r-bioc-bitseq →
1.38.0+dfsg-1 →
armhf → 2021-12-04 05:58:26
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| r-bioc-bitseq 1.38.0+dfsg-1 (armhf) Sat, 04 Dec 2021 05:37:20 +0000 |
+==============================================================================+
Package: r-bioc-bitseq
Version: 1.38.0+dfsg-1
Source Version: 1.38.0+dfsg-1
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-e7de09ec-c4a1-4736-b7f3-ba6fe4c218b2' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-bitseq-bsi6na/resolver-5Edyc9' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [12.6 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [13.5 MB]
Fetched 26.1 MB in 14s (1857 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| 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 759 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main r-bioc-bitseq 1.38.0+dfsg-1 (dsc) [2199 B]
Get:2 http://172.17.4.1/private bookworm-staging/main r-bioc-bitseq 1.38.0+dfsg-1 (tar) [751 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main r-bioc-bitseq 1.38.0+dfsg-1 (diff) [5924 B]
Fetched 759 kB in 0s (2782 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-bitseq-bsi6na/r-bioc-bitseq-1.38.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-bitseq-bsi6na' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-bioc-rsamtools (>= 1.99.3), r-bioc-s4vectors, r-bioc-iranges, r-bioc-rhtslib, libboost-dev, libcurl4-openssl-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-bioc-rsamtools (>= 1.99.3), r-bioc-s4vectors, r-bioc-iranges, r-bioc-rhtslib, libboost-dev, libcurl4-openssl-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [437 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [521 B]
Fetched 1915 B in 0s (47.9 kB/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils ca-certificates
dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism dwz file
fontconfig fontconfig-config fonts-dejavu-core gcc-10-base gettext
gettext-base gfortran gfortran-11 groff-base icu-devtools intltool-debian
libalgorithm-c3-perl libarchive-zip-perl libb-hooks-endofscope-perl
libb-hooks-op-check-perl libblas-dev libblas3 libboost-dev libboost1.74-dev
libbrotli1 libbsd0 libbz2-dev libcairo2 libclass-c3-perl libclass-load-perl
libclass-load-xs-perl libcurl3-gnutls libcurl4 libcurl4-openssl-dev
libdata-optlist-perl libdatrie1 libdebhelper-perl libdeflate0
libdevel-callchecker-perl libdevel-globaldestruction-perl
libdevel-overloadinfo-perl libdevel-stacktrace-perl
libdist-checkconflicts-perl libdynaloader-functions-perl libelf1
libencode-locale-perl libeval-closure-perl libexpat1
libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1
libfreetype6 libfribidi0 libgcc-10-dev libgfortran-11-dev libgfortran5
libglib2.0-0 libgraphite2-3 libharfbuzz0b libhttp-date-perl
libhttp-message-perl libice6 libicu-dev libicu67 libio-html-perl libjbig0
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev liblapack-dev liblapack3
liblwp-mediatypes-perl liblzma-dev libmagic-mgc libmagic1 libmd0
libmodule-implementation-perl libmodule-runtime-conflicts-perl
libmodule-runtime-perl libmoose-perl libmro-compat-perl
libnamespace-clean-perl libncurses-dev libncurses5-dev libncurses6
libnghttp2-14 libpackage-deprecationmanager-perl libpackage-stash-perl
libpackage-stash-xs-perl libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl
libparams-util-perl libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-dev
libpcre2-posix3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1
libpixman-1-0 libpng-dev libpng16-16 libpsl5 libreadline-dev librtmp1
libscalar-list-utils-perl libsigsegv2 libsm6 libssh2-1 libstdc++-10-dev
libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl
libsub-install-perl libsub-name-perl libsub-override-perl libswitch-perl
libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtool
libtry-tiny-perl libuchardet0 liburi-perl libvariable-magic-perl libwebp6
libwww-curl-perl libwww-curl-simple-perl libx11-6 libx11-data libxau6
libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2
libxmuu1 libxrender1 libxss1 libxt6 m4 man-db openssl 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-rhtslib r-bioc-rsamtools
r-bioc-s4vectors r-bioc-xvector r-bioc-zlibbioc r-cran-bh r-cran-bitops
r-cran-crayon 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 debtags dh-make
postgresql-client-common gettext-doc libasprintf-dev libgettextpo-dev
gfortran-doc gfortran-11-doc libcoarrays-dev groff liblapack-doc
libboost-doc libboost1.74-doc libboost-atomic1.74-dev
libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev
libboost-contract1.74-dev libboost-coroutine1.74-dev
libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev
libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev
libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev
libboost-program-options1.74-dev libboost-python1.74-dev
libboost-random1.74-dev libboost-regex1.74-dev
libboost-serialization1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev
libssl-dev icu-doc liblzma-doc ncurses-doc libscalar-number-perl
readline-doc libstdc++-10-doc tcl8.6 tk8.6 libtool-doc gcj-jdk
libbusiness-isbn-perl libwww-perl libcurl4-gnutls-dev m4-doc apparmor less
www-browser libmail-box-perl elpa-ess r-doc-info | r-doc-pdf r-mathlib
r-base-html texlive-base texlive-latex-base texlive-plain-generic
texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils
texlive-latex-recommended texlive-latex-extra texinfo r-bioc-biobase
r-bioc-delayedarray r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2
r-bioc-annotate r-cran-foreach r-cran-bbmisc r-bioc-variantannotation
r-bioc-genomicalignments r-bioc-shortread r-cran-codetools r-bioc-biocstyle
r-cran-knitr r-cran-data.table r-bioc-bsgenome r-bioc-genomicfeatures
r-cran-runit r-cran-matrix r-bioc-summarizedexperiment r-bioc-rtracklayer
r-bioc-gviz r-bioc-annotationhub r-bioc-dexseq r-bioc-edger r-bioc-keggrest
r-cran-digest r-cran-rmarkdown r-bioc-graph r-cran-rstudioapi r-cran-shiny
r-cran-jsonlite r-cran-xml r-cran-rmpi r-cran-rsprng r-cran-rlecuyer
Recommended packages:
devscripts cme git-buildpackage curl | wget | lynx bzip2-doc
libclass-c3-xs-perl libdevel-lexalias-perl libarchive-cpio-perl
libglib2.0-data shared-mime-info xdg-user-dirs libclone-perl
libdevel-partialdump-perl libgpm2 libpng-tools publicsuffix libltdl-dev
libmail-sendmail-perl r-recommended r-doc-html r-cran-runit r-cran-batchjobs
r-cran-doparallel r-cran-batchtools r-cran-rmpi r-cran-testthat r-cran-withr
r-cran-mockery r-cran-testit r-cran-codetools r-cran-survival
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 bsdextrautils ca-certificates
dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism dwz file
fontconfig fontconfig-config fonts-dejavu-core gcc-10-base gettext
gettext-base gfortran gfortran-11 groff-base icu-devtools intltool-debian
libalgorithm-c3-perl libarchive-zip-perl libb-hooks-endofscope-perl
libb-hooks-op-check-perl libblas-dev libblas3 libboost-dev libboost1.74-dev
libbrotli1 libbsd0 libbz2-dev libcairo2 libclass-c3-perl libclass-load-perl
libclass-load-xs-perl libcurl3-gnutls libcurl4 libcurl4-openssl-dev
libdata-optlist-perl libdatrie1 libdebhelper-perl libdeflate0
libdevel-callchecker-perl libdevel-globaldestruction-perl
libdevel-overloadinfo-perl libdevel-stacktrace-perl
libdist-checkconflicts-perl libdynaloader-functions-perl libelf1
libencode-locale-perl libeval-closure-perl libexpat1
libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1
libfreetype6 libfribidi0 libgcc-10-dev libgfortran-11-dev libgfortran5
libglib2.0-0 libgraphite2-3 libharfbuzz0b libhttp-date-perl
libhttp-message-perl libice6 libicu-dev libicu67 libio-html-perl libjbig0
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev liblapack-dev liblapack3
liblwp-mediatypes-perl liblzma-dev libmagic-mgc libmagic1 libmd0
libmodule-implementation-perl libmodule-runtime-conflicts-perl
libmodule-runtime-perl libmoose-perl libmro-compat-perl
libnamespace-clean-perl libncurses-dev libncurses5-dev libncurses6
libnghttp2-14 libpackage-deprecationmanager-perl libpackage-stash-perl
libpackage-stash-xs-perl libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl
libparams-util-perl libpcre16-3 libpcre2-16-0 libpcre2-32-0 libpcre2-dev
libpcre2-posix3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1
libpixman-1-0 libpng-dev libpng16-16 libpsl5 libreadline-dev librtmp1
libscalar-list-utils-perl libsigsegv2 libsm6 libssh2-1 libstdc++-10-dev
libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl
libsub-install-perl libsub-name-perl libsub-override-perl libswitch-perl
libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtool
libtry-tiny-perl libuchardet0 liburi-perl libvariable-magic-perl libwebp6
libwww-curl-perl libwww-curl-simple-perl libx11-6 libx11-data libxau6
libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2
libxmuu1 libxrender1 libxss1 libxt6 m4 man-db openssl 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-rhtslib r-bioc-rsamtools
r-bioc-s4vectors r-bioc-xvector r-bioc-zlibbioc r-cran-bh r-cran-bitops
r-cran-crayon r-cran-formatr r-cran-futile.logger r-cran-futile.options
r-cran-lambda.r r-cran-rcurl r-cran-snow sbuild-build-depends-main-dummy ucf
unzip x11-common xauth xdg-utils zip zlib1g-dev
0 upgraded, 195 newly installed, 0 to remove and 0 not upgraded.
