r-bioc-bitseq →
1.26.1+dfsg-1 →
armhf → 2019-01-14 07:00:28
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| r-bioc-bitseq 1.26.1+dfsg-1 (armhf) Mon, 14 Jan 2019 06:45:44 +0000 |
+==============================================================================+
Package: r-bioc-bitseq
Version: 1.26.1+dfsg-1
Source Version: 1.26.1+dfsg-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-b8a5a70e-fae2-4b58-a288-d8c2ded3243d' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.1 MB]
Fetched 24.5 MB in 9s (2634 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: 'r-bioc-bitseq' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/r-pkg-team/r-bioc-bitseq.git
Please use:
git clone https://salsa.debian.org/r-pkg-team/r-bioc-bitseq.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 757 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main r-bioc-bitseq 1.26.1+dfsg-1 (dsc) [2161 B]
Get:2 http://172.17.0.1/private buster-staging/main r-bioc-bitseq 1.26.1+dfsg-1 (tar) [750 kB]
Get:3 http://172.17.0.1/private buster-staging/main r-bioc-bitseq 1.26.1+dfsg-1 (diff) [5348 B]
Fetched 757 kB in 0s (4141 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-bitseq-zdWYfC/r-bioc-bitseq-1.26.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-bitseq-zdWYfC' 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-wGHJsD/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-wGHJsD/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-wGHJsD/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-wGHJsD/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-wGHJsD/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-wGHJsD/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-wGHJsD/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-wGHJsD/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (10.9 kB/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 packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libgpg-error-l10n libnss-systemd libpam-systemd libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 1 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-wGHJsD/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 (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15814 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)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), dh-r, r-base-dev, r-bioc-rsamtools, r-bioc-zlibbioc, r-bioc-s4vectors, r-bioc-iranges, libboost-dev
Filtered Build-Depends: debhelper (>= 11~), dh-r, r-base-dev, r-bioc-rsamtools, r-bioc-zlibbioc, r-bioc-s4vectors, r-bioc-iranges, libboost-dev
dpkg-deb: building package 'sbuild-build-depends-r-bioc-bitseq-dummy' in '/<<BUILDDIR>>/resolver-wGHJsD/apt_archive/sbuild-build-depends-r-bioc-bitseq-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-r-bioc-bitseq-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-wGHJsD/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-wGHJsD/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-wGHJsD/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-wGHJsD/apt_archive ./ Sources [541 B]
Get:5 copy:/<<BUILDDIR>>/resolver-wGHJsD/apt_archive ./ Packages [625 B]
Fetched 2499 B in 0s (12.9 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install r-bioc-bitseq build dependencies (apt-based resolver)
-------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
dbus dbus-user-session e2fsprogs-l10n krb5-locales libgpg-error-l10n
libnss-systemd libpam-systemd systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils dctrl-tools debhelper
dh-autoreconf dh-r dh-strip-nondeterminism dwz file fontconfig
fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-8
groff-base icu-devtools intltool-debian libarchive-zip-perl libblas-dev
libblas3 libboost-dev libboost1.67-dev libbsd0 libbz2-dev libcairo2
libcroco3 libcurl4 libdatrie1 libelf1 libfile-stripnondeterminism-perl
libfile-which-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran-8-dev
libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libice6 libicu-dev
libicu63 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
liblapack-dev liblapack3 liblzma-dev libmagic-mgc libmagic1 libncurses-dev
libncurses5-dev libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev
libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev libpsl5
