r-bioc-bitseq →
1.30.0+dfsg-1 →
armhf → 2019-11-18 11:27:12
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| r-bioc-bitseq 1.30.0+dfsg-1 (armhf) Mon, 18 Nov 2019 10:55:42 +0000 |
+==============================================================================+
Package: r-bioc-bitseq
Version: 1.30.0+dfsg-1
Source Version: 1.30.0+dfsg-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bullseye-staging-armhf-sbuild-1a6f2ea4-47dd-4bff-be28-bce5c0740610' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.4 MB in 27s (914 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 757 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main r-bioc-bitseq 1.30.0+dfsg-1 (dsc) [2199 B]
Get:2 http://172.17.0.1/private bullseye-staging/main r-bioc-bitseq 1.30.0+dfsg-1 (tar) [750 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main r-bioc-bitseq 1.30.0+dfsg-1 (diff) [5452 B]
Fetched 757 kB in 0s (4982 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-bitseq-GuMKVH/r-bioc-bitseq-1.30.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-bitseq-GuMKVH' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-3mPWL7/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-3mPWL7/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-3mPWL7/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-3mPWL7/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-3mPWL7/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-3mPWL7/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-3mPWL7/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-3mPWL7/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-3mPWL7/apt_archive ./ Packages [430 B]
Fetched 2106 B in 1s (2723 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-3mPWL7/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-3mPWL7/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 2 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-3mPWL7/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12227 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), 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
Filtered Build-Depends: debhelper-compat (= 12), 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
dpkg-deb: building package 'sbuild-build-depends-r-bioc-bitseq-dummy' in '/<<BUILDDIR>>/resolver-3mPWL7/apt_archive/sbuild-build-depends-r-bioc-bitseq-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-r-bioc-bitseq-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-3mPWL7/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-3mPWL7/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-3mPWL7/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-3mPWL7/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-3mPWL7/apt_archive ./ Sources [565 B]
Get:5 copy:/<<BUILDDIR>>/resolver-3mPWL7/apt_archive ./ Packages [646 B]
Fetched 2544 B in 1s (3149 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-3mPWL7/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-3mPWL7/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install r-bioc-bitseq build dependencies (apt-based resolver)
-------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils ca-certificates
dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism dwz file
fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base gfortran
gfortran-9 groff-base icu-devtools intltool-debian libarchive-zip-perl
libblas-dev libblas3 libboost-dev libboost1.67-dev libbrotli1 libbsd0
libbz2-dev libcairo2 libcroco3 libcurl4 libcurl4-openssl-dev libdatrie1
libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
libfile-which-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran-9-dev
libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b
libice6 libicu-dev libicu63 libjbig0 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
liblapack-dev liblapack3 liblzma-dev libmagic-mgc libmagic1 libncurses-dev
libncurses5-dev libncurses6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre2-16-0
libpcre2-32-0 libpcre2-dev libpcre2-posix0 libpcre3-dev libpcre32-3
libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev libpng16-16 libpsl5
libreadline-dev librtmp1 libsigsegv2 libsm6 libssh2-1 libssl1.1
libsub-override-perl libswitch-perl libtcl8.6 libthai-data libthai0 libtiff5
libtinfo5 libtk8.6 libtool libuchardet0 libwebp6 libx11-6 libx11-data
libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2
libxml2 libxmuu1 libxrender1 libxss1 libxt6 m4 man-db 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-bitops r-cran-formatr
r-cran-futile.logger r-cran-futile.options r-cran-lambda.r r-cran-rcurl
r-cran-snow sensible-utils ucf unzip x11-common xauth xdg-utils zip
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation debtags dh-make gettext-doc libasprintf-dev libgettextpo-dev
gfortran-doc gfortran-9-doc libgfortran5-dbg libcoarrays-dev groff
liblapack-doc libboost-doc libboost1.67-doc libboost-atomic1.67-dev
libboost-chrono1.67-dev libboost-container1.67-dev libboost-context1.67-dev
libboost-coroutine1.67-dev libboost-date-time1.67-dev
libboost-exception1.67-dev libboost-fiber1.67-dev
libboost-filesystem1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev
libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
libboost-program-options1.67-dev libboost-python1.67-dev
libboost-random1.67-dev libboost-regex1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-system1.67-dev libboost-test1.67-dev
libboost-thread1.67-dev libboost-timer1.67-dev libboost-type-erasure1.67-dev
libboost-wave1.67-dev libboost1.67-tools-dev libmpfrc++-dev libntl-dev
libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev
libssl-dev krb5-doc krb5-user icu-doc liblzma-doc ncurses-doc readline-doc
tcl8.6 tk8.6 libtool-doc gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl 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-cran-knitr
r-cran-data.table r-bioc-bsgenome r-bioc-genomicfeatures r-cran-matrix
r-bioc-rtracklayer r-bioc-gviz r-bioc-annotationhub r-bioc-edger
r-bioc-summarizedexperiment r-bioc-graph r-cran-shiny r-cran-rmarkdown
r-cran-jsonlite r-cran-xml r-cran-rmpi r-cran-rsprng r-cran-rlecuyer
Recommended packages:
devscripts curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales 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-digest r-bioc-annotate r-bioc-summarizedexperiment
r-bioc-shortread r-cran-testit r-cran-codetools r-cran-survival
r-cran-testthat libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl
x11-utils x11-xserver-utils
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils ca-certificates
dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism dwz file
fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base gfortran
gfortran-9 groff-base icu-devtools intltool-debian libarchive-zip-perl
libblas-dev libblas3 libboost-dev libboost1.67-dev libbrotli1 libbsd0
libbz2-dev libcairo2 libcroco3 libcurl4 libcurl4-openssl-dev libdatrie1
libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
libfile-which-perl libfontconfig1 libfreetype6 libfribidi0 libgfortran-9-dev
libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b
libice6 libicu-dev libicu63 libjbig0 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
liblapack-dev liblapack3 liblzma-dev libmagic-mgc libmagic1 libncurses-dev
libncurses5-dev libncurses6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre2-16-0
libpcre2-32-0 libpcre2-dev libpcre2-posix0 libpcre3-dev libpcre32-3
libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev libpng16-16 libpsl5
libreadline-dev librtmp1 libsigsegv2 libsm6 libssh2-1 libssl1.1
libsub-override-perl libswitch-perl libtcl8.6 libthai-data libthai0 libtiff5
libtinfo5 libtk8.6 libtool libuchardet0 libwebp6 libx11-6 libx11-data
libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2
libxml2 libxmuu1 libxrender1 libxss1 libxt6 m4 man-db 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-bitops r-cran-formatr
r-cran-futile.logger r-cran-futile.options r-cran-lambda.r r-cran-rcurl
r-cran-snow sbuild-build-depends-r-bioc-bitseq-dummy sensible-utils ucf
unzip x11-common xauth xdg-utils zip zlib1g-dev
0 upgraded, 154 newly installed, 0 to remove and 2 not upgraded.