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Get:2 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-4 [135 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.4-1 [31.6 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf gcc-10-base armhf 10.3.0-12+rpi1 [206 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-2 [295 kB]
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Get:10 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-2 [65.8 kB]
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Get:12 http://172.17.4.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.1 [823 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf openssl armhf 1.1.1l-1 [815 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf ca-certificates all 20210119 [158 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf dctrl-tools armhf 2.24-3 [94.2 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
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Get:34 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
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Get:36 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf zip armhf 3.0-12 [209 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf unzip armhf 6.0-26 [151 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libpaper1 armhf 1.1.28 [20.5 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libpaper-utils armhf 1.1.28 [17.7 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.0-1 [108 kB]
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Get:72 http://172.17.4.1/private bookworm-staging/main armhf fontconfig armhf 2.13.1-4.2 [416 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libfribidi0 armhf 1.0.8-2 [63.5 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libgraphite2-3 armhf 1.3.14-1 [70.3 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libharfbuzz0b armhf 2.7.4-1 [1422 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libthai-data all 0.1.28-4.1 [171 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libdatrie1 armhf 0.2.13-2 [39.7 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libthai0 armhf 0.1.28-4.1 [51.4 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libpango-1.0-0 armhf 1.48.10+ds1-1 [184 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libpangoft2-1.0-0 armhf 1.48.10+ds1-1 [66.6 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libpangocairo-1.0-0 armhf 1.48.10+ds1-1 [56.8 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libtcl8.6 armhf 8.6.12+dfsg-1 [906 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.8-1 [44.1 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libwebp6 armhf 0.6.1-2.1 [225 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf libtiff5 armhf 4.3.0-2 [272 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf x11-common all 1:7.7+23 [252 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libtk8.6 armhf 8.6.12-1 [680 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libice6 armhf 2:1.0.10-1 [51.7 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libxt6 armhf 1:1.2.0-1 [159 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf r-base-core armhf 4.1.2-1 [25.4 MB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libgfortran-11-dev armhf 11.2.0-10+rpi1 [280 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf gfortran-11 armhf 11.2.0-10+rpi1 [43.8 MB]
Get:97 http://172.17.4.1/private bookworm-staging/main armhf gfortran armhf 4:11.2.0-2+rpi1 [1428 B]
Get:98 http://172.17.4.1/private bookworm-staging/main armhf libblas-dev armhf 3.10.0-1 [113 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf liblapack-dev armhf 3.10.0-1 [2872 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3-1 [79.8 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf libncurses-dev armhf 6.3-1 [290 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf libncurses5-dev armhf 6.3-1 [932 B]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf libreadline-dev armhf 8.1-2 [121 kB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo-dev armhf 1:2.1.2-1 [261 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf libjpeg-dev armhf 1:2.1.2-1 [74.7 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf libpcre2-16-0 armhf 10.39-3 [200 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf libpcre2-32-0 armhf 10.39-3 [190 kB]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf libpcre2-posix3 armhf 10.39-3 [51.8 kB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf libpcre2-dev armhf 10.39-3 [629 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf libpcre16-3 armhf 2:8.39-13 [235 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf libpcre32-3 armhf 2:8.39-13 [228 kB]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf libpcrecpp0v5 armhf 2:8.39-13 [150 kB]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf libpcre3-dev armhf 2:8.39-13 [566 kB]
Get:114 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:115 http://172.17.4.1/private bookworm-staging/main armhf libpng-dev armhf 1.6.37-3 [277 kB]
Get:116 http://172.17.4.1/private bookworm-staging/main armhf libbz2-dev armhf 1.0.8-4 [28.0 kB]
Get:117 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2 [219 kB]
Get:118 http://172.17.4.1/private bookworm-staging/main armhf icu-devtools armhf 67.1-7 [172 kB]
Get:119 http://172.17.4.1/private bookworm-staging/main armhf libicu-dev armhf 67.1-7 [9228 kB]
Get:120 http://172.17.4.1/private bookworm-staging/main armhf libxmuu1 armhf 2:1.1.2-2+b3 [23.4 kB]
Get:121 http://172.17.4.1/private bookworm-staging/main armhf xauth armhf 1:1.1-1 [36.6 kB]
Get:122 http://172.17.4.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:123 http://172.17.4.1/private bookworm-staging/main armhf r-base-dev all 4.1.2-1 [4484 B]
Get:124 http://172.17.4.1/private bookworm-staging/main armhf libfile-which-perl all 1.23-1 [16.6 kB]
Get:125 http://172.17.4.1/private bookworm-staging/main armhf libswitch-perl all 2.17-2.1 [20.0 kB]
Get:126 http://172.17.4.1/private bookworm-staging/main armhf libencode-locale-perl all 1.05-1.1 [13.2 kB]
Get:127 http://172.17.4.1/private bookworm-staging/main armhf libtimedate-perl all 2.3300-2 [39.3 kB]
Get:128 http://172.17.4.1/private bookworm-staging/main armhf libhttp-date-perl all 6.05-1 [10.4 kB]
Get:129 http://172.17.4.1/private bookworm-staging/main armhf libio-html-perl all 1.004-2 [16.1 kB]
Get:130 http://172.17.4.1/private bookworm-staging/main armhf liblwp-mediatypes-perl all 6.04-1 [19.9 kB]
Get:131 http://172.17.4.1/private bookworm-staging/main armhf liburi-perl all 5.10-1 [91.0 kB]
Get:132 http://172.17.4.1/private bookworm-staging/main armhf libhttp-message-perl all 6.35-1 [80.5 kB]
Get:133 http://172.17.4.1/private bookworm-staging/main armhf libparams-util-perl armhf 1.102-1+b1 [24.6 kB]
Get:134 http://172.17.4.1/private bookworm-staging/main armhf libsub-install-perl all 0.928-1.1 [10.8 kB]