libreadline-dev librtmp1 libsigsegv2 libsm6 libssh2-1 libswitch-perl
libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0
libwebp6 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1
libxdmcp6 libxext6 libxft2 libxml2 libxmuu1 libxrender1 libxss1 libxt6 m4
man-db pkg-config po-debconf r-base-core r-base-dev r-bioc-biocgenerics
r-bioc-biocparallel r-bioc-biostrings r-bioc-genomeinfodb
r-bioc-genomeinfodbdata r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools
r-bioc-s4vectors r-bioc-xvector r-bioc-zlibbioc r-cran-bitops r-cran-formatr
r-cran-futile.logger r-cran-futile.options r-cran-lambda.r r-cran-rcurl
r-cran-snow ucf unzip x11-common xauth xdg-utils zip zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation debtags dh-make gettext-doc libasprintf-dev libgettextpo-dev
gfortran-doc gfortran-8-doc libgfortran5-dbg libcoarrays-dev groff
liblapack-doc libboost-doc libboost1.67-doc libboost-atomic1.67-dev
libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev
libboost-coroutine1.67-dev libboost-date-time1.67-dev
libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev
libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
libboost-program-options1.67-dev libboost-python1.67-dev
libboost-random1.67-dev libboost-regex1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
icu-doc liblzma-doc ncurses-doc readline-doc tcl8.6 tk8.6 libtool-doc
gcj-jdk m4-doc apparmor less www-browser libmail-box-perl ess r-doc-info
| r-doc-pdf r-mathlib r-base-html texlive-base texlive-latex-base
texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra
texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo
r-bioc-biobase r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2
r-bioc-annotate r-cran-foreach r-cran-batchjobs r-cran-bbmisc
r-cran-doparallel r-cran-rmpi r-bioc-variantannotation
r-bioc-genomicalignments r-bioc-shortread r-cran-codetools r-cran-runit
r-cran-knitr r-cran-batchtools r-cran-data.table r-bioc-bsgenome
r-bioc-genomicfeatures r-cran-matrix r-bioc-rtracklayer r-bioc-gviz
r-bioc-annotationhub r-bioc-edger r-bioc-summarizedexperiment
r-bioc-delayedarray r-bioc-graph r-cran-shiny r-cran-rmarkdown
r-cran-jsonlite r-cran-xml r-cran-rsprng r-cran-rlecuyer
Recommended packages:
devscripts curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs libpng-tools publicsuffix libltdl-dev
libmail-sendmail-perl r-recommended r-doc-html r-cran-runit r-cran-digest
r-bioc-annotate r-bioc-summarizedexperiment r-bioc-shortread r-cran-testit
r-cran-codetools r-cran-survival r-cran-testthat libfile-mimeinfo-perl
libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils dctrl-tools debhelper
dh-autoreconf dh-r dh-strip-nondeterminism dwz file fontconfig
fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-8
groff-base icu-devtools intltool-debian libarchive-zip-perl libblas-dev
libblas3 libboost-dev libboost1.67-dev libbsd0 libbz2-dev libcairo2
libcroco3 libcurl4 libdatrie1 libelf1 libfile-stripnondeterminism-perl
libfile-which-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran-8-dev
libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libice6 libicu-dev
libicu63 libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
liblapack-dev liblapack3 liblzma-dev libmagic-mgc libmagic1 libncurses-dev
libncurses5-dev libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev
libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev libpsl5
libreadline-dev librtmp1 libsigsegv2 libsm6 libssh2-1 libswitch-perl
libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0
libwebp6 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1
libxdmcp6 libxext6 libxft2 libxml2 libxmuu1 libxrender1 libxss1 libxt6 m4
man-db pkg-config po-debconf r-base-core r-base-dev r-bioc-biocgenerics
r-bioc-biocparallel r-bioc-biostrings r-bioc-genomeinfodb
r-bioc-genomeinfodbdata r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools
r-bioc-s4vectors r-bioc-xvector r-bioc-zlibbioc r-cran-bitops r-cran-formatr
r-cran-futile.logger r-cran-futile.options r-cran-lambda.r r-cran-rcurl
r-cran-snow sbuild-build-depends-r-bioc-bitseq-dummy ucf unzip x11-common
xauth xdg-utils zip zlib1g-dev
0 upgraded, 132 newly installed, 0 to remove and 1 not upgraded.
Need to get 119 MB/122 MB of archives.