Need to get 134 MB of archives.
After this operation, 429 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-3mPWL7/apt_archive ./ sbuild-build-depends-r-bioc-bitseq-dummy 0.invalid.0 [936 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-3 [782 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-1 [1261 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-6 [253 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-6 [111 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libswitch-perl all 2.17-2 [20.5 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0038+nmu1 [69.0 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf openssl armhf 1.1.1d-2 [806 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates all 20190110 [157 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf dctrl-tools armhf 2.24-3 [94.2 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.1-1 [23.5 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.1-1 [14.4 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-2 [136 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.7.1 [173 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.2-3 [1137 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b2 [571 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20191019-1 [79.5 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.1 [997 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf unzip armhf 6.0-25 [152 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libpaper1 armhf 1.1.28 [20.5 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libpaper-utils armhf 1.1.28 [17.7 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf xdg-utils all 1.1.3-1 [73.3 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.8.0-8 [107 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-1 [274 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.10.1-2 [330 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-2 [280 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-2 [327 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libpixman-1-0 armhf 0.36.0-1 [458 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.13.1-2 [132 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.8-1 [298 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.8-1 [691 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libxcb-render0 armhf 1.13.1-2 [108 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libxcb-shm0 armhf 1.13.1-2 [99.3 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libcairo2 armhf 1.16.0-4 [599 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-5 [257 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6-6 [14.0 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-6+b1 [61.5 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-6+b1 [112 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-6+b1 [316 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-6+b1 [134 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.39.2-1 [71.3 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.66.0-1+b1 [297 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 9.2.1-17+rpi1 [231 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.8.0-8 [1568 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf fontconfig armhf 2.13.1-2 [404 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libfribidi0 armhf 1.0.7-1.1 [62.8 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libthai-data all 0.1.28-3 [170 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libdatrie1 armhf 0.2.12-3+b1 [36.4 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libthai0 armhf 0.1.28-3 [51.0 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libpango-1.0-0 armhf 1.42.4-7+b1 [168 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libgraphite2-3 armhf 1.3.13-11 [70.1 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libharfbuzz0b armhf 2.6.4-1+rpi1 [1308 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libpangoft2-1.0-0 armhf 1.42.4-7+b1 [62.2 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libpangocairo-1.0-0 armhf 1.42.4-7+b1 [51.9 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libtcl8.6 armhf 8.6.9+dfsg-2 [878 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libwebp6 armhf 0.6.1-2 [228 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libtiff5 armhf 4.1.0-1 [249 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf x11-common all 1:7.7+20 [252 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libtk8.6 armhf 8.6.9-2 [664 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libice6 armhf 2:1.0.9-2 [51.6 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libxt6 armhf 1:1.1.5-1+b3 [156 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf r-base-core armhf 3.6.1-7 [24.3 MB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-9-dev armhf 9.2.1-17+rpi1 [279 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf gfortran-9 armhf 9.2.1-17+rpi1 [7451 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:9.2.1-3+rpi1 [1432 B]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.8.0-8 [112 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.8.0-8 [2839 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libncurses-dev armhf 6.1+20191019-1 [284 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf libncurses5-dev armhf 6.1+20191019-1 [940 B]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf libreadline-dev armhf 8.0-3 [114 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2+b1 [179 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf libjpeg-dev all 1:1.5.2-2 [57.5 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-16-0 armhf 10.32-5 [175 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-32-0 armhf 10.32-5 [168 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-posix0 armhf 10.32-5 [38.3 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf libpcre2-dev armhf 10.32-5 [572 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libpcre16-3 armhf 2:8.39-12 [234 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf libpcre32-3 armhf 2:8.39-12 [227 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf libpcrecpp0v5 armhf 2:8.39-12 [150 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf libpcre3-dev armhf 2:8.39-12 [564 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf libpng-dev armhf 1.6.37-1 [275 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-2 [27.7 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf icu-devtools armhf 63.2-2 [163 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf libicu-dev armhf 63.2-2 [8846 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf libxmuu1 armhf 2:1.1.2-2+b3 [23.4 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf xauth armhf 1:1.0.10-1 [36.4 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29-6 [59.8 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf r-base-dev all 3.6.1-7 [4488 B]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf libfile-which-perl all 1.23-1 [16.6 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf dh-r all 20190917 [36.2 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf libboost1.67-dev armhf 1.67.0-13 [8386 kB]
Get:134 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.67.0.2+b3 [4464 B]
Get:135 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-openssl-dev armhf 7.66.0-1+b1 [370 kB]
Get:136 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biocgenerics all 0.32.0-1 [639 kB]
Get:137 http://172.17.0.1/private bullseye-staging/main armhf r-cran-formatr all 1.7-1 [152 kB]
Get:138 http://172.17.0.1/private bullseye-staging/main armhf r-cran-lambda.r all 1.2.4-1 [119 kB]
Get:139 http://172.17.0.1/private bullseye-staging/main armhf r-cran-futile.options all 1.0.1-2 [19.8 kB]
Get:140 http://172.17.0.1/private bullseye-staging/main armhf r-cran-futile.logger all 1.4.3-3 [102 kB]
Get:141 http://172.17.0.1/private bullseye-staging/main armhf r-cran-snow all 1:0.4.3-1 [108 kB]
Get:142 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biocparallel armhf 1.20.0-1 [1070 kB]
Get:143 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-s4vectors armhf 0.24.0-1 [1944 kB]
Get:144 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-iranges armhf 2.20.0-1 [2217 kB]
Get:145 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-zlibbioc all 1.32.0+dfsg-1 [8780 B]
Get:146 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-xvector armhf 0.26.0-1 [610 kB]
Get:147 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-biostrings armhf 2.54.0-1 [14.1 MB]
Get:148 http://172.17.0.1/private bullseye-staging/main armhf r-cran-bitops armhf 1.0-6-4 [23.9 kB]
Get:149 http://172.17.0.1/private bullseye-staging/main armhf r-cran-rcurl armhf 1.95-4.12-1 [722 kB]
Get:150 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomeinfodbdata all 1.2.2-1 [10.2 MB]
Get:151 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomeinfodb all 1.22.0-1 [3687 kB]
Get:152 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-genomicranges armhf 1.38.0+dfsg-1 [1828 kB]
Get:153 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-rhtslib armhf 1.18.0+dfsg-1 [964 kB]
Get:154 http://172.17.0.1/private bullseye-staging/main armhf r-bioc-rsamtools armhf 2.2.1-1 [3657 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 134 MB in 14s (9761 kB/s)
Selecting previously unselected package libbsd0:armhf.