Get:135 http://172.17.4.1/private bookworm-staging/main armhf libdata-optlist-perl all 0.112-1 [11.8 kB]
Get:136 http://172.17.4.1/private bookworm-staging/main armhf libb-hooks-op-check-perl armhf 0.22-1+b4 [11.0 kB]
Get:137 http://172.17.4.1/private bookworm-staging/main armhf libdynaloader-functions-perl all 0.003-1.1 [12.7 kB]
Get:138 http://172.17.4.1/private bookworm-staging/main armhf libdevel-callchecker-perl armhf 0.008-1+b2 [15.7 kB]
Get:139 http://172.17.4.1/private bookworm-staging/main armhf libparams-classify-perl armhf 0.015-1+b3 [24.6 kB]
Get:140 http://172.17.4.1/private bookworm-staging/main armhf libmodule-runtime-perl all 0.016-1 [19.4 kB]
Get:141 http://172.17.4.1/private bookworm-staging/main armhf libtry-tiny-perl all 0.31-1 [24.2 kB]
Get:142 http://172.17.4.1/private bookworm-staging/main armhf libmodule-implementation-perl all 0.09-1.1 [12.4 kB]
Get:143 http://172.17.4.1/private bookworm-staging/main armhf libscalar-list-utils-perl armhf 1:1.59-1 [60.8 kB]
Get:144 http://172.17.4.1/private bookworm-staging/main armhf libpackage-stash-perl all 0.39-1 [21.9 kB]
Get:145 http://172.17.4.1/private bookworm-staging/main armhf libclass-load-perl all 0.25-1 [16.1 kB]
Get:146 http://172.17.4.1/private bookworm-staging/main armhf libclass-load-xs-perl armhf 0.10-1+b4 [14.3 kB]
Get:147 http://172.17.4.1/private bookworm-staging/main armhf libsub-exporter-progressive-perl all 0.001013-1 [7588 B]
Get:148 http://172.17.4.1/private bookworm-staging/main armhf libdevel-globaldestruction-perl all 0.14-1.1 [8312 B]
Get:149 http://172.17.4.1/private bookworm-staging/main armhf libalgorithm-c3-perl all 0.11-1 [11.7 kB]
Get:150 http://172.17.4.1/private bookworm-staging/main armhf libclass-c3-perl all 0.35-1 [22.9 kB]
Get:151 http://172.17.4.1/private bookworm-staging/main armhf libmro-compat-perl all 0.13-1 [12.2 kB]
Get:152 http://172.17.4.1/private bookworm-staging/main armhf libdevel-overloadinfo-perl all 0.007-1 [7896 B]
Get:153 http://172.17.4.1/private bookworm-staging/main armhf libdevel-stacktrace-perl all 2.0400-1 [28.6 kB]
Get:154 http://172.17.4.1/private bookworm-staging/main armhf libsub-exporter-perl all 0.988-1 [51.9 kB]
Get:155 http://172.17.4.1/private bookworm-staging/main armhf libeval-closure-perl all 0.14-1 [11.5 kB]
Get:156 http://172.17.4.1/private bookworm-staging/main armhf libdist-checkconflicts-perl all 0.11-1.1 [10.2 kB]
Get:157 http://172.17.4.1/private bookworm-staging/main armhf libmodule-runtime-conflicts-perl all 0.003-1.1 [7156 B]
Get:158 http://172.17.4.1/private bookworm-staging/main armhf libsub-name-perl armhf 0.26-1+b1 [13.2 kB]
Get:159 http://172.17.4.1/private bookworm-staging/main armhf libpackage-deprecationmanager-perl all 0.17-1.1 [16.6 kB]
Get:160 http://172.17.4.1/private bookworm-staging/main armhf libpackage-stash-xs-perl armhf 0.29-1+b2 [18.5 kB]
Get:161 http://172.17.4.1/private bookworm-staging/main armhf libmoose-perl armhf 2.2200-1 [803 kB]
Get:162 http://172.17.4.1/private bookworm-staging/main armhf libvariable-magic-perl armhf 0.62-1+b3 [43.0 kB]
Get:163 http://172.17.4.1/private bookworm-staging/main armhf libb-hooks-endofscope-perl all 0.25-1 [19.5 kB]
Get:164 http://172.17.4.1/private bookworm-staging/main armhf libsub-identify-perl armhf 0.14-1+b3 [11.6 kB]
Get:165 http://172.17.4.1/private bookworm-staging/main armhf libnamespace-clean-perl all 0.27-1 [17.3 kB]
Get:166 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.79.1-2 [317 kB]
Get:167 http://172.17.4.1/private bookworm-staging/main armhf libwww-curl-perl armhf 4.17-7+b1 [58.9 kB]
Get:168 http://172.17.4.1/private bookworm-staging/main armhf libwww-curl-simple-perl all 0.100191-2 [12.5 kB]
Get:169 http://172.17.4.1/private bookworm-staging/main armhf dh-r all 20210816 [41.6 kB]
Get:170 http://172.17.4.1/private bookworm-staging/main armhf libgcc-10-dev armhf 10.3.0-12+rpi1 [679 kB]
Get:171 http://172.17.4.1/private bookworm-staging/main armhf libstdc++-10-dev armhf 10.3.0-12+rpi1 [1758 kB]
Get:172 http://172.17.4.1/private bookworm-staging/main armhf libboost1.74-dev armhf 1.74.0-13 [9537 kB]
Get:173 http://172.17.4.1/private bookworm-staging/main armhf libboost-dev armhf 1.74.0.3+b2 [4824 B]
Get:174 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-openssl-dev armhf 7.79.1-2 [396 kB]
Get:175 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-biocgenerics all 0.40.0-1 [587 kB]
Get:176 http://172.17.4.1/private bookworm-staging/main armhf r-cran-formatr all 1.11-1 [147 kB]
Get:177 http://172.17.4.1/private bookworm-staging/main armhf r-cran-lambda.r all 1.2.4-2 [118 kB]
Get:178 http://172.17.4.1/private bookworm-staging/main armhf r-cran-futile.options all 1.0.1-3 [20.0 kB]
Get:179 http://172.17.4.1/private bookworm-staging/main armhf r-cran-futile.logger all 1.4.3-4 [98.4 kB]
Get:180 http://172.17.4.1/private bookworm-staging/main armhf r-cran-snow all 1:0.4.4-1 [99.0 kB]
Get:181 http://172.17.4.1/private bookworm-staging/main armhf r-cran-bh all 1.74.0-2 [5524 B]
Get:182 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-biocparallel armhf 1.28.2-2 [1362 kB]
Get:183 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-s4vectors armhf 0.32.3-1 [2066 kB]
Get:184 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-iranges armhf 2.28.0-1 [2218 kB]
Get:185 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-zlibbioc all 1.40.0+dfsg-1 [9040 B]
Get:186 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-xvector armhf 0.34.0-1 [605 kB]
Get:187 http://172.17.4.1/private bookworm-staging/main armhf r-cran-bitops armhf 1.0-7-1 [30.1 kB]
Get:188 http://172.17.4.1/private bookworm-staging/main armhf r-cran-rcurl armhf 1.98-1.5-1 [800 kB]
Get:189 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-genomeinfodbdata all 1.2.7-1 [11.2 MB]
Get:190 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-genomeinfodb all 1.30.0-1 [3914 kB]
Get:191 http://172.17.4.1/private bookworm-staging/main armhf r-cran-crayon all 1.4.2-1 [158 kB]
Get:192 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-biostrings armhf 2.62.0-1 [14.2 MB]
Get:193 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-genomicranges armhf 1.46.1+dfsg-1 [1863 kB]
Get:194 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-rhtslib armhf 1.26.0+dfsg-1 [946 kB]
Get:195 http://172.17.4.1/private bookworm-staging/main armhf r-bioc-rsamtools armhf 2.10.0-1 [3537 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 178 MB in 27s (6580 kB/s)
Selecting previously unselected package bsdextrautils.
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Preparing to unpack .../000-bsdextrautils_2.37.2-4_armhf.deb ...
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Unpacking man-db (2.9.4-2) ...
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Unpacking gettext-base (0.21-4) ...
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Unpacking libsigsegv2:armhf (2.13-1) ...