After this operation, 395 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-wGHJsD/apt_archive ./ sbuild-build-depends-r-bioc-bitseq-dummy 0.invalid.0 [908 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-2 [782 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-2 [25.1 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.5-1 [1231 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libswitch-perl all 2.17-2 [20.5 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf ucf all 3.0038+nmu1 [69.0 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf dctrl-tools armhf 2.24-3 [94.2 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-6 [547 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.0.0-1 [19.5 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.0.0-1 [12.5 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.175-2 [157 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.2-3 [1076 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-5 [7976 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf debhelper all 12 [1002 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libpaper1 armhf 1.1.26 [20.0 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libpaper-utils armhf 1.1.26 [17.5 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf xdg-utils all 1.1.3-1 [73.3 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.2.0-13+rpi1 [205 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-2 [103 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libfreetype6 armhf 2.9.1-3 [318 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.13.1-2 [280 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libfontconfig1 armhf 2.13.1-2 [327 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libpixman-1-0 armhf 0.36.0-1 [458 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libxcb1 armhf 1.13.1-2 [132 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libx11-data all 2:1.6.7-1 [298 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libx11-6 armhf 2:1.6.7-1 [689 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libxcb-render0 armhf 1.13.1-2 [108 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libxcb-shm0 armhf 1.13.1-2 [99.3 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libcairo2 armhf 1.16.0-2 [602 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.35.1-1 [70.8 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libcurl4 armhf 7.62.0-1 [286 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-2 [1493 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf fontconfig armhf 2.13.1-2 [404 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libfribidi0 armhf 1.0.5-3 [61.9 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libthai-data all 0.1.28-1 [170 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libdatrie1 armhf 0.2.12-1 [35.8 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libthai0 armhf 0.1.28-1 [50.9 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libpango-1.0-0 armhf 1.42.4-6 [168 kB]
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Get:65 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 2.3.0-1 [1130 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libpangoft2-1.0-0 armhf 1.42.4-6 [61.9 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libpangocairo-1.0-0 armhf 1.42.4-6 [51.6 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libtcl8.6 armhf 8.6.9+dfsg-1 [878 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.10-3 [235 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libtk8.6 armhf 8.6.9-1 [666 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf r-base-core armhf 3.5.2-1 [23.6 MB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libgfortran-8-dev armhf 8.2.0-13+rpi1 [248 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf gfortran-8 armhf 8.2.0-13+rpi1 [5816 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:8.2.0-2+rpi1 [1432 B]
Get:77 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.8.0-2 [113 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.8.0-2 [1551 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20181013-1 [278 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1+20181013-1 [940 B]
Get:81 http://172.17.0.1/private buster-staging/main armhf libreadline-dev armhf 7.0-5 [110 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-11+rpi1 [234 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-11+rpi1 [227 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-11+rpi1 [150 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-11+rpi1 [565 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libpng-dev armhf 1.6.36-2 [280 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-9 [27.7 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 63.1-5 [166 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 63.1-5 [8845 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf libxmuu1 armhf 2:1.1.2-2 [23.0 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf xauth armhf 1:1.0.10-1 [36.4 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf r-base-dev all 3.5.2-1 [4480 B]
Get:94 http://172.17.0.1/private buster-staging/main armhf libfile-which-perl all 1.23-1 [16.6 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf dh-r all 20181206 [34.9 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf libboost1.67-dev armhf 1.67.0-11 [8386 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.67.0.1+b1 [4140 B]
Get:98 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocgenerics all 0.28.0-2 [644 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf r-cran-formatr all 1.5-3 [149 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf r-cran-lambda.r all 1.2.3-2 [117 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.options all 1.0.1-2 [19.8 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.logger all 1.4.3-3 [102 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf r-cran-snow all 1:0.4.3-1 [108 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocparallel armhf 1.16.5-1 [1057 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf r-bioc-s4vectors armhf 0.20.1-2 [1807 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf r-bioc-iranges armhf 2.16.0-1 [2121 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf r-bioc-xvector armhf 0.22.0-1 [596 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf r-bioc-biostrings armhf 2.50.2-1 [14.1 MB]
Get:109 http://172.17.0.1/private buster-staging/main armhf r-cran-bitops armhf 1.0-6-4 [23.9 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf r-cran-rcurl armhf 1.95-4.11-1 [711 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodbdata all 1.2.0-1 [9196 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodb all 1.18.1-1 [3692 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicranges armhf 1.34.0+dfsg-1 [1765 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf r-bioc-rsamtools armhf 1.34.0-1 [3492 kB]
Get:115 http://172.17.0.1/private buster-staging/main armhf r-bioc-zlibbioc all 1.28.0+dfsg-1 [8540 B]
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Setting up libxft2:armhf (2.3.2-2) ...
Setting up fontconfig (2.13.1-2) ...
Regenerating fonts cache... done.
Setting up liblapack-dev:armhf (3.8.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up gfortran (4:8.2.0-2+rpi1) ...
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Setting up r-base-core (3.5.2-1) ...
Creating config file /etc/R/Renviron with new version
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Setting up r-bioc-biostrings (2.50.2-1) ...
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Setting up r-bioc-rsamtools (1.34.0-1) ...
Setting up dh-autoreconf (19) ...
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Setting up debhelper (12) ...
Setting up dh-r (20181206) ...