(Reading database ... 12227 files and directories currently installed.)
Preparing to unpack .../000-libbsd0_0.10.0-1_armhf.deb ...
Unpacking libbsd0:armhf (0.10.0-1) ...
Selecting previously unselected package libtinfo5:armhf.
Preparing to unpack .../001-libtinfo5_6.1+20191019-1_armhf.deb ...
Unpacking libtinfo5:armhf (6.1+20191019-1) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../002-bsdmainutils_11.1.2_armhf.deb ...
Unpacking bsdmainutils (11.1.2) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../003-libuchardet0_0.0.6-3_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.6-3) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../004-groff-base_1.22.4-3_armhf.deb ...
Unpacking groff-base (1.22.4-3) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../005-libpipeline1_1.5.1-2_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.1-2) ...
Selecting previously unselected package man-db.
Preparing to unpack .../006-man-db_2.9.0-1_armhf.deb ...
Unpacking man-db (2.9.0-1) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../007-sensible-utils_0.0.12_all.deb ...
Unpacking sensible-utils (0.0.12) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../008-libmagic-mgc_1%3a5.37-6_armhf.deb ...
Unpacking libmagic-mgc (1:5.37-6) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../009-libmagic1_1%3a5.37-6_armhf.deb ...
Unpacking libmagic1:armhf (1:5.37-6) ...
Selecting previously unselected package file.
Preparing to unpack .../010-file_1%3a5.37-6_armhf.deb ...
Unpacking file (1:5.37-6) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../011-gettext-base_0.19.8.1-9_armhf.deb ...
Unpacking gettext-base (0.19.8.1-9) ...
Selecting previously unselected package libswitch-perl.
Preparing to unpack .../012-libswitch-perl_2.17-2_all.deb ...
Unpacking libswitch-perl (2.17-2) ...
Selecting previously unselected package ucf.
Preparing to unpack .../013-ucf_3.0038+nmu1_all.deb ...
Moving old data out of the way
Unpacking ucf (3.0038+nmu1) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../014-libsigsegv2_2.12-2_armhf.deb ...
Unpacking libsigsegv2:armhf (2.12-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../015-m4_1.4.18-4_armhf.deb ...
Unpacking m4 (1.4.18-4) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../016-autoconf_2.69-11_all.deb ...
Unpacking autoconf (2.69-11) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../017-autotools-dev_20180224.1_all.deb ...
Unpacking autotools-dev (20180224.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../018-automake_1%3a1.16.1-4_all.deb ...
Unpacking automake (1:1.16.1-4) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../019-autopoint_0.19.8.1-9_all.deb ...
Unpacking autopoint (0.19.8.1-9) ...
Selecting previously unselected package libssl1.1:armhf.
Preparing to unpack .../020-libssl1.1_1.1.1d-2_armhf.deb ...
Unpacking libssl1.1:armhf (1.1.1d-2) ...
Selecting previously unselected package openssl.
Preparing to unpack .../021-openssl_1.1.1d-2_armhf.deb ...
Unpacking openssl (1.1.1d-2) ...
Selecting previously unselected package ca-certificates.
Preparing to unpack .../022-ca-certificates_20190110_all.deb ...
Unpacking ca-certificates (20190110) ...
Selecting previously unselected package dctrl-tools.
Preparing to unpack .../023-dctrl-tools_2.24-3_armhf.deb ...
Unpacking dctrl-tools (2.24-3) ...
Selecting previously unselected package libtool.
Preparing to unpack .../024-libtool_2.4.6-11_all.deb ...
Unpacking libtool (2.4.6-11) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../025-dh-autoreconf_19_all.deb ...
Unpacking dh-autoreconf (19) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../026-libarchive-zip-perl_1.67-1_all.deb ...
Unpacking libarchive-zip-perl (1.67-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../027-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../028-libfile-stripnondeterminism-perl_1.6.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.6.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../029-dh-strip-nondeterminism_1.6.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.6.1-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../030-libelf1_0.176-1.1_armhf.deb ...
Unpacking libelf1:armhf (0.176-1.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../031-dwz_0.13-2_armhf.deb ...
Unpacking dwz (0.13-2) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../032-libdebhelper-perl_12.7.1_all.deb ...