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Preparing to unpack .../012-m4_1.4.18-5_armhf.deb ...
Unpacking m4 (1.4.18-5) ...
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Unpacking autoconf (2.71-2) ...
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Unpacking automake (1:1.16.5-1.1) ...
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Unpacking openssl (1.1.1l-1) ...
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Unpacking ca-certificates (20210119) ...
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Unpacking libdebhelper-perl (13.5.2) ...
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Unpacking libfile-stripnondeterminism-perl (1.12.1-1) ...
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Unpacking dh-strip-nondeterminism (1.12.1-1) ...
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Unpacking libelf1:armhf (0.186-1) ...
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Unpacking unzip (6.0-26) ...
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Unpacking libpaper-utils (1.1.28) ...
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Setting up libexpat1:armhf (2.4.1-3) ...
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Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up bsdextrautils (2.37.2-4) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
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Setting up libdatrie1:armhf (0.2.13-2) ...
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Setting up libsub-identify-perl (0.14-1+b3) ...
Setting up libglib2.0-0:armhf (2.70.1-1) ...
No schema files found: doing nothing.
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Setting up unzip (6.0-26) ...
Setting up libdebhelper-perl (13.5.2) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up liblwp-mediatypes-perl (6.04-1) ...
Setting up x11-common (1:7.7+23) ...
invoke-rc.d: could not determine current runlevel
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of restart.
Setting up libtry-tiny-perl (0.31-1) ...
Setting up libnghttp2-14:armhf (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.41-2) ...
Setting up libdeflate0:armhf (1.8-1) ...
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Setting up libencode-locale-perl (1.05-1.1) ...
Setting up file (1:5.41-2) ...
Setting up libjbig0:armhf (2.1-3.1+b2) ...
Setting up libpcre2-16-0:armhf (10.39-3) ...
Setting up libsub-install-perl (0.928-1.1) ...
Setting up gcc-10-base:armhf (10.3.0-12+rpi1) ...
Setting up zip (3.0-12) ...
Setting up libpackage-stash-xs-perl (0.29-1+b2) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libpcre2-32-0:armhf (10.39-3) ...
Setting up libblas3:armhf (3.10.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
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update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up dctrl-tools (2.24-3) ...
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Creating config file /etc/papersize with new version
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libncurses-dev:armhf (6.3-1) ...
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Setting up libtool (2.4.6-15) ...
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Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.79.1-2) ...
Setting up libxcb-shm0:armhf (1.14-3) ...
Setting up libpaper-utils (1.1.28) ...
Setting up libclass-c3-perl (0.35-1) ...
Setting up libreadline-dev:armhf (8.1-2) ...
Setting up libdevel-callchecker-perl (0.008-1+b2) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libthai0:armhf (0.1.28-4.1) ...
Setting up ca-certificates (20210119) ...
Updating certificates in /etc/ssl/certs...
129 added, 0 removed; done.
Setting up libfreetype6:armhf (2.11.0+dfsg-1) ...
Setting up liblapack-dev:armhf (3.10.0-1) ...
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 libdata-optlist-perl (0.112-1) ...
Setting up gfortran-11 (11.2.0-10+rpi1) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.1-1) ...
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Setting up groff-base (1.22.4-7) ...
Setting up libncurses5-dev:armhf (6.3-1) ...
Setting up libcurl4:armhf (7.79.1-2) ...
Setting up libx11-6:armhf (2:1.7.2-2) ...
Setting up libharfbuzz0b:armhf (2.7.4-1) ...
Setting up libfontconfig1:armhf (2.13.1-4.2) ...
Setting up libmro-compat-perl (0.13-1) ...
Setting up libsm6:armhf (2:1.2.3-1) ...
Setting up libxmuu1:armhf (2:1.1.2-2+b3) ...
Setting up libsub-exporter-perl (0.988-1) ...
Setting up libhttp-message-perl (6.35-1) ...
Setting up libeval-closure-perl (0.14-1) ...
Setting up automake (1:1.16.5-1.1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up fontconfig (2.13.1-4.2) ...
Regenerating fonts cache... done.
Setting up libstdc++-10-dev:armhf (10.3.0-12+rpi1) ...
Setting up libboost1.74-dev:armhf (1.74.0-13) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libparams-classify-perl (0.015-1+b3) ...
Setting up libpango-1.0-0:armhf (1.48.10+ds1-1) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up libwww-curl-perl (4.17-7+b1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran (4:11.2.0-2+rpi1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libcairo2:armhf (1.16.0-5) ...
Setting up dh-autoreconf (20) ...
Setting up libmodule-runtime-perl (0.016-1) ...
Setting up libcurl4-openssl-dev:armhf (7.79.1-2) ...
Setting up libdist-checkconflicts-perl (0.11-1.1) ...
Setting up libxt6:armhf (1:1.2.0-1) ...
Setting up xauth (1:1.1-1) ...
Setting up libboost-dev:armhf (1.74.0.3+b2) ...
Setting up libxss1:armhf (1:1.2.3-1) ...
Setting up libpangoft2-1.0-0:armhf (1.48.10+ds1-1) ...
Setting up libpangocairo-1.0-0:armhf (1.48.10+ds1-1) ...
Setting up r-cran-bh (1.74.0-2) ...
Setting up libxft2:armhf (2.3.2-2) ...
Setting up libmodule-implementation-perl (0.09-1.1) ...
Setting up libpackage-stash-perl (0.39-1) ...
Setting up libtk8.6:armhf (8.6.12-1) ...
Setting up debhelper (13.5.2) ...
Setting up libmodule-runtime-conflicts-perl (0.003-1.1) ...
Setting up libclass-load-perl (0.25-1) ...
Setting up r-base-core (4.1.2-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-cran-crayon (1.4.2-1) ...
Setting up r-cran-futile.options (1.0.1-3) ...
Setting up r-cran-formatr (1.11-1) ...
Setting up libpackage-deprecationmanager-perl (0.17-1.1) ...
Setting up libdevel-overloadinfo-perl (0.007-1) ...
Setting up libclass-load-xs-perl (0.10-1+b4) ...
Setting up libb-hooks-endofscope-perl (0.25-1) ...
Setting up r-bioc-genomeinfodbdata (1.2.7-1) ...
Setting up r-bioc-biocgenerics (0.40.0-1) ...
Setting up r-base-dev (4.1.2-1) ...
Setting up libmoose-perl:armhf (2.2200-1) ...
Setting up r-cran-lambda.r (1.2.4-2) ...
Setting up r-cran-snow (1:0.4.4-1) ...
Setting up r-cran-bitops (1.0-7-1) ...
Setting up r-bioc-zlibbioc (1.40.0+dfsg-1) ...
Setting up r-bioc-s4vectors (0.32.3-1) ...
Setting up r-cran-futile.logger (1.4.3-4) ...
Setting up libnamespace-clean-perl (0.27-1) ...
Setting up r-bioc-iranges (2.28.0-1) ...
Setting up r-cran-rcurl (1.98-1.5-1) ...
Setting up r-bioc-biocparallel (1.28.2-2) ...
Setting up libwww-curl-simple-perl (0.100191-2) ...
Setting up r-bioc-rhtslib (1.26.0+dfsg-1) ...
Setting up r-bioc-genomeinfodb (1.30.0-1) ...
Setting up r-bioc-xvector (0.34.0-1) ...
Setting up dh-r (20210816) ...
Setting up r-bioc-genomicranges (1.46.1+dfsg-1) ...
Setting up r-bioc-biostrings (2.62.0-1) ...
Setting up r-bioc-rsamtools (2.10.0-1) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...