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Processing triggers for libc-bin (2.28-2) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-11+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-13+rpi1 gcc-8_8.2.0-13+rpi1 libc6-dev_2.28-2 libstdc++-8-dev_8.2.0-13+rpi1 libstdc++6_8.2.0-13+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~alpha3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-11+rpi1 binutils-arm-linux-gnueabihf_2.31.1-11+rpi1 binutils-common_2.31.1-11+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-13+rpi1 dash_0.5.10.2-4 dbus_1.12.12-1 dbus-user-session_1.12.12-1 dctrl-tools_2.24-3 debconf_1.5.69 debhelper_12 debianutils_4.8.6 dh-autoreconf_19 dh-r_20181206 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.155-1 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 e2fsprogs-l10n_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20181018-1 fontconfig_2.13.1-2 fontconfig-config_2.13.1-2 fonts-dejavu-core_2.37-1 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-13+rpi1 gcc_4:8.2.0-2+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-13+rpi1 gcc-8-base_8.2.0-13+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gfortran_4:8.2.0-2+rpi1 gfortran-8_8.2.0-13+rpi1 gnupg_2.2.12-1+rpi1 gnupg-agent_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.1-3 groff-base_1.22.4-2 gzip_1.9-3 hostname_3.21 icu-devtools_63.1-5 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56+nmu1 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-2 krb5-locales_1.16.2-1 libacl1_2.2.52-3 libapparmor1_2.13.2-3 libapt-pkg5.0_1.8.0~alpha3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-13+rpi1 libassuan0_2.5.2-1 libatomic1_8.2.0-13+rpi1 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libxt6_1:1.1.5-1 libzstd1_1.3.8+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.5-1 mawk_1.3.3-17 mount_2.33.1-0.1 multiarch-support_2.28-2 nano_3.2-1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 netbase_5.5 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.24_5.24.1-7 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 r-base-core_3.5.2-1 r-base-dev_3.5.2-1 r-bioc-biocgenerics_0.28.0-2 r-bioc-biocparallel_1.16.5-1 r-bioc-biostrings_2.50.2-1 r-bioc-genomeinfodb_1.18.1-1 r-bioc-genomeinfodbdata_1.2.0-1 r-bioc-genomicranges_1.34.0+dfsg-1 r-bioc-iranges_2.16.0-1 r-bioc-rsamtools_1.34.0-1 r-bioc-s4vectors_0.20.1-2 r-bioc-xvector_0.22.0-1 r-bioc-zlibbioc_1.28.0+dfsg-1 r-cran-bitops_1.0-6-4 r-cran-formatr_1.5-3 r-cran-futile.logger_1.4.3-3 r-cran-futile.options_1.0.1-2 r-cran-lambda.r_1.2.3-2 r-cran-rcurl_1.95-4.11-1 r-cran-snow_1:0.4.3-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-bitseq-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_240-2+rpi1 systemd-sysv_240-2+rpi1 sysvinit-utils_2.93-3 tar_1.30+dfsg-4 tzdata_2018i-1 ucf_3.0038+nmu1 udev_240-2+rpi1 unzip_6.0-21 util-linux_2.33.1-0.1 x11-common_1:7.7+19 xauth_1:1.0.10-1 xdg-utils_1.1.3-1 xz-utils_5.2.2-1.3 zip_3.0-11 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Jan 9 07:06:07 2019 UTC
gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54
gpgv: issuer "daissi@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./r-bioc-bitseq_1.26.1+dfsg-1.dsc
dpkg-source: info: extracting r-bioc-bitseq in /<<BUILDDIR>>/r-bioc-bitseq-1.26.1+dfsg
dpkg-source: info: unpacking r-bioc-bitseq_1.26.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking r-bioc-bitseq_1.26.1+dfsg-1.debian.tar.xz
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-b8a5a70e-fae2-4b58-a288-d8c2ded3243d
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package r-bioc-bitseq
dpkg-buildpackage: info: source version 1.26.1+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --buildsystem R
dh_auto_clean -O--buildsystem=R
dh_autoreconf_clean -O--buildsystem=R
dh_clean -O--buildsystem=R
debian/rules build-arch
dh build-arch --buildsystem R
dh_update_autotools_config -a -O--buildsystem=R
dh_autoreconf -a -O--buildsystem=R
dh_auto_configure -a -O--buildsystem=R
dh_auto_build -a -O--buildsystem=R
dh_auto_test -a -O--buildsystem=R
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --buildsystem R
dh_testroot -a -O--buildsystem=R
dh_prep -a -O--buildsystem=R
dh_auto_install -a -O--buildsystem=R
I: R Package: BitSeq Version: 1.26.1
I: Building using R version 3.5.2-1
I: R API version: r-api-3.5
I: Using built-time from d/changelog: Wed, 09 Jan 2019 07:50:30 +0100
mkdir -p /<<BUILDDIR>>/r-bioc-bitseq-1.26.1\+dfsg/debian/r-bioc-bitseq/usr/lib/R/site-library
R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-bitseq-1.26.1\+dfsg/debian/r-bioc-bitseq/usr/lib/R/site-library --clean . "--built-timestamp='Wed, 09 Jan 2019 07:50:30 +0100'"
* installing *source* package 'BitSeq' ...
