:19,
from src/mode_rtc/rtc_data.h:36,
from src/mode_rtc/rtc_sampling.cpp:16:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from lib/OTools/otools.h:26,
from src/mode_rtc/../common/data.h:19,
from src/mode_rtc/rtc_data.h:36,
from src/mode_rtc/rtc_sampling.cpp:16:
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/algorithm:62,
from lib/OTools/otools.h:29,
from src/mode_rtc/../common/data.h:19,
from src/mode_rtc/rtc_data.h:36,
from src/mode_rtc/rtc_sampling.cpp:16:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from lib/OTools/otools.h:26,
from src/mode_rtc/../common/data.h:19,
from src/mode_rtc/rtc_data.h:36,
from src/mode_rtc/rtc_sampling.cpp:16:
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/vector.tcc: In member function 'void trans_data::buildNullDistribution(std::string)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
g++ -std=c++0x -o obj/trans_analysis_pass.o -c src/mode_trans/trans_analysis_pass.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/trans_chunking.o -c src/mode_trans/trans_chunking.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
In file included from /usr/include/c++/9/vector:67,
from lib/OTools/otools.h:20,
from src/mode_rtc/../common/data.h:19,
from src/mode_rtc/rtc_data.h:36,
from src/mode_rtc/rtc_common.cpp:16:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void rtc_data::calculateRTC(std::string)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pairsToTestForRTC*, std::vector<pairsToTestForRTC> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from lib/OTools/otools.h:29,
from src/mode_rtc/../common/data.h:19,
from src/mode_rtc/rtc_data.h:36,
from src/mode_rtc/rtc_common.cpp:16:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=c++0x -o obj/trans_initilization.o -c src/mode_trans/trans_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/trans_learn_beta.o -c src/mode_trans/trans_learn_beta.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/trans_main.o -c src/mode_trans/trans_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/trans_managment.o -c src/mode_trans/trans_managment.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/trans_read_covariates.o -c src/mode_trans/trans_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
In file included from src/mode_trans/trans_analysis_pass.cpp:16:
src/mode_trans/trans_data.h: In member function 'double trans_data::fastCorrelation(std::vector<float>&, float*)':
src/mode_trans/trans_data.h:122:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
122 | case 3: sum0 += P[i+2] * G[i+2];
| ~~~~~^~~~~~~~~~~~~~~~~~
src/mode_trans/trans_data.h:123:2: note: here
123 | case 2: sum0 += P[i+1] * G[i+1];
| ^~~~
src/mode_trans/trans_data.h:123:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
123 | case 2: sum0 += P[i+1] * G[i+1];
| ~~~~~^~~~~~~~~~~~~~~~~~
src/mode_trans/trans_data.h:124:2: note: here
124 | case 1: sum0 += P[i+0] * G[i+0];
| ^~~~
g++ -std=c++0x -o obj/trans_read_phenotypes.o -c src/mode_trans/trans_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/trans_read_samples.o -c src/mode_trans/trans_read_samples.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/union_initilization.o -c src/mode_union/union_initilization.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/union_main.o -c src/mode_union/union_main.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/union_management.o -c src/mode_union/union_management.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/union_read_covariates.o -c src/mode_union/union_read_covariates.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/union_read_genotypes.o -c src/mode_union/union_read_genotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/union_read_get_hotspots.o -c src/mode_union/union_read_get_hotspots.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
g++ -std=c++0x -o obj/union_read_phenotypes.o -c src/mode_union/union_read_phenotypes.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
src/mode_union/union_read_genotypes.cpp: In member function 'void union_data::readGenotypesVCF(std::string, std::string)':
src/mode_union/union_read_genotypes.cpp:76:27: warning: this statement may fall through [-Wimplicit-fallthrough=]
76 | case not_bgzf: vrb.error("File not compressed with bgzip!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_union/union_read_genotypes.cpp:77:3: note: here