Unpacking libdebhelper-perl (12.7.1) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../033-libglib2.0-0_2.62.2-3_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.62.2-3) ...
Selecting previously unselected package libicu63:armhf.
Preparing to unpack .../034-libicu63_63.2-2_armhf.deb ...
Unpacking libicu63:armhf (63.2-2) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../035-libxml2_2.9.4+dfsg1-7+b2_armhf.deb ...
Unpacking libxml2:armhf (2.9.4+dfsg1-7+b2) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../036-libcroco3_0.6.13-1_armhf.deb ...
Unpacking libcroco3:armhf (0.6.13-1) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../037-libncurses6_6.1+20191019-1_armhf.deb ...
Unpacking libncurses6:armhf (6.1+20191019-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../038-gettext_0.19.8.1-9_armhf.deb ...
Unpacking gettext (0.19.8.1-9) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../039-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../040-po-debconf_1.0.21_all.deb ...
Unpacking po-debconf (1.0.21) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../041-debhelper_12.7.1_all.deb ...
Unpacking debhelper (12.7.1) ...
Selecting previously unselected package zip.
Preparing to unpack .../042-zip_3.0-11_armhf.deb ...
Unpacking zip (3.0-11) ...
Selecting previously unselected package unzip.
Preparing to unpack .../043-unzip_6.0-25_armhf.deb ...
Unpacking unzip (6.0-25) ...
Selecting previously unselected package libpaper1:armhf.
Preparing to unpack .../044-libpaper1_1.1.28_armhf.deb ...
Unpacking libpaper1:armhf (1.1.28) ...
Selecting previously unselected package libpaper-utils.
Preparing to unpack .../045-libpaper-utils_1.1.28_armhf.deb ...
Unpacking libpaper-utils (1.1.28) ...
Selecting previously unselected package xdg-utils.
Preparing to unpack .../046-xdg-utils_1.1.3-1_all.deb ...
Unpacking xdg-utils (1.1.3-1) ...
Selecting previously unselected package libblas3:armhf.
Preparing to unpack .../047-libblas3_3.8.0-8_armhf.deb ...
Unpacking libblas3:armhf (3.8.0-8) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../048-libexpat1_2.2.9-1_armhf.deb ...
Unpacking libexpat1:armhf (2.2.9-1) ...
Selecting previously unselected package libpng16-16:armhf.
Preparing to unpack .../049-libpng16-16_1.6.37-1_armhf.deb ...
Unpacking libpng16-16:armhf (1.6.37-1) ...
Selecting previously unselected package libfreetype6:armhf.
Preparing to unpack .../050-libfreetype6_2.10.1-2_armhf.deb ...
Unpacking libfreetype6:armhf (2.10.1-2) ...
Selecting previously unselected package fonts-dejavu-core.
Preparing to unpack .../051-fonts-dejavu-core_2.37-1_all.deb ...
Unpacking fonts-dejavu-core (2.37-1) ...
Selecting previously unselected package fontconfig-config.
Preparing to unpack .../052-fontconfig-config_2.13.1-2_all.deb ...
Unpacking fontconfig-config (2.13.1-2) ...
Selecting previously unselected package libfontconfig1:armhf.
Preparing to unpack .../053-libfontconfig1_2.13.1-2_armhf.deb ...
Unpacking libfontconfig1:armhf (2.13.1-2) ...
Selecting previously unselected package libpixman-1-0:armhf.
Preparing to unpack .../054-libpixman-1-0_0.36.0-1_armhf.deb ...
Unpacking libpixman-1-0:armhf (0.36.0-1) ...
Selecting previously unselected package libxau6:armhf.
Preparing to unpack .../055-libxau6_1%3a1.0.8-1+b2_armhf.deb ...
Unpacking libxau6:armhf (1:1.0.8-1+b2) ...
Selecting previously unselected package libxdmcp6:armhf.
Preparing to unpack .../056-libxdmcp6_1%3a1.1.2-3_armhf.deb ...
Unpacking libxdmcp6:armhf (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:armhf.
Preparing to unpack .../057-libxcb1_1.13.1-2_armhf.deb ...
Unpacking libxcb1:armhf (1.13.1-2) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../058-libx11-data_2%3a1.6.8-1_all.deb ...
Unpacking libx11-data (2:1.6.8-1) ...
Selecting previously unselected package libx11-6:armhf.
Preparing to unpack .../059-libx11-6_2%3a1.6.8-1_armhf.deb ...
Unpacking libx11-6:armhf (2:1.6.8-1) ...
Selecting previously unselected package libxcb-render0:armhf.
Preparing to unpack .../060-libxcb-render0_1.13.1-2_armhf.deb ...
Unpacking libxcb-render0:armhf (1.13.1-2) ...
Selecting previously unselected package libxcb-shm0:armhf.
Preparing to unpack .../061-libxcb-shm0_1.13.1-2_armhf.deb ...
Unpacking libxcb-shm0:armhf (1.13.1-2) ...
Selecting previously unselected package libxext6:armhf.
Preparing to unpack .../062-libxext6_2%3a1.3.3-1+b2_armhf.deb ...
Unpacking libxext6:armhf (2:1.3.3-1+b2) ...
Selecting previously unselected package libxrender1:armhf.
Preparing to unpack .../063-libxrender1_1%3a0.9.10-1_armhf.deb ...
Unpacking libxrender1:armhf (1:0.9.10-1) ...
Selecting previously unselected package libcairo2:armhf.
Preparing to unpack .../064-libcairo2_1.16.0-4_armhf.deb ...
Unpacking libcairo2:armhf (1.16.0-4) ...
Selecting previously unselected package libbrotli1:armhf.
Preparing to unpack .../065-libbrotli1_1.0.7-5_armhf.deb ...
Unpacking libbrotli1:armhf (1.0.7-5) ...
Selecting previously unselected package libkeyutils1:armhf.
Preparing to unpack .../066-libkeyutils1_1.6-6_armhf.deb ...
Unpacking libkeyutils1:armhf (1.6-6) ...