configure: Version def: -DBS_VERSION=\"1.26.1\"
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for g++ option to support OpenMP... -fopenmp
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/Makevars.win
** libs
make[1]: Entering directory '/<<BUILDDIR>>/r-bioc-bitseq-1.26.1+dfsg/src'
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ArgumentParser.cpp -o ArgumentParser.o
In file included from /usr/include/c++/8/vector:69,
from ArgumentParser.h:6,
from ArgumentParser.cpp:5:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: 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
/usr/include/c++/8/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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CollapsedSampler.cpp -o CollapsedSampler.o
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c FileHeader.cpp -o FileHeader.o
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c GibbsParameters.cpp -o GibbsParameters.o
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c GibbsSampler.cpp -o GibbsSampler.o
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MyTimer.cpp -o MyTimer.o
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PosteriorSamples.cpp -o PosteriorSamples.o
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_BitSeq.cpp -o R_init_BitSeq.o
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ReadDistribution.cpp -o ReadDistribution.o
In file included from /usr/include/c++/8/vector:69,
from ReadDistribution.h:4,
from ReadDistribution.cpp:7:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:478:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ReadDistribution.h:4,
from ReadDistribution.cpp:7:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void ReadDistribution::updateMismatchFreq(bam1_t*)':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
from ReadDistribution.h:5,
from ReadDistribution.cpp:7:
/usr/include/c++/8/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 long int&>, std::tuple<>}; _Key = long int; _Val = std::pair<const long int, double>; _KeyOfValue = std::_Select1st<std::pair<const long int, double> >; _Compare = std::less<long int>; _Alloc = std::allocator<std::pair<const long int, double> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from ReadDistribution.h:5,
from ReadDistribution.cpp:7:
/usr/include/c++/8/bits/stl_map.h: In member function 'double ReadDistribution::getWeightNorm(long int, ns_rD::readT, long int)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h: In member function 'bool ReadDistribution::observed(ns_rD::fragmentP)':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:64,
from ReadDistribution.h:4,
from ReadDistribution.cpp:7:
/usr/include/c++/8/bits/stl_vector.h: In constructor 'ReadDistribution::ReadDistribution()':
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
^~~~~~~~~~~~~~
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Sampler.cpp -o Sampler.o
In file included from /usr/include/c++/8/vector:69,
from Sampler.h:4,
from Sampler.cpp:5:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: 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
In file included from /usr/include/c++/8/vector:64,
from Sampler.h:4,
from Sampler.cpp:5:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void Sampler::appendFile()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SimpleSparse.cpp -o SimpleSparse.o
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c TagAlignments.cpp -o TagAlignments.o
In file included from /usr/include/c++/8/vector:69,
from TagAlignments.h:5,
from TagAlignments.cpp:3:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from TagAlignments.h:5,
from TagAlignments.cpp:3:
/usr/include/c++/8/bits/stl_vector.h: In member function 'void TagAlignments::pushAlignmentL(long int, double)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c TranscriptExpression.cpp -o TranscriptExpression.o
In file included from /usr/include/c++/8/algorithm:62,
from TranscriptExpression.cpp:1:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from TranscriptExpression.cpp:1:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >; _Distance = int; _Tp = trExpInfoT; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from TranscriptExpression.cpp:1:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'void TranscriptExpression::doSort(bool)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c TranscriptInfo.cpp -o TranscriptInfo.o
In file included from /usr/include/c++/8/vector:69,
from TranscriptInfo.h:4,
from TranscriptInfo.cpp:4:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const transcriptT&}; _Tp = transcriptT; _Alloc = std::allocator<transcriptT>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<transcriptT>::iterator' {aka '__gnu_cxx::__normal_iterator<transcriptT*, std::vector<transcriptT> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from TranscriptInfo.h:4,
from TranscriptInfo.cpp:4:
/usr/include/c++/8/bits/stl_vector.h: In member function 'bool TranscriptInfo::setInfo(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, std::vector<long int>)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<transcriptT*, std::vector<transcriptT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function 'bool TranscriptInfo::readInfo(std::__cxx11::string)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<transcriptT*, std::vector<transcriptT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c TranscriptSequence.cpp -o TranscriptSequence.o
In file included from /usr/include/c++/8/vector:69,