Processing triggers for ca-certificates (20210119) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.37-7+rpi1 dpkg-dev_1.20.9+rpi1 g++-11_11.2.0-10+rpi1 gcc-11_11.2.0-10+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-10-dev_10.3.0-12+rpi1 libstdc++-11-dev_11.2.0-10+rpi1 libstdc++6_11.2.0-10+rpi1 linux-libc-dev_5.14.16-1+rpi1
Package versions: adduser_3.118 apt_2.3.13 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-5 binutils_2.37-7+rpi1 binutils-arm-linux-gnueabihf_2.37-7+rpi1 binutils-common_2.37-7+rpi1 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 ca-certificates_20210119 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.2.0-10+rpi1 dash_0.5.11+git20210903+057cd650a4ed-3 dctrl-tools_2.24-3 debconf_1.5.79 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-r_20210816 dh-strip-nondeterminism_1.12.1-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.41-2 findutils_4.8.0-1 fontconfig_2.13.1-4.2 fontconfig-config_2.13.1-4.2 fonts-dejavu-core_2.37-2 g++_4:11.2.0-2+rpi1 g++-11_11.2.0-10+rpi1 gcc_4:11.2.0-2+rpi1 gcc-10-base_10.3.0-12+rpi1 gcc-11_11.2.0-10+rpi1 gcc-11-base_11.2.0-10+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 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+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
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Hash: SHA512
Format: 3.0 (quilt)
Source: r-bioc-bitseq
Binary: r-bioc-bitseq
Architecture: any
Version: 1.38.0+dfsg-1
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://bioconductor.org/packages/BitSeq/
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-bioc-bitseq
Vcs-Git: https://salsa.debian.org/r-pkg-team/r-bioc-bitseq.git
Testsuite: autopkgtest-pkg-r
Build-Depends: debhelper-compat (= 13), dh-r, r-base-dev, r-bioc-rsamtools (>= 1.99.3), r-bioc-s4vectors, r-bioc-iranges, r-bioc-rhtslib, libboost-dev, libcurl4-openssl-dev
Package-List:
r-bioc-bitseq deb gnu-r optional arch=any
Checksums-Sha1:
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8d2b09d3230030594c65ba4c9afc45ab4b200cc6 5924 r-bioc-bitseq_1.38.0+dfsg-1.debian.tar.xz
Checksums-Sha256:
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Files:
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cbe38cefe0c28bc67256b5841d396f39 5924 r-bioc-bitseq_1.38.0+dfsg-1.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.ix_Mc6Cg/trustedkeys.kbx': General error
gpgv: Signature made Thu Nov 25 11:16:30 2021 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "nilesh@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./r-bioc-bitseq_1.38.0+dfsg-1.dsc
dpkg-source: info: extracting r-bioc-bitseq in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-bitseq_1.38.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking r-bioc-bitseq_1.38.0+dfsg-1.debian.tar.xz
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=1b2d35e96e094e0c905e1f5e00ab4580
JOURNAL_STREAM=8:29072680
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-e7de09ec-c4a1-4736-b7f3-ba6fe4c218b2
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c163189
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package r-bioc-bitseq
dpkg-buildpackage: info: source version 1.38.0+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
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 binary-arch
dh binary-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
dh_testroot -a -O--buildsystem=R
dh_prep -a -O--buildsystem=R
dh_auto_install --destdir=debian/r-bioc-bitseq/ -a -O--buildsystem=R
I: R Package: BitSeq Version: 1.38.0
I: Building using R version 4.1.2-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Thu, 25 Nov 2021 16:41:18 +0530
mkdir -p /<<BUILDDIR>>/r-bioc-bitseq-1.38.0\+dfsg/debian/r-bioc-bitseq/usr/lib/R/site-library
R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-bitseq-1.38.0\+dfsg/debian/r-bioc-bitseq/usr/lib/R/site-library --clean . "--built-timestamp='Thu, 25 Nov 2021 16:41:18 +0530'"
* installing *source* package ‘BitSeq’ ...
** using staged installation
configure: Version def: -DBS_VERSION=\"1.38.0\"
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 the compiler supports GNU C++... yes
checking whether g++ -std=gnu++14 accepts -g... yes
checking for g++ -std=gnu++14 option to enable C++11 features... none needed
checking for g++ -std=gnu++14 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 '/<<PKGBUILDDIR>>/src'
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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++/11/vector:72,
from ArgumentParser.h:6,
from ArgumentParser.cpp:5:
/usr/include/c++/11/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++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
/usr/include/c++/11/bits/vector.tcc: In function ‘std::vector<double> tokenizeD(const string&, const string&)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CollapsedSampler.cpp -o CollapsedSampler.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c FileHeader.cpp -o FileHeader.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c GibbsParameters.cpp -o GibbsParameters.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c GibbsSampler.cpp -o GibbsSampler.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MyTimer.cpp -o MyTimer.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PosteriorSamples.cpp -o PosteriorSamples.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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++/11/vector:72,
from ReadDistribution.h:4,
from ReadDistribution.cpp:7:
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from ReadDistribution.h:4,
from ReadDistribution.cpp:7:
/usr/include/c++/11/bits/stl_vector.h: In constructor ‘ReadDistribution::ReadDistribution()’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void ReadDistribution::updateMismatchFreq(bam1_t*)’:
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:60,
from ReadDistribution.h:5,
from ReadDistribution.cpp:7:
/usr/include/c++/11/bits/stl_tree.h: In 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++/11/bits/stl_tree.h:2426:7: 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’ changed in GCC 7.1
2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from ReadDistribution.h:5,
from ReadDistribution.cpp:7:
/usr/include/c++/11/bits/stl_map.h: In member function ‘double ReadDistribution::getWeightNorm(long int, ns_rD::readT, long int)’:
/usr/include/c++/11/bits/stl_map.h:501:44: 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’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h: In member function ‘bool ReadDistribution::observed(ns_rD::fragmentP)’:
/usr/include/c++/11/bits/stl_map.h:501:44: 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’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: 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’ changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rhtslib_bam_plbuf.c -o Rhtslib_bam_plbuf.o
gcc -std=gnu99 -std=gnu11 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rhtslib_sam.c -o Rhtslib_sam.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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++/11/vector:72,
from Sampler.h:4,
from Sampler.cpp:5:
/usr/include/c++/11/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++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from Sampler.h:4,
from Sampler.cpp:5:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void Sampler::appendFile()’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SimpleSparse.cpp -o SimpleSparse.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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++/11/vector:72,
from TagAlignments.h:5,
from TagAlignments.cpp:3:
/usr/include/c++/11/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++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from TagAlignments.h:5,