Selecting previously unselected package libkrb5support0:armhf.
Preparing to unpack .../067-libkrb5support0_1.17-6+b1_armhf.deb ...
Unpacking libkrb5support0:armhf (1.17-6+b1) ...
Selecting previously unselected package libk5crypto3:armhf.
Preparing to unpack .../068-libk5crypto3_1.17-6+b1_armhf.deb ...
Unpacking libk5crypto3:armhf (1.17-6+b1) ...
Selecting previously unselected package libkrb5-3:armhf.
Preparing to unpack .../069-libkrb5-3_1.17-6+b1_armhf.deb ...
Unpacking libkrb5-3:armhf (1.17-6+b1) ...
Selecting previously unselected package libgssapi-krb5-2:armhf.
Preparing to unpack .../070-libgssapi-krb5-2_1.17-6+b1_armhf.deb ...
Unpacking libgssapi-krb5-2:armhf (1.17-6+b1) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../071-libnghttp2-14_1.39.2-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.39.2-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../072-libpsl5_0.20.2-2_armhf.deb ...
Unpacking libpsl5:armhf (0.20.2-2) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../073-librtmp1_2.4+20151223.gitfa8646d.1-2+b1_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../074-libssh2-1_1.8.0-2.1_armhf.deb ...
Unpacking libssh2-1:armhf (1.8.0-2.1) ...
Selecting previously unselected package libcurl4:armhf.
Preparing to unpack .../075-libcurl4_7.66.0-1+b1_armhf.deb ...
Unpacking libcurl4:armhf (7.66.0-1+b1) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
Preparing to unpack .../076-libjpeg62-turbo_1%3a1.5.2-2+b1_armhf.deb ...
Unpacking libjpeg62-turbo:armhf (1:1.5.2-2+b1) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../077-libgfortran5_9.2.1-17+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (9.2.1-17+rpi1) ...
Selecting previously unselected package liblapack3:armhf.
Preparing to unpack .../078-liblapack3_3.8.0-8_armhf.deb ...
Unpacking liblapack3:armhf (3.8.0-8) ...
Selecting previously unselected package fontconfig.
Preparing to unpack .../079-fontconfig_2.13.1-2_armhf.deb ...
Unpacking fontconfig (2.13.1-2) ...
Selecting previously unselected package libfribidi0:armhf.
Preparing to unpack .../080-libfribidi0_1.0.7-1.1_armhf.deb ...
Unpacking libfribidi0:armhf (1.0.7-1.1) ...
Selecting previously unselected package libthai-data.
Preparing to unpack .../081-libthai-data_0.1.28-3_all.deb ...
Unpacking libthai-data (0.1.28-3) ...
Selecting previously unselected package libdatrie1:armhf.
Preparing to unpack .../082-libdatrie1_0.2.12-3+b1_armhf.deb ...
Unpacking libdatrie1:armhf (0.2.12-3+b1) ...
Selecting previously unselected package libthai0:armhf.
Preparing to unpack .../083-libthai0_0.1.28-3_armhf.deb ...
Unpacking libthai0:armhf (0.1.28-3) ...
Selecting previously unselected package libpango-1.0-0:armhf.
Preparing to unpack .../084-libpango-1.0-0_1.42.4-7+b1_armhf.deb ...
Unpacking libpango-1.0-0:armhf (1.42.4-7+b1) ...
Selecting previously unselected package libgraphite2-3:armhf.
Preparing to unpack .../085-libgraphite2-3_1.3.13-11_armhf.deb ...
Unpacking libgraphite2-3:armhf (1.3.13-11) ...
Selecting previously unselected package libharfbuzz0b:armhf.
Preparing to unpack .../086-libharfbuzz0b_2.6.4-1+rpi1_armhf.deb ...
Unpacking libharfbuzz0b:armhf (2.6.4-1+rpi1) ...
Selecting previously unselected package libpangoft2-1.0-0:armhf.
Preparing to unpack .../087-libpangoft2-1.0-0_1.42.4-7+b1_armhf.deb ...
Unpacking libpangoft2-1.0-0:armhf (1.42.4-7+b1) ...
Selecting previously unselected package libpangocairo-1.0-0:armhf.
Preparing to unpack .../088-libpangocairo-1.0-0_1.42.4-7+b1_armhf.deb ...
Unpacking libpangocairo-1.0-0:armhf (1.42.4-7+b1) ...
Selecting previously unselected package libtcl8.6:armhf.
Preparing to unpack .../089-libtcl8.6_8.6.9+dfsg-2_armhf.deb ...
Unpacking libtcl8.6:armhf (8.6.9+dfsg-2) ...
Selecting previously unselected package libjbig0:armhf.
Preparing to unpack .../090-libjbig0_2.1-3.1+b2_armhf.deb ...
Unpacking libjbig0:armhf (2.1-3.1+b2) ...
Selecting previously unselected package libwebp6:armhf.
Preparing to unpack .../091-libwebp6_0.6.1-2_armhf.deb ...
Unpacking libwebp6:armhf (0.6.1-2) ...
Selecting previously unselected package libtiff5:armhf.
Preparing to unpack .../092-libtiff5_4.1.0-1_armhf.deb ...
Unpacking libtiff5:armhf (4.1.0-1) ...
Selecting previously unselected package libxft2:armhf.
Preparing to unpack .../093-libxft2_2.3.2-2_armhf.deb ...
Unpacking libxft2:armhf (2.3.2-2) ...
Selecting previously unselected package x11-common.
Preparing to unpack .../094-x11-common_1%3a7.7+20_all.deb ...
Unpacking x11-common (1:7.7+20) ...
Selecting previously unselected package libxss1:armhf.
Preparing to unpack .../095-libxss1_1%3a1.2.3-1_armhf.deb ...
Unpacking libxss1:armhf (1:1.2.3-1) ...
Selecting previously unselected package libtk8.6:armhf.
Preparing to unpack .../096-libtk8.6_8.6.9-2_armhf.deb ...