from TranscriptSequence.h:6,
from TranscriptSequence.cpp:6:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const trSeqInfoT&}; _Tp = trSeqInfoT; _Alloc = std::allocator<trSeqInfoT>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<trSeqInfoT>::iterator' {aka '__gnu_cxx::__normal_iterator<trSeqInfoT*, std::vector<trSeqInfoT> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from TranscriptSequence.h:6,
from TranscriptSequence.cpp:6:
/usr/include/c++/8/bits/stl_vector.h: In member function 'bool TranscriptSequence::readSequence(std::__cxx11::string, refFormatT)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trSeqInfoT*, std::vector<trSeqInfoT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c VariationalBayes.cpp -o VariationalBayes.o
In file included from /usr/include/c++/8/vector:69,
from /usr/include/boost/random/detail/polynomial.hpp:18,
from /usr/include/boost/random/mersenne_twister.hpp:32,
from VariationalBayes.h:4,
from VariationalBayes.cpp:12:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {boost::random::gamma_distribution<double>::param_type}; _Tp = boost::random::gamma_distribution<double>::param_type; _Alloc = std::allocator<boost::random::gamma_distribution<double>::param_type>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<boost::random::gamma_distribution<double>::param_type>::iterator' {aka '__gnu_cxx::__normal_iterator<boost::random::gamma_distribution<double>::param_type*, std::vector<boost::random::gamma_distribution<double>::param_type> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void VariationalBayes::generateSamples(long int, const string&, const std::vector<double>*, std::ofstream*)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::random::gamma_distribution<double>::param_type*, std::vector<boost::random::gamma_distribution<double>::param_type> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c common.cpp -o common.o
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c estimateDE.cpp -o estimateDE.o
estimateDE.cpp:57:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
estimateDE.cpp:57:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:532:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
estimateExpression.cpp:532:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from estimateExpression.cpp:1:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from estimateExpression.cpp:1:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from estimateExpression.cpp:1:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'void MCMC(TagAlignments*, gibbsParameters&, ArgumentParser&)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c estimateHyperPar.cpp -o estimateHyperPar.o
estimateHyperPar.cpp:62:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
estimateHyperPar.cpp:62:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /usr/include/boost/random/detail/polynomial.hpp:18,
from /usr/include/boost/random/mersenne_twister.hpp:32,
from estimateHyperPar.cpp:10:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ns_params::paramT&}; _Tp = ns_params::paramT; _Alloc = std::allocator<ns_params::paramT>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<ns_params::paramT>::iterator' {aka '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:159:5: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from estimateHyperPar.cpp:6:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from estimateHyperPar.cpp:6:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Distance = int; _Tp = ns_params::paramT; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from estimateHyperPar.cpp:6:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /usr/include/boost/random/detail/polynomial.hpp:18,
from /usr/include/boost/random/mersenne_twister.hpp:32,
from estimateHyperPar.cpp:10:
/usr/include/c++/8/bits/stl_vector.h: In function 'int estimateHyperPar(int*, char**)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from estimateHyperPar.cpp:6:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /usr/include/boost/random/detail/polynomial.hpp:18,
from /usr/include/boost/random/mersenne_twister.hpp:32,
from estimateHyperPar.cpp:10:
/usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
{ return _M_erase(begin() + (__position - cbegin())); }
^
/usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
{ return _M_erase(begin() + (__position - cbegin())); }
^
/usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
{ return _M_erase(begin() + (__position - cbegin())); }
^
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c estimateVBExpression.cpp -o estimateVBExpression.o
estimateVBExpression.cpp:126:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
estimateVBExpression.cpp:126:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getGeneExpression.cpp -o getGeneExpression.o
getGeneExpression.cpp:33:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
getGeneExpression.cpp:33:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getVariance.cpp -o getVariance.o
getVariance.cpp:28:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
getVariance.cpp:28:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
getWithinGeneExpression.cpp:54:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
getWithinGeneExpression.cpp:54:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lowess.cpp -o lowess.o
In file included from /usr/include/c++/8/algorithm:62,