77 | case idx_load_failed: vrb.error("Impossible to load index file!");
| ^~~~
src/mode_union/union_read_genotypes.cpp:77:34: warning: this statement may fall through [-Wimplicit-fallthrough=]
77 | case idx_load_failed: vrb.error("Impossible to load index file!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_union/union_read_genotypes.cpp:78:3: note: here
78 | case file_type_error: vrb.error("File format not detected by htslib!");
| ^~~~
src/mode_union/union_read_genotypes.cpp:78:34: warning: this statement may fall through [-Wimplicit-fallthrough=]
78 | case file_type_error: vrb.error("File format not detected by htslib!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_union/union_read_genotypes.cpp:79:3: note: here
79 | default : vrb.error("Unknown error!");
| ^~~~~~~
src/mode_union/union_read_genotypes.cpp: In member function 'void union_data::scanGenotypesVCF(std::string)':
src/mode_union/union_read_genotypes.cpp:248:37: warning: this statement may fall through [-Wimplicit-fallthrough=]
248 | case not_bgzf: vrb.error("File not compressed with bgzip!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_union/union_read_genotypes.cpp:249:13: note: here
249 | case idx_load_failed: vrb.error("Impossible to load index file!");
| ^~~~
src/mode_union/union_read_genotypes.cpp:249:44: warning: this statement may fall through [-Wimplicit-fallthrough=]
249 | case idx_load_failed: vrb.error("Impossible to load index file!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_union/union_read_genotypes.cpp:250:13: note: here
250 | case file_type_error: vrb.error("File format not detected by htslib!");
| ^~~~
src/mode_union/union_read_genotypes.cpp:250:44: warning: this statement may fall through [-Wimplicit-fallthrough=]
250 | case file_type_error: vrb.error("File format not detected by htslib!");
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/mode_union/union_read_genotypes.cpp:251:13: note: here
251 | default : vrb.error("Unknown error!");
| ^~~~~~~
g++ -std=c++0x -o obj/union_union.o -c src/mode_union/union_union.cpp -O3 -Wall -Wextra -Wno-sign-compare -Wno-unused-local-typedefs -Wno-deprecated -Wno-unused-parameter -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/qtltools-1.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/eigen3 -Ilib/OTools -Ilib
In file included from src/mode_union/union_union.cpp:16:
src/mode_union/union_data.h: In member function 'double union_data::getCorrelation(std::vector<float>&, std::vector<float>&)':
src/mode_union/union_data.h:189:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
189 | case 3: sum0 += vec1[i+2] * vec2[i+2];
src/mode_union/union_data.h:190:2: note: here
190 | case 2: sum0 += vec1[i+1] * vec2[i+1];
| ^~~~
src/mode_union/union_data.h:190:15: warning: this statement may fall through [-Wimplicit-fallthrough=]
190 | case 2: sum0 += vec1[i+1] * vec2[i+1];
src/mode_union/union_data.h:191:2: note: here
191 | case 1: sum0 += vec1[i+0] * vec2[i+0];
| ^~~~
In file included from /usr/include/c++/9/vector:72,
from lib/OTools/otools.h:20,
from src/mode_union/../common/data.h:19,
from src/mode_union/union_data.h:20,
from src/mode_union/union_union.cpp:16:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from lib/OTools/otools.h:20,
from src/mode_union/../common/data.h:19,
from src/mode_union/union_data.h:20,
from src/mode_union/union_union.cpp:16:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void union_data::find_unions(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -std=c++0x obj/QTLtools.o obj/data.o obj/ase_main.o obj/ase_read_genotypes.o obj/ase_read_sequences.o obj/bamstat_main.o obj/bamstat_read_annotations.o obj/bamstat_read_bam.o obj/bamstat_write_output.o obj/cis_chunking.o obj/cis_collapse_phenotypes.o obj/cis_conditionnal_pass.o obj/cis_initilization.o obj/cis_learn_beta.o obj/cis_learn_dof.o obj/cis_main.o obj/cis_management.o obj/cis_nominal_pass.o obj/cis_permutation_pass.o obj/cis_read_covariates.o obj/cis_read_genotypes.o obj/cis_read_phenotypes.o obj/cis_read_thresholds.o obj/correct_main.o obj/correct_management.o obj/correct_processing.o obj/correct_read_covariates.o obj/extract_main.o obj/extract_managment.o obj/extract_read_data.o obj/extract_write.o obj/fdensity_main.o obj/fdensity_process.o obj/fdensity_read_annotation.o obj/fdensity_read_qtl.o obj/fenrich_main.o