Unpacking libtk8.6:armhf (8.6.9-2) ...
Selecting previously unselected package libice6:armhf.
Preparing to unpack .../097-libice6_2%3a1.0.9-2_armhf.deb ...
Unpacking libice6:armhf (2:1.0.9-2) ...
Selecting previously unselected package libsm6:armhf.
Preparing to unpack .../098-libsm6_2%3a1.2.3-1_armhf.deb ...
Unpacking libsm6:armhf (2:1.2.3-1) ...
Selecting previously unselected package libxt6:armhf.
Preparing to unpack .../099-libxt6_1%3a1.1.5-1+b3_armhf.deb ...
Unpacking libxt6:armhf (1:1.1.5-1+b3) ...
Selecting previously unselected package r-base-core.
Preparing to unpack .../100-r-base-core_3.6.1-7_armhf.deb ...
Unpacking r-base-core (3.6.1-7) ...
Selecting previously unselected package libgfortran-9-dev:armhf.
Preparing to unpack .../101-libgfortran-9-dev_9.2.1-17+rpi1_armhf.deb ...
Unpacking libgfortran-9-dev:armhf (9.2.1-17+rpi1) ...
Selecting previously unselected package gfortran-9.
Preparing to unpack .../102-gfortran-9_9.2.1-17+rpi1_armhf.deb ...
Unpacking gfortran-9 (9.2.1-17+rpi1) ...
Selecting previously unselected package gfortran.
Preparing to unpack .../103-gfortran_4%3a9.2.1-3+rpi1_armhf.deb ...
Unpacking gfortran (4:9.2.1-3+rpi1) ...
Selecting previously unselected package libblas-dev:armhf.
Preparing to unpack .../104-libblas-dev_3.8.0-8_armhf.deb ...
Unpacking libblas-dev:armhf (3.8.0-8) ...
Selecting previously unselected package liblapack-dev:armhf.
Preparing to unpack .../105-liblapack-dev_3.8.0-8_armhf.deb ...
Unpacking liblapack-dev:armhf (3.8.0-8) ...
Selecting previously unselected package libncurses-dev:armhf.
Preparing to unpack .../106-libncurses-dev_6.1+20191019-1_armhf.deb ...
Unpacking libncurses-dev:armhf (6.1+20191019-1) ...
Selecting previously unselected package libncurses5-dev:armhf.
Preparing to unpack .../107-libncurses5-dev_6.1+20191019-1_armhf.deb ...
Unpacking libncurses5-dev:armhf (6.1+20191019-1) ...
Selecting previously unselected package libreadline-dev:armhf.
Preparing to unpack .../108-libreadline-dev_8.0-3_armhf.deb ...
Unpacking libreadline-dev:armhf (8.0-3) ...
Selecting previously unselected package libjpeg62-turbo-dev:armhf.
Preparing to unpack .../109-libjpeg62-turbo-dev_1%3a1.5.2-2+b1_armhf.deb ...
Unpacking libjpeg62-turbo-dev:armhf (1:1.5.2-2+b1) ...
Selecting previously unselected package libjpeg-dev.
Preparing to unpack .../110-libjpeg-dev_1%3a1.5.2-2_all.deb ...
Unpacking libjpeg-dev (1:1.5.2-2) ...
Selecting previously unselected package libpcre2-16-0:armhf.
Preparing to unpack .../111-libpcre2-16-0_10.32-5_armhf.deb ...
Unpacking libpcre2-16-0:armhf (10.32-5) ...
Selecting previously unselected package libpcre2-32-0:armhf.
Preparing to unpack .../112-libpcre2-32-0_10.32-5_armhf.deb ...
Unpacking libpcre2-32-0:armhf (10.32-5) ...
Selecting previously unselected package libpcre2-posix0:armhf.
Preparing to unpack .../113-libpcre2-posix0_10.32-5_armhf.deb ...
Unpacking libpcre2-posix0:armhf (10.32-5) ...
Selecting previously unselected package libpcre2-dev:armhf.
Preparing to unpack .../114-libpcre2-dev_10.32-5_armhf.deb ...
Unpacking libpcre2-dev:armhf (10.32-5) ...
Selecting previously unselected package libpcre16-3:armhf.
Preparing to unpack .../115-libpcre16-3_2%3a8.39-12_armhf.deb ...
Unpacking libpcre16-3:armhf (2:8.39-12) ...
Selecting previously unselected package libpcre32-3:armhf.
Preparing to unpack .../116-libpcre32-3_2%3a8.39-12_armhf.deb ...
Unpacking libpcre32-3:armhf (2:8.39-12) ...
Selecting previously unselected package libpcrecpp0v5:armhf.
Preparing to unpack .../117-libpcrecpp0v5_2%3a8.39-12_armhf.deb ...
Unpacking libpcrecpp0v5:armhf (2:8.39-12) ...
Selecting previously unselected package libpcre3-dev:armhf.
Preparing to unpack .../118-libpcre3-dev_2%3a8.39-12_armhf.deb ...
Unpacking libpcre3-dev:armhf (2:8.39-12) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../119-zlib1g-dev_1%3a1.2.11.dfsg-1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Selecting previously unselected package libpng-dev:armhf.
Preparing to unpack .../120-libpng-dev_1.6.37-1_armhf.deb ...
Unpacking libpng-dev:armhf (1.6.37-1) ...
Selecting previously unselected package libbz2-dev:armhf.
Preparing to unpack .../121-libbz2-dev_1.0.8-2_armhf.deb ...
Unpacking libbz2-dev:armhf (1.0.8-2) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../122-liblzma-dev_5.2.4-1_armhf.deb ...
Unpacking liblzma-dev:armhf (5.2.4-1) ...
Selecting previously unselected package icu-devtools.
Preparing to unpack .../123-icu-devtools_63.2-2_armhf.deb ...
Unpacking icu-devtools (63.2-2) ...
Selecting previously unselected package libicu-dev:armhf.