from lowess.cpp:17:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: 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++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from lowess.cpp:17:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from lowess.cpp:17:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'void lowess(const std::vector<double>&, const std::vector<double>&, double, long int, double, std::vector<double>&, std::vector<double>&, std::vector<double>&)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c misc.cpp -o misc.o
In file included from /usr/include/c++/8/vector:69,
from ArgumentParser.h:6,
from misc.h:6,
from misc.cpp:5:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ns_params::paramT&}; _Tp = ns_params::paramT; _Alloc = std::allocator<ns_params::paramT>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<ns_params::paramT>::iterator' {aka '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from misc.cpp:1:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from misc.cpp:1:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from misc.cpp:1:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'void ns_misc::computeCI(double, std::vector<double>*, double*, double*)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from misc.cpp:1:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Distance = int; _Tp = ns_params::paramT; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from misc.cpp:1:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ArgumentParser.h:6,
from misc.h:6,
from misc.cpp:5:
/usr/include/c++/8/bits/stl_vector.h: In function 'bool ns_params::readParams(const string&, std::vector<ns_params::paramT>*, std::ofstream*)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from misc.cpp:1:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c parseAlignment.cpp -o parseAlignment.o
parseAlignment.cpp:102:38: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
parseAlignment.cpp:102:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
^~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ArgumentParser.h:6,
from parseAlignment.cpp:7:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {ns_parseAlignment::TagAlignment}; _Tp = ns_parseAlignment::TagAlignment; _Alloc = std::allocator<ns_parseAlignment::TagAlignment>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<ns_parseAlignment::TagAlignment>::iterator' {aka '__gnu_cxx::__normal_iterator<ns_parseAlignment::TagAlignment*, std::vector<ns_parseAlignment::TagAlignment> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'int parseAlignment(int*, char**)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_parseAlignment::TagAlignment*, std::vector<ns_parseAlignment::TagAlignment> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
g++ -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.26.1\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rsamtools/include" -I"/usr/lib/R/site-library/zlibbioc/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c transposeFiles.cpp -o transposeFiles.o
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o BitSeq.so ArgumentParser.o CollapsedSampler.o FileHeader.o GibbsParameters.o GibbsSampler.o MyTimer.o PosteriorSamples.o R_init_BitSeq.o ReadDistribution.o Sampler.o SimpleSparse.o TagAlignments.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o VariationalBayes.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o estimateVBExpression.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o misc.o parseAlignment.o transposeFiles.o /usr/lib/R/site-library/Rsamtools/usrlib//libbam.a /usr/lib/R/site-library/Rsamtools/usrlib//libbcf.a /usr/lib/R/site-library/Rsamtools/usrlib//libtabix.a -lz -pthread -fopenmp -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/<<BUILDDIR>>/r-bioc-bitseq-1.26.1+dfsg/src'
make[1]: Entering directory '/<<BUILDDIR>>/r-bioc-bitseq-1.26.1+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/r-bioc-bitseq-1.26.1+dfsg/src'
installing to /<<BUILDDIR>>/r-bioc-bitseq-1.26.1+dfsg/debian/r-bioc-bitseq/usr/lib/R/site-library/BitSeq/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BitSeq)
rm -f /<<BUILDDIR>>/r-bioc-bitseq-1.26.1\+dfsg/debian/r-bioc-bitseq/usr/lib/R/site-library/BitSeq/LICENSE
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 292.
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 293.
Use of uninitialized value $dep_line in split at /usr/share/perl5/Dpkg/Deps.pm line 296.
I: Using r-bioc-rsamtools for Depends:Rsamtools
I: Using r-bioc-zlibbioc for Depends:zlibbioc
I: Using r-bioc-edger for Suggests:edgeR
W: Cannot find a debian package for Suggests:DESeq
W: Cannot find a debian package for Suggests:BiocStyle
I: Using r-bioc-s4vectors for Imports:S4Vectors
I: Using r-bioc-iranges for Imports:IRanges
I: BioConductor API version: r-api-bioc-3.8
Create lintian-override for package-contains-documentation-outside-usr-share-doc
dh_installdocs -a -O--buildsystem=R
dh_installchangelogs -a -O--buildsystem=R
dh_installinit -a -O--buildsystem=R
dh_lintian -a -O--buildsystem=R
dh_perl -a -O--buildsystem=R
dh_link -a -O--buildsystem=R
dh_strip_nondeterminism -a -O--buildsystem=R
dh_compress -a -O--buildsystem=R
dh_fixperms -a -O--buildsystem=R
dh_missing -a -O--buildsystem=R
dh_strip -a -O--buildsystem=R
dh_makeshlibs -a -O--buildsystem=R
dh_shlibdeps -a -O--buildsystem=R
dh_installdeb -a -O--buildsystem=R
dh_gencontrol -a -O--buildsystem=R
dh_md5sums -a -O--buildsystem=R
dh_builddeb -a -O--buildsystem=R
dpkg-deb: building package 'r-bioc-bitseq-dbgsym' in '../r-bioc-bitseq-dbgsym_1.26.1+dfsg-1_armhf.deb'.