from TagAlignments.cpp:3:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘void TagAlignments::pushAlignmentL(long int, double)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from TranscriptExpression.cpp:1:
/usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >’ changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from TranscriptExpression.cpp:1:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >’ changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >’ changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >’ changed in GCC 7.1
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In member function ‘void TranscriptExpression::doSort(bool)’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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++/11/vector:72,
from TranscriptInfo.h:4,
from TranscriptInfo.cpp:4:
/usr/include/c++/11/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++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<transcriptT>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from TranscriptInfo.h:4,
from TranscriptInfo.cpp:4:
/usr/include/c++/11/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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<transcriptT*, std::vector<transcriptT> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h: In member function ‘bool TranscriptInfo::readInfo(std::string)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<transcriptT*, std::vector<transcriptT> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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++/11/vector:72,
from TranscriptSequence.h:6,
from TranscriptSequence.cpp:6:
/usr/include/c++/11/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++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<trSeqInfoT>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from TranscriptSequence.h:6,
from TranscriptSequence.cpp:6:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘bool TranscriptSequence::readSequence(std::string, refFormatT)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<trSeqInfoT*, std::vector<trSeqInfoT> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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++/11/vector:72,
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++/11/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++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<boost::random::gamma_distribution<double>::param_type>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void VariationalBayes::generateSamples(long int, const string&, const std::vector<double>*, std::ofstream*)’:
/usr/include/c++/11/bits/vector.tcc:121:28: 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
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c common.cpp -o common.o
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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]
57 | if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
| ^~~~~~~~
estimateDE.cpp:57:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
57 | if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
| ^~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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]
532 | if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
| ^~~~~~~~
estimateExpression.cpp:532:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
532 | if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from estimateExpression.cpp:1:
/usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from estimateExpression.cpp:1:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘void MCMC(TagAlignments*, gibbsParameters&, ArgumentParser&)’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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]
62 | if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
| ^~~~~~~~
estimateHyperPar.cpp:62:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
62 | if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
| ^~~~~~~~
In file included from /usr/include/c++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from estimateHyperPar.cpp:6:
/usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from estimateHyperPar.cpp:6:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: 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++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: 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++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
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++/11/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++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<ns_params::paramT>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/vector.tcc:171:5: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h: In function ‘int estimateHyperPar(int*, char**)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from estimateHyperPar.cpp:6:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
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++/11/bits/stl_vector.h:1431:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1431:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1431:24: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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]
126 | if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
| ^~~~~~~~
estimateVBExpression.cpp:126:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
126 | if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
| ^~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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]
33 | if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
| ^~~~~~~~
getGeneExpression.cpp:33:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
33 | if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
| ^~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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]
28 | if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
| ^~~~~~~~
getVariance.cpp:28:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
28 | if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
| ^~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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]
54 | if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
| ^~~~~~~~
getWithinGeneExpression.cpp:54:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
54 | if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
| ^~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from lowess.cpp:17:
/usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from lowess.cpp:17:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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++/11/bits/stl_algo.h:61,
from /usr/include/c++/11/algorithm:62,
from misc.cpp:1:
/usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_heap.h:223:5: 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++/11/algorithm:62,
from misc.cpp:1:
/usr/include/c++/11/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++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
1799 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
1819 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1819:5: 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++/11/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++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
1925 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1925:5: 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++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h: In function ‘void ns_misc::computeCI(double, std::vector<double>*, double*, double*)’:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from ArgumentParser.h:6,
from misc.h:6,
from misc.cpp:5:
/usr/include/c++/11/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++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<ns_params::paramT>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from ArgumentParser.h:6,