Preparing to unpack .../124-libicu-dev_63.2-2_armhf.deb ...
Unpacking libicu-dev:armhf (63.2-2) ...
Selecting previously unselected package libxmuu1:armhf.
Preparing to unpack .../125-libxmuu1_2%3a1.1.2-2+b3_armhf.deb ...
Unpacking libxmuu1:armhf (2:1.1.2-2+b3) ...
Selecting previously unselected package xauth.
Preparing to unpack .../126-xauth_1%3a1.0.10-1_armhf.deb ...
Unpacking xauth (1:1.0.10-1) ...
Selecting previously unselected package pkg-config.
Preparing to unpack .../127-pkg-config_0.29-6_armhf.deb ...
Unpacking pkg-config (0.29-6) ...
Selecting previously unselected package r-base-dev.
Preparing to unpack .../128-r-base-dev_3.6.1-7_all.deb ...
Unpacking r-base-dev (3.6.1-7) ...
Selecting previously unselected package libfile-which-perl.
Preparing to unpack .../129-libfile-which-perl_1.23-1_all.deb ...
Unpacking libfile-which-perl (1.23-1) ...
Selecting previously unselected package dh-r.
Preparing to unpack .../130-dh-r_20190917_all.deb ...
Unpacking dh-r (20190917) ...
Selecting previously unselected package libboost1.67-dev:armhf.
Preparing to unpack .../131-libboost1.67-dev_1.67.0-13_armhf.deb ...
Unpacking libboost1.67-dev:armhf (1.67.0-13) ...
Selecting previously unselected package libboost-dev:armhf.
Preparing to unpack .../132-libboost-dev_1.67.0.2+b3_armhf.deb ...
Unpacking libboost-dev:armhf (1.67.0.2+b3) ...
Selecting previously unselected package libcurl4-openssl-dev:armhf.
Preparing to unpack .../133-libcurl4-openssl-dev_7.66.0-1+b1_armhf.deb ...
Unpacking libcurl4-openssl-dev:armhf (7.66.0-1+b1) ...
Selecting previously unselected package r-bioc-biocgenerics.
Preparing to unpack .../134-r-bioc-biocgenerics_0.32.0-1_all.deb ...
Unpacking r-bioc-biocgenerics (0.32.0-1) ...
Selecting previously unselected package r-cran-formatr.
Preparing to unpack .../135-r-cran-formatr_1.7-1_all.deb ...
Unpacking r-cran-formatr (1.7-1) ...
Selecting previously unselected package r-cran-lambda.r.
Preparing to unpack .../136-r-cran-lambda.r_1.2.4-1_all.deb ...
Unpacking r-cran-lambda.r (1.2.4-1) ...
Selecting previously unselected package r-cran-futile.options.
Preparing to unpack .../137-r-cran-futile.options_1.0.1-2_all.deb ...
Unpacking r-cran-futile.options (1.0.1-2) ...
Selecting previously unselected package r-cran-futile.logger.
Preparing to unpack .../138-r-cran-futile.logger_1.4.3-3_all.deb ...
Unpacking r-cran-futile.logger (1.4.3-3) ...
Selecting previously unselected package r-cran-snow.
Preparing to unpack .../139-r-cran-snow_1%3a0.4.3-1_all.deb ...
Unpacking r-cran-snow (1:0.4.3-1) ...
Selecting previously unselected package r-bioc-biocparallel.
Preparing to unpack .../140-r-bioc-biocparallel_1.20.0-1_armhf.deb ...
Unpacking r-bioc-biocparallel (1.20.0-1) ...
Selecting previously unselected package r-bioc-s4vectors.
Preparing to unpack .../141-r-bioc-s4vectors_0.24.0-1_armhf.deb ...
Unpacking r-bioc-s4vectors (0.24.0-1) ...
Selecting previously unselected package r-bioc-iranges.
Preparing to unpack .../142-r-bioc-iranges_2.20.0-1_armhf.deb ...
Unpacking r-bioc-iranges (2.20.0-1) ...
Selecting previously unselected package r-bioc-zlibbioc.
Preparing to unpack .../143-r-bioc-zlibbioc_1.32.0+dfsg-1_all.deb ...
Unpacking r-bioc-zlibbioc (1.32.0+dfsg-1) ...
Selecting previously unselected package r-bioc-xvector.
Preparing to unpack .../144-r-bioc-xvector_0.26.0-1_armhf.deb ...
Unpacking r-bioc-xvector (0.26.0-1) ...
Selecting previously unselected package r-bioc-biostrings.
Preparing to unpack .../145-r-bioc-biostrings_2.54.0-1_armhf.deb ...
Unpacking r-bioc-biostrings (2.54.0-1) ...
Selecting previously unselected package r-cran-bitops.
Preparing to unpack .../146-r-cran-bitops_1.0-6-4_armhf.deb ...
Unpacking r-cran-bitops (1.0-6-4) ...
Selecting previously unselected package r-cran-rcurl.
Preparing to unpack .../147-r-cran-rcurl_1.95-4.12-1_armhf.deb ...
Unpacking r-cran-rcurl (1.95-4.12-1) ...
Selecting previously unselected package r-bioc-genomeinfodbdata.
Preparing to unpack .../148-r-bioc-genomeinfodbdata_1.2.2-1_all.deb ...
Unpacking r-bioc-genomeinfodbdata (1.2.2-1) ...
Selecting previously unselected package r-bioc-genomeinfodb.
Preparing to unpack .../149-r-bioc-genomeinfodb_1.22.0-1_all.deb ...
Unpacking r-bioc-genomeinfodb (1.22.0-1) ...
Selecting previously unselected package r-bioc-genomicranges.
Preparing to unpack .../150-r-bioc-genomicranges_1.38.0+dfsg-1_armhf.deb ...
Unpacking r-bioc-genomicranges (1.38.0+dfsg-1) ...
Selecting previously unselected package r-bioc-rhtslib.