obj/fenrich_management.o obj/fenrich_process.o obj/fenrich_read_annotation.o obj/fenrich_read_qtl.o obj/fenrich_read_tss.o obj/genrich_binning_process.o obj/genrich_main.o obj/genrich_process.o obj/genrich_read_auxillliary_data.o obj/genrich_read_phenotypes.o obj/genrich_read_reference_genotypes.o obj/genrich_routines.o obj/gwas_analysis_pass.o obj/gwas_initilization.o obj/gwas_main.o obj/gwas_managment.o obj/gwas_read_covariates.o obj/gwas_read_phenotypes.o obj/match_main.o obj/match_managment.o obj/match_process.o obj/match_read_genotypes.o obj/match_read_sequences.o obj/pca_main.o obj/pca_management.o obj/pca_pca.o obj/pca_read_data.o obj/quan_main.o obj/quan_readBAM.o obj/quan_readGTF.o obj/quan_writeResults.o obj/quan_xxhash.o obj/rep_initilization.o obj/rep_main.o obj/rep_management.o obj/rep_nominal_pass.o obj/rep_read_covariates.o obj/rep_read_genotypes.o obj/rep_read_phenotypes.o obj/rep_read_qtls.o obj/rtc_chunking.o obj/rtc_collapse_phenotypes.o obj/rtc_common.o obj/rtc_gwas_cis.o obj/rtc_gwas_trans.o obj/rtc_initilization.o obj/rtc_main.o obj/rtc_management.o obj/rtc_mergeQTL_cis.o obj/rtc_mergeQTL_trans.o obj/rtc_read_covariates.o obj/rtc_read_genotypes.o obj/rtc_read_get_hotspots.o obj/rtc_read_phenotypes.o obj/rtc_sampling.o obj/trans_adjust.o obj/trans_analysis_pass.o obj/trans_chunking.o obj/trans_initilization.o obj/trans_learn_beta.o obj/trans_main.o obj/trans_managment.o obj/trans_read_covariates.o obj/trans_read_phenotypes.o obj/trans_read_samples.o obj/union_initilization.o obj/union_main.o obj/union_management.o obj/union_read_covariates.o obj/union_read_genotypes.o obj/union_read_get_hotspots.o obj/union_read_phenotypes.o obj/union_union.o -lRmath -lhts -lboost_iostreams -lboost_program_options -o bin/QTLtools -lz -lgsl -lblas -lbz2 -lm -lpthread -Wl,-z,relro -Wl,-z,now
make[2]: Leaving directory '/<<BUILDDIR>>/qtltools-1.2+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/qtltools-1.2+dfsg'
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
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/qtltools-1.2+dfsg'
cd debian/upstream.example && find -type f | LC_ALL=C sort | tar -T - --sort=name --mode=go=rX,u+rw,a-s --owner=root --group=root --numeric-owner -Jcvf examples.tar.xz
./genes.50percent.chr22.bed.gz
./genes.50percent.chr22.bed.gz.tbi
./genes.covariates.pc50.txt.gz
./genes.simulated.chr22.bed.gz
./genes.simulated.chr22.bed.gz.tbi
./genotypes.chr22.vcf.gz
./genotypes.chr22.vcf.gz.tbi
dh_install
make[1]: Leaving directory '/<<BUILDDIR>>/qtltools-1.2+dfsg'
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dwz: debian/qtltools/usr/bin/QTLtools: .debug_info section not present
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/qtltools/usr/bin/QTLtools 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/qtltools/usr/bin/QTLtools was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/qtltools/usr/bin/QTLtools was not linked against libblas.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'qtltools-dbgsym' in '../qtltools-dbgsym_1.2+dfsg-2+b3_armhf.deb'.
dpkg-deb: building package 'qtltools' in '../qtltools_1.2+dfsg-2+b3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../qtltools_1.2+dfsg-2+b3_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 2020-06-10T06:43:47Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
qtltools_1.2+dfsg-2+b3_armhf.changes:
-------------------------------------
Format: 1.8
Date: Wed, 25 Dec 2019 22:27:16 +0100
Source: qtltools (1.2+dfsg-2)
Binary: qtltools qtltools-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 1.2+dfsg-2+b3
Distribution: bullseye-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
qtltools - Tool set for molecular QTL discovery and analysis
Changes:
qtltools (1.2+dfsg-2+b3) bullseye-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild for boost 1.71
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Files:
e788b69f03a6344b3bbe3b770af94475 61024 debug optional qtltools-dbgsym_1.2+dfsg-2+b3_armhf.deb
a6afa9fea2bddc3e80e64614185d6612 6462 science optional qtltools_1.2+dfsg-2+b3_armhf.buildinfo
91a25e29c2fd2f27e678e5a46df14bfd 530404 science optional qtltools_1.2+dfsg-2+b3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
qtltools-dbgsym_1.2+dfsg-2+b3_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 61024 bytes: control archive=544 bytes.