from misc.h:6,
from misc.cpp:5:
/usr/include/c++/11/bits/stl_vector.h: In function ‘bool ns_params::readParams(const string&, std::vector<ns_params::paramT>*, std::ofstream*)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/algorithm:62,
from misc.cpp:1:
/usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
1954 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1955 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1956 | __comp);
| ~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >’ changed in GCC 7.1
1871 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -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]
102 | if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
| ^~~~~~~~
parseAlignment.cpp:102:47: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
102 | if(args.verbose)buildTime(argv[0],__DATE__,__TIME__);
| ^~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from ArgumentParser.h:6,
from parseAlignment.cpp:7:
/usr/include/c++/11/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++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<ns_parseAlignment::TagAlignment>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In function ‘int parseAlignment(int*, char**)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<ns_parseAlignment::TagAlignment*, std::vector<ns_parseAlignment::TagAlignment> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DPACKAGE_NAME=\"BitSeq\" -DPACKAGE_TARNAME=\"bitseq\" -DPACKAGE_VERSION=\"1.10.x\" -DPACKAGE_STRING=\"BitSeq\ 1.10.x\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DBS_VERSION=\"1.38.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I'/usr/lib/R/site-library/Rhtslib/include' -I. -fopenmp -fpic -g -O2 -ffile-prefix-map=/build/r-base-4lrxNK/r-base-4.1.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c transposeFiles.cpp -o transposeFiles.o
g++ -std=gnu++14 -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 Rhtslib_bam_plbuf.o Rhtslib_sam.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/Rhtslib/usrlib/libhts.a -lcurl -fopenmp -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
installing to /<<PKGBUILDDIR>>/debian/r-bioc-bitseq/usr/lib/R/site-library/00LOCK-r-bioc-bitseq-1.38.0+dfsg/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BitSeq)
rm -f /<<BUILDDIR>>/r-bioc-bitseq-1.38.0\+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 299.
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 300.
Use of uninitialized value $dep_line in split at /usr/share/perl5/Dpkg/Deps.pm line 303.
I: Using r-bioc-rsamtools for Depends:Rsamtools (>= 1.99.3)
I: Using r-bioc-biocstyle for Suggests:BiocStyle
I: Using r-bioc-s4vectors for Imports:S4Vectors
I: Using r-bioc-iranges for Imports:IRanges
I: Using r-bioc-rhtslib for LinkingTo:Rhtslib (>= 1.15.5)
I: BioConductor API version: r-api-bioc-3.14
I: Use r-bioc-bitseq as Debian binary package for variables substitution
dh_installdocs -a -O--buildsystem=R
dh_installchangelogs -a -O--buildsystem=R
dh_installsystemduser -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_dwz -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' in '../r-bioc-bitseq_1.38.0+dfsg-1_armhf.deb'.
dpkg-deb: building package 'r-bioc-bitseq-dbgsym' in '../r-bioc-bitseq-dbgsym_1.38.0+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> >../r-bioc-bitseq_1.38.0+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)
--------------------------------------------------------------------------------
Build finished at 2021-12-04T05:58:20Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
r-bioc-bitseq_1.38.0+dfsg-1_armhf.changes:
------------------------------------------
Format: 1.8
Date: Thu, 25 Nov 2021 16:41:18 +0530
Source: r-bioc-bitseq
Binary: r-bioc-bitseq r-bioc-bitseq-dbgsym
Architecture: armhf
Version: 1.38.0+dfsg-1
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Description:
r-bioc-bitseq - transcript expression inference and analysis for RNA-seq data
Changes:
r-bioc-bitseq (1.38.0+dfsg-1) unstable; urgency=medium
.
* Team upload.
* New upstream version 1.38.0+dfsg
* d/control: Run dh-update-R
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Files:
ad8eeb05fcd9e525ea02ece1e37a5565 3157256 debug optional r-bioc-bitseq-dbgsym_1.38.0+dfsg-1_armhf.deb
1733f746b71c7238ca34d82ef3926095 10415 gnu-r optional r-bioc-bitseq_1.38.0+dfsg-1_armhf.buildinfo
a39110a8074ffe310ee1bc9dea393676 1063752 gnu-r optional r-bioc-bitseq_1.38.0+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: r-bioc-bitseq
Binary: r-bioc-bitseq r-bioc-bitseq-dbgsym
Architecture: armhf
Version: 1.38.0+dfsg-1
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Checksums-Sha1:
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Checksums-Sha256:
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Sat, 04 Dec 2021 05:58:18 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.71-2),
automake (= 1:1.16.5-1.1),
autopoint (= 0.21-4),
autotools-dev (= 20180224.1+nmu1),
base-files (= 12+rpi1),
base-passwd (= 3.5.52),
bash (= 5.1-5),
binutils (= 2.37-7+rpi1),
binutils-arm-linux-gnueabihf (= 2.37-7+rpi1),
binutils-common (= 2.37-7+rpi1),
bsdextrautils (= 2.37.2-4),
bsdutils (= 1:2.37.2-4),
build-essential (= 12.9),
bzip2 (= 1.0.8-4),
ca-certificates (= 20210119),
coreutils (= 8.32-4.1),
cpp (= 4:11.2.0-2+rpi1),
cpp-11 (= 11.2.0-10+rpi1),
dash (= 0.5.11+git20210903+057cd650a4ed-3),
dctrl-tools (= 2.24-3),
debconf (= 1.5.79),
debhelper (= 13.5.2),
debianutils (= 4.11.2),
dh-autoreconf (= 20),
dh-r (= 20210816),
dh-strip-nondeterminism (= 1.12.1-1),
diffutils (= 1:3.7-5),
dpkg (= 1.20.9+rpi1),
dpkg-dev (= 1.20.9+rpi1),
dwz (= 0.14-1),
file (= 1:5.41-2),
findutils (= 4.8.0-1),
fontconfig (= 2.13.1-4.2),
fontconfig-config (= 2.13.1-4.2),
fonts-dejavu-core (= 2.37-2),
g++ (= 4:11.2.0-2+rpi1),
g++-11 (= 11.2.0-10+rpi1),
gcc (= 4:11.2.0-2+rpi1),
gcc-10-base (= 10.3.0-12+rpi1),
gcc-11 (= 11.2.0-10+rpi1),
gcc-11-base (= 11.2.0-10+rpi1),
gettext (= 0.21-4),
gettext-base (= 0.21-4),
gfortran (= 4:11.2.0-2+rpi1),
gfortran-11 (= 11.2.0-10+rpi1),
grep (= 3.7-1),
groff-base (= 1.22.4-7),
gzip (= 1.10-4),
hostname (= 3.23),
icu-devtools (= 67.1-7),
init-system-helpers (= 1.60),
intltool-debian (= 0.35.0+20060710.5),
libacl1 (= 2.3.1-1),
libalgorithm-c3-perl (= 0.11-1),
libarchive-zip-perl (= 1.68-1),
libasan6 (= 11.2.0-10+rpi1),
libatomic1 (= 11.2.0-10+rpi1),
libattr1 (= 1:2.5.1-1),
libaudit-common (= 1:3.0.6-1),
libaudit1 (= 1:3.0.6-1),
libb-hooks-endofscope-perl (= 0.25-1),
libb-hooks-op-check-perl (= 0.22-1+b4),
libbinutils (= 2.37-7+rpi1),
libblas-dev (= 3.10.0-1),
libblas3 (= 3.10.0-1),
libblkid1 (= 2.37.2-4),
libboost-dev (= 1.74.0.3+b2),
libboost1.74-dev (= 1.74.0-13),
libbrotli1 (= 1.0.9-2+b1),
libbsd0 (= 0.11.3-1),
libbz2-1.0 (= 1.0.8-4),
libbz2-dev (= 1.0.8-4),
libc-bin (= 2.32-4+rpi1),
libc-dev-bin (= 2.32-4+rpi1),
libc6 (= 2.32-4+rpi1),
libc6-dev (= 2.32-4+rpi1),
libcairo2 (= 1.16.0-5),
libcap-ng0 (= 0.7.9-2.2+b1),
libcap2 (= 1:2.44-1),
libcc1-0 (= 11.2.0-10+rpi1),
libclass-c3-perl (= 0.35-1),
libclass-load-perl (= 0.25-1),
libclass-load-xs-perl (= 0.10-1+b4),
libcom-err2 (= 1.46.4-1),
libcrypt-dev (= 1:4.4.26-1),
libcrypt1 (= 1:4.4.26-1),
libctf-nobfd0 (= 2.37-7+rpi1),
libctf0 (= 2.37-7+rpi1),
libcurl3-gnutls (= 7.79.1-2),
libcurl4 (= 7.79.1-2),
libcurl4-openssl-dev (= 7.79.1-2),
libdata-optlist-perl (= 0.112-1),
libdatrie1 (= 0.2.13-2),
libdb5.3 (= 5.3.28+dfsg1-0.8),
libdebconfclient0 (= 0.261),
libdebhelper-perl (= 13.5.2),
libdeflate0 (= 1.8-1),
libdevel-callchecker-perl (= 0.008-1+b2),
libdevel-globaldestruction-perl (= 0.14-1.1),
libdevel-overloadinfo-perl (= 0.007-1),
libdevel-stacktrace-perl (= 2.0400-1),
libdist-checkconflicts-perl (= 0.11-1.1),
libdpkg-perl (= 1.20.9+rpi1),
libdynaloader-functions-perl (= 0.003-1.1),
libelf1 (= 0.186-1),
libencode-locale-perl (= 1.05-1.1),