dpkg-deb: building package 'r-bioc-bitseq' in '../r-bioc-bitseq_1.26.1+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../r-bioc-bitseq_1.26.1+dfsg-1_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)
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Build finished at 2019-01-14T07:00:26Z
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r-bioc-bitseq_1.26.1+dfsg-1_armhf.changes:
------------------------------------------
Format: 1.8
Date: Wed, 09 Jan 2019 07:50:30 +0100
Source: r-bioc-bitseq
Binary: r-bioc-bitseq
Architecture: armhf
Version: 1.26.1+dfsg-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Dylan Aïssi <daissi@debian.org>
Description:
r-bioc-bitseq - transcript expression inference and analysis for RNA-seq data
Changes:
r-bioc-bitseq (1.26.1+dfsg-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
* Standards-Version: 4.3.0
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r-bioc-bitseq-dbgsym_1.26.1+dfsg-1_armhf.deb
--------------------------------------------
new Debian package, version 2.0.
size 3454984 bytes: control archive=544 bytes.
401 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: r-bioc-bitseq-dbgsym
Source: r-bioc-bitseq
Version: 1.26.1+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 3479
Depends: r-bioc-bitseq (= 1.26.1+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for r-bioc-bitseq
Build-Ids: e189ffeb1b570e575917f6ee68bbdb5c1932d815
drwxr-xr-x root/root 0 2019-01-09 06:50 ./
drwxr-xr-x root/root 0 2019-01-09 06:50 ./usr/
drwxr-xr-x root/root 0 2019-01-09 06:50 ./usr/lib/
drwxr-xr-x root/root 0 2019-01-09 06:50 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-01-09 06:50 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-01-09 06:50 ./usr/lib/debug/.build-id/e1/
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lrwxrwxrwx root/root 0 2019-01-09 06:50 ./usr/share/doc/r-bioc-bitseq-dbgsym -> r-bioc-bitseq
r-bioc-bitseq_1.26.1+dfsg-1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 942552 bytes: control archive=1940 bytes.
1220 bytes, 22 lines control
2937 bytes, 37 lines md5sums
Package: r-bioc-bitseq
Version: 1.26.1+dfsg-1
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 5493
Depends: r-base-core (>= 3.5.2-1), r-api-3.5, r-api-bioc-3.8, r-bioc-rsamtools, r-bioc-zlibbioc, r-bioc-s4vectors, r-bioc-iranges, libc6 (>= 2.23), libgcc1 (>= 1:3.5), libgomp1 (>= 4.9), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3)
Suggests: r-bioc-edger
Section: gnu-r
Priority: optional
Homepage: https://bioconductor.org/packages/BitSeq/
Description: transcript expression inference and analysis for RNA-seq data
The BitSeq package is targeted for transcript expression
analysis and differential expression analysis of RNA-seq data
in two stage process. In the first stage it uses Bayesian
inference methodology to infer expression of individual
transcripts from individual RNA-seq experiments. The second
stage of BitSeq embraces the differential expression analysis
of transcript expression. Providing expression estimates from
replicates of multiple conditions, Log-Normal model of the
estimates is used for inferring the condition mean transcript
expression and ranking the transcripts based on the likelihood
of differential expression.
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drwxr-xr-x root/root 0 2019-01-09 06:50 ./usr/lib/R/site-library/BitSeq/html/
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drwxr-xr-x root/root 0 2019-01-09 06:50 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 152 2019-01-09 06:50 ./usr/share/lintian/overrides/r-bioc-bitseq
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| Summary |
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Build Architecture: armhf
Build-Space: 19180
Build-Time: 197
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 666
Job: r-bioc-bitseq_1.26.1+dfsg-1
Machine Architecture: armhf
Package: r-bioc-bitseq
Package-Time: 882
Source-Version: 1.26.1+dfsg-1
Space: 19180
Status: successful
Version: 1.26.1+dfsg-1
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Finished at 2019-01-14T07:00:26Z
Build needed 00:14:42, 19180k disk space