399 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: qtltools-dbgsym
Source: qtltools (1.2+dfsg-2)
Version: 1.2+dfsg-2+b3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 469
Depends: qtltools (= 1.2+dfsg-2+b3)
Section: debug
Priority: optional
Description: debug symbols for qtltools
Build-Ids: 5c70230fa3fa78c9113bea77a639ced87a4cf45a
drwxr-xr-x root/root 0 2019-12-25 21:27 ./
drwxr-xr-x root/root 0 2019-12-25 21:27 ./usr/
drwxr-xr-x root/root 0 2019-12-25 21:27 ./usr/lib/
drwxr-xr-x root/root 0 2019-12-25 21:27 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-12-25 21:27 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-12-25 21:27 ./usr/lib/debug/.build-id/5c/
-rw-r--r-- root/root 469676 2019-12-25 21:27 ./usr/lib/debug/.build-id/5c/70230fa3fa78c9113bea77a639ced87a4cf45a.debug
drwxr-xr-x root/root 0 2019-12-25 21:27 ./usr/share/
drwxr-xr-x root/root 0 2019-12-25 21:27 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-12-25 21:27 ./usr/share/doc/qtltools-dbgsym -> qtltools
qtltools_1.2+dfsg-2+b3_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 530404 bytes: control archive=984 bytes.
967 bytes, 18 lines control
345 bytes, 5 lines md5sums
Package: qtltools
Source: qtltools (1.2+dfsg-2)
Version: 1.2+dfsg-2+b3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1882
Depends: libblas3 | libblas.so.3, libboost-iostreams1.71.0, libboost-program-options1.71.0, libc6 (>= 2.29), libgcc-s1 (>= 4.0), libgsl25 (>= 2.6), libhts3 (>= 1.10), libstdc++6 (>= 5.2), r-mathlib
Suggests: qtltools-example
Section: science
Priority: optional
Homepage: https://qtltools.github.io/qtltools/
Description: Tool set for molecular QTL discovery and analysis
QTLtools is a tool set for molecular Quantitative Trait Loci (QTL) discovery
and analysis. It allows user to go from the raw sequence data to collection of
molecular QTL in few easy-to-perform steps. QTLtools contains multiple methods
to prepare the data, to discover proximal and distal molecular QTL and to
finally integrate them with GWAS variants and functional annotations of the
genome.
drwxr-xr-x root/root 0 2019-12-25 21:27 ./
drwxr-xr-x root/root 0 2019-12-25 21:27 ./usr/
drwxr-xr-x root/root 0 2019-12-25 21:27 ./usr/bin/
-rwxr-xr-x root/root 1910280 2019-12-25 21:27 ./usr/bin/QTLtools
drwxr-xr-x root/root 0 2019-12-25 21:27 ./usr/share/
drwxr-xr-x root/root 0 2019-12-25 21:27 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-12-25 21:27 ./usr/share/doc/qtltools/
-rw-r--r-- root/root 218 2019-12-25 21:27 ./usr/share/doc/qtltools/changelog.Debian.armhf.gz
-rw-r--r-- root/root 770 2019-12-25 21:27 ./usr/share/doc/qtltools/changelog.Debian.gz
-rw-r--r-- root/root 2843 2019-12-25 14:43 ./usr/share/doc/qtltools/copyright
drwxr-xr-x root/root 0 2019-12-25 21:27 ./usr/share/man/
drwxr-xr-x root/root 0 2019-12-25 21:27 ./usr/share/man/man1/
-rw-r--r-- root/root 1601 2019-12-25 21:27 ./usr/share/man/man1/QTLtools.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 57040
Build-Time: 7816
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 369
Job: qtltools_1.2+dfsg-2
Machine Architecture: armhf
Package: qtltools
Package-Time: 8243
Source-Version: 1.2+dfsg-2
Space: 57040
Status: successful
Version: 1.2+dfsg-2+b3
--------------------------------------------------------------------------------
Finished at 2020-06-10T06:43:47Z
Build needed 02:17:23, 57040k disc space