libeval-closure-perl (= 0.14-1),
libexpat1 (= 2.4.1-3),
libffi8 (= 3.4.2-3),
libfile-stripnondeterminism-perl (= 1.12.1-1),
libfile-which-perl (= 1.23-1),
libfontconfig1 (= 2.13.1-4.2),
libfreetype6 (= 2.11.0+dfsg-1),
libfribidi0 (= 1.0.8-2),
libgcc-10-dev (= 10.3.0-12+rpi1),
libgcc-11-dev (= 11.2.0-10+rpi1),
libgcc-s1 (= 11.2.0-10+rpi1),
libgcrypt20 (= 1.9.4-3),
libgdbm-compat4 (= 1.22-1),
libgdbm6 (= 1.22-1),
libgfortran-11-dev (= 11.2.0-10+rpi1),
libgfortran5 (= 11.2.0-10+rpi1),
libglib2.0-0 (= 2.70.1-1),
libgmp10 (= 2:6.2.1+dfsg-3),
libgnutls30 (= 3.7.2-2),
libgomp1 (= 11.2.0-10+rpi1),
libgpg-error0 (= 1.42-3),
libgraphite2-3 (= 1.3.14-1),
libgssapi-krb5-2 (= 1.18.3-7),
libharfbuzz0b (= 2.7.4-1),
libhogweed6 (= 3.7.3-1),
libhttp-date-perl (= 6.05-1),
libhttp-message-perl (= 6.35-1),
libice6 (= 2:1.0.10-1),
libicu-dev (= 67.1-7),
libicu67 (= 67.1-7),
libidn2-0 (= 2.3.2-2),
libio-html-perl (= 1.004-2),
libisl23 (= 0.24-2),
libjbig0 (= 2.1-3.1+b2),
libjpeg-dev (= 1:2.1.2-1),
libjpeg62-turbo (= 1:2.1.2-1),
libjpeg62-turbo-dev (= 1:2.1.2-1),
libk5crypto3 (= 1.18.3-7),
libkeyutils1 (= 1.6.1-2),
libkrb5-3 (= 1.18.3-7),
libkrb5support0 (= 1.18.3-7),
liblapack-dev (= 3.10.0-1),
liblapack3 (= 3.10.0-1),
libldap-2.4-2 (= 2.4.59+dfsg-1),
liblwp-mediatypes-perl (= 6.04-1),
liblz4-1 (= 1.9.3-2),
liblzma-dev (= 5.2.5-2),
liblzma5 (= 5.2.5-2),
libmagic-mgc (= 1:5.41-2),
libmagic1 (= 1:5.41-2),
libmd0 (= 1.0.4-1),
libmodule-implementation-perl (= 0.09-1.1),
libmodule-runtime-conflicts-perl (= 0.003-1.1),
libmodule-runtime-perl (= 0.016-1),
libmoose-perl (= 2.2200-1),
libmount1 (= 2.37.2-4),
libmpc3 (= 1.2.1-1),
libmpfr6 (= 4.1.0-3),
libmro-compat-perl (= 0.13-1),
libnamespace-clean-perl (= 0.27-1),
libncurses-dev (= 6.3-1),
libncurses5-dev (= 6.3-1),
libncurses6 (= 6.3-1),
libncursesw6 (= 6.3-1),
libnettle8 (= 3.7.3-1),
libnghttp2-14 (= 1.43.0-1),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libp11-kit0 (= 0.24.0-5),
libpackage-deprecationmanager-perl (= 0.17-1.1),
libpackage-stash-perl (= 0.39-1),
libpackage-stash-xs-perl (= 0.29-1+b2),
libpam-modules (= 1.4.0-10),
libpam-modules-bin (= 1.4.0-10),
libpam-runtime (= 1.4.0-10),
libpam0g (= 1.4.0-10),
libpango-1.0-0 (= 1.48.10+ds1-1),
libpangocairo-1.0-0 (= 1.48.10+ds1-1),
libpangoft2-1.0-0 (= 1.48.10+ds1-1),
libpaper-utils (= 1.1.28),
libpaper1 (= 1.1.28),
libparams-classify-perl (= 0.015-1+b3),
libparams-util-perl (= 1.102-1+b1),
libpcre16-3 (= 2:8.39-13),
libpcre2-16-0 (= 10.39-3),
libpcre2-32-0 (= 10.39-3),
libpcre2-8-0 (= 10.39-3),
libpcre2-dev (= 10.39-3),
libpcre2-posix3 (= 10.39-3),
libpcre3 (= 2:8.39-13),
libpcre3-dev (= 2:8.39-13),
libpcre32-3 (= 2:8.39-13),
libpcrecpp0v5 (= 2:8.39-13),
libperl5.32 (= 5.32.1-6),
libpipeline1 (= 1.5.4-1),
libpixman-1-0 (= 0.40.0-1),
libpng-dev (= 1.6.37-3),
libpng16-16 (= 1.6.37-3),
libpsl5 (= 0.21.0-1.2),
libreadline-dev (= 8.1-2),
libreadline8 (= 8.1-2),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.27+dfsg2-2),
libsasl2-modules-db (= 2.1.27+dfsg2-2),
libscalar-list-utils-perl (= 1:1.59-1),
libseccomp2 (= 2.5.3-2+rpi1),
libselinux1 (= 3.3-1),
libsigsegv2 (= 2.13-1),
libsm6 (= 2:1.2.3-1),
libsmartcols1 (= 2.37.2-4),
libssh2-1 (= 1.10.0-2),
libssl1.1 (= 1.1.1l-1),
libstdc++-10-dev (= 10.3.0-12+rpi1),
libstdc++-11-dev (= 11.2.0-10+rpi1),
libstdc++6 (= 11.2.0-10+rpi1),
libsub-exporter-perl (= 0.988-1),
libsub-exporter-progressive-perl (= 0.001013-1),
libsub-identify-perl (= 0.14-1+b3),
libsub-install-perl (= 0.928-1.1),
libsub-name-perl (= 0.26-1+b1),
libsub-override-perl (= 0.09-2),
libswitch-perl (= 2.17-2.1),
libsystemd0 (= 249.7-1+rpi1),
libtasn1-6 (= 4.18.0-4),
libtcl8.6 (= 8.6.12+dfsg-1),
libthai-data (= 0.1.28-4.1),
libthai0 (= 0.1.28-4.1),
libtiff5 (= 4.3.0-2),
libtimedate-perl (= 2.3300-2),
libtinfo6 (= 6.3-1),
libtirpc-common (= 1.3.2-2),
libtirpc-dev (= 1.3.2-2),
libtirpc3 (= 1.3.2-2),
libtk8.6 (= 8.6.12-1),
libtool (= 2.4.6-15),
libtry-tiny-perl (= 0.31-1),
libubsan1 (= 11.2.0-10+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 249.7-1+rpi1),
libunistring2 (= 0.9.10-6),
liburi-perl (= 5.10-1),
libuuid1 (= 2.37.2-4),
libvariable-magic-perl (= 0.62-1+b3),
libwebp6 (= 0.6.1-2.1),
libwww-curl-perl (= 4.17-7+b1),
libwww-curl-simple-perl (= 0.100191-2),
libx11-6 (= 2:1.7.2-2),
libx11-data (= 2:1.7.2-2),
libxau6 (= 1:1.0.9-1),
libxcb-render0 (= 1.14-3),
libxcb-shm0 (= 1.14-3),
libxcb1 (= 1.14-3),
libxdmcp6 (= 1:1.1.2-3),
libxext6 (= 2:1.3.4-1),
libxft2 (= 2.3.2-2),
libxml2 (= 2.9.12+dfsg-5),
libxmuu1 (= 2:1.1.2-2+b3),
libxrender1 (= 1:0.9.10-1),
libxss1 (= 1:1.2.3-1),
libxt6 (= 1:1.2.0-1),
libzstd1 (= 1.4.8+dfsg-3+rpi1),
linux-libc-dev (= 5.14.16-1+rpi1),
login (= 1:4.8.1-2),
lsb-base (= 11.1.0+rpi1),
m4 (= 1.4.18-5),
make (= 4.3-4.1),
man-db (= 2.9.4-2),
mawk (= 1.3.4.20200120-2),
ncurses-base (= 6.3-1),
ncurses-bin (= 6.3-1),
openssl (= 1.1.1l-1),
patch (= 2.7.6-7),
perl (= 5.32.1-6),
perl-base (= 5.32.1-6),
perl-modules-5.32 (= 5.32.1-6),
pkg-config (= 0.29.2-1),
po-debconf (= 1.0.21+nmu1),
r-base-core (= 4.1.2-1),
r-base-dev (= 4.1.2-1),
r-bioc-biocgenerics (= 0.40.0-1),
r-bioc-biocparallel (= 1.28.2-2),
r-bioc-biostrings (= 2.62.0-1),
r-bioc-genomeinfodb (= 1.30.0-1),
r-bioc-genomeinfodbdata (= 1.2.7-1),
r-bioc-genomicranges (= 1.46.1+dfsg-1),
r-bioc-iranges (= 2.28.0-1),
r-bioc-rhtslib (= 1.26.0+dfsg-1),
r-bioc-rsamtools (= 2.10.0-1),
r-bioc-s4vectors (= 0.32.3-1),
r-bioc-xvector (= 0.34.0-1),
r-bioc-zlibbioc (= 1.40.0+dfsg-1),
r-cran-bh (= 1.74.0-2),
r-cran-bitops (= 1.0-7-1),
r-cran-crayon (= 1.4.2-1),
r-cran-formatr (= 1.11-1),
r-cran-futile.logger (= 1.4.3-4),
r-cran-futile.options (= 1.0.1-3),
r-cran-lambda.r (= 1.2.4-2),
r-cran-rcurl (= 1.98-1.5-1),
r-cran-snow (= 1:0.4.4-1),
readline-common (= 8.1-2),
rpcsvc-proto (= 1.4.2-4),
sed (= 4.8-1),
sensible-utils (= 0.0.17),
sysvinit-utils (= 3.00-1),
tar (= 1.34+dfsg-1),
tzdata (= 2021e-1),
ucf (= 3.0043),
unzip (= 6.0-26),
util-linux (= 2.37.2-4),
x11-common (= 1:7.7+23),
xauth (= 1:1.1-1),
xdg-utils (= 1.1.3-4.1),
xz-utils (= 5.2.5-2),
zip (= 3.0-12),
zlib1g (= 1:1.2.11.dfsg-2),
zlib1g-dev (= 1:1.2.11.dfsg-2)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1637838678"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
r-bioc-bitseq-dbgsym_1.38.0+dfsg-1_armhf.deb
--------------------------------------------
new Debian package, version 2.0.
size 3157256 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: 1.38.0+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 3201
Depends: r-bioc-bitseq (= 1.38.0+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for r-bioc-bitseq
Build-Ids: 9657ebf4a05fbe969c8e711b481725af18dab614
drwxr-xr-x root/root 0 2021-11-25 11:11 ./
drwxr-xr-x root/root 0 2021-11-25 11:11 ./usr/
drwxr-xr-x root/root 0 2021-11-25 11:11 ./usr/lib/
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r-bioc-bitseq_1.38.0+dfsg-1_armhf.deb
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Package: r-bioc-bitseq
Version: 1.38.0+dfsg-1
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 5820
Depends: r-base-core (>= 4.1.2-1), r-api-4.0, r-api-bioc-3.14, r-bioc-rsamtools (>= 1.99.3), r-bioc-s4vectors, r-bioc-iranges, r-bioc-rhtslib (>= 1.15.5), libc6 (>= 2.29), libcurl4 (>= 7.18.0), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libstdc++6 (>= 11)
Suggests: r-bioc-biocstyle
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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Build Architecture: armhf
Build Type: any
Build-Space: 18992
Build-Time: 227
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 997
Job: r-bioc-bitseq_1.38.0+dfsg-1
Machine Architecture: armhf
Package: r-bioc-bitseq
Package-Time: 1260
Source-Version: 1.38.0+dfsg-1
Space: 18992
Status: successful
Version: 1.38.0+dfsg-1
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Finished at 2021-12-04T05:58:20Z
Build needed 00:21:00, 18992k disk space