Preparing to unpack .../151-r-bioc-rhtslib_1.18.0+dfsg-1_armhf.deb ...
Unpacking r-bioc-rhtslib (1.18.0+dfsg-1) ...
Selecting previously unselected package r-bioc-rsamtools.
Preparing to unpack .../152-r-bioc-rsamtools_2.2.1-1_armhf.deb ...
Unpacking r-bioc-rsamtools (2.2.1-1) ...
Selecting previously unselected package sbuild-build-depends-r-bioc-bitseq-dummy.
Preparing to unpack .../153-sbuild-build-depends-r-bioc-bitseq-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-r-bioc-bitseq-dummy (0.invalid.0) ...
Setting up libboost1.67-dev:armhf (1.67.0-13) ...
Setting up libexpat1:armhf (2.2.9-1) ...
Setting up libpcrecpp0v5:armhf (2:8.39-12) ...
Setting up libpipeline1:armhf (1.5.1-2) ...
Setting up libgraphite2-3:armhf (1.3.13-11) ...
Setting up libpixman-1-0:armhf (0.36.0-1) ...
Setting up libfile-which-perl (1.23-1) ...
Setting up libxau6:armhf (1:1.0.8-1+b2) ...
Setting up libkeyutils1:armhf (1.6-6) ...
Setting up libpsl5:armhf (0.20.2-2) ...
Setting up libpcre16-3:armhf (2:8.39-12) ...
Setting up libdatrie1:armhf (0.2.12-3+b1) ...
Setting up libmagic-mgc (1:5.37-6) ...
Setting up libarchive-zip-perl (1.67-1) ...
Setting up libglib2.0-0:armhf (2.62.2-3) ...
No schema files found: doing nothing.
Setting up libssl1.1:armhf (1.1.1d-2) ...
Setting up unzip (6.0-25) ...
Setting up libdebhelper-perl (12.7.1) ...
Setting up libbrotli1:armhf (1.0.7-5) ...
Setting up x11-common (1:7.7+20) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
invoke-rc.d: could not determine current runlevel
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libnghttp2-14:armhf (1.39.2-1) ...
Setting up libmagic1:armhf (1:5.37-6) ...
Setting up gettext-base (0.19.8.1-9) ...
Setting up file (1:5.37-6) ...
Setting up libjbig0:armhf (2.1-3.1+b2) ...
Setting up libpcre2-16-0:armhf (10.32-5) ...
Setting up libicu63:armhf (63.2-2) ...
Setting up libkrb5support0:armhf (1.17-6+b1) ...
Setting up zip (3.0-11) ...
Setting up autotools-dev (20180224.1) ...
Setting up libpcre2-32-0:armhf (10.32-5) ...
Setting up libblas3:armhf (3.8.0-8) ...
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
Setting up libjpeg62-turbo:armhf (1:1.5.2-2+b1) ...
Setting up libpcre2-posix0:armhf (10.32-5) ...
Setting up libswitch-perl (2.17-2) ...
Setting up libx11-data (2:1.6.8-1) ...
Setting up libjpeg62-turbo-dev:armhf (1:1.5.2-2+b1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Setting up libncurses6:armhf (6.1+20191019-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libfribidi0:armhf (1.0.7-1.1) ...
Setting up libpng16-16:armhf (1.6.37-1) ...
Setting up libpcre32-3:armhf (2:8.39-12) ...
Setting up libtcl8.6:armhf (8.6.9+dfsg-2) ...
Setting up autopoint (0.19.8.1-9) ...
Setting up libwebp6:armhf (0.6.1-2) ...
Setting up icu-devtools (63.2-2) ...
Setting up pkg-config (0.29-6) ...
Setting up fonts-dejavu-core (2.37-1) ...
Setting up libk5crypto3:armhf (1.17-6+b1) ...
Setting up libgfortran5:armhf (9.2.1-17+rpi1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up sensible-utils (0.0.12) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libthai-data (0.1.28-3) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-6+b1) ...
Setting up libboost-dev:armhf (1.67.0.2+b3) ...
Setting up libtiff5:armhf (4.1.0-1) ...
Setting up openssl (1.1.1d-2) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20191019-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libicu-dev:armhf (63.2-2) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7+b2) ...
Setting up xdg-utils (1.1.3-1) ...
Setting up libblas-dev:armhf (3.8.0-8) ...
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) ...
Setting up libbz2-dev:armhf (1.0.8-2) ...
Setting up libfile-stripnondeterminism-perl (1.6.1-1) ...
Setting up libice6:armhf (2:1.0.9-2) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up liblapack3:armhf (3.8.0-8) ...
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 (6.1+20191019-1) ...
Setting up libxcb1:armhf (1.13.1-2) ...
Setting up libpcre2-dev:armhf (10.32-5) ...
Setting up libtool (2.4.6-11) ...
Setting up libxcb-render0:armhf (1.13.1-2) ...
Setting up libpcre3-dev:armhf (2:8.39-12) ...
Setting up libpng-dev:armhf (1.6.37-1) ...
Setting up libjpeg-dev (1:1.5.2-2) ...
Setting up libgfortran-9-dev:armhf (9.2.1-17+rpi1) ...
Setting up m4 (1.4.18-4) ...
Setting up libxcb-shm0:armhf (1.13.1-2) ...
Setting up libreadline-dev:armhf (8.0-3) ...
Setting up libthai0:armhf (0.1.28-3) ...
Setting up ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
128 added, 0 removed; done.
Setting up libfreetype6:armhf (2.10.1-2) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up liblapack-dev:armhf (3.8.0-8) ...
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 libgssapi-krb5-2:armhf (1.17-6+b1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up ucf (3.0038+nmu1) ...
Setting up autoconf (2.69-11) ...
Setting up dwz (0.13-2) ...
Setting up groff-base (1.22.4-3) ...
Setting up libncurses5-dev:armhf (6.1+20191019-1) ...
Setting up libcurl4:armhf (7.66.0-1+b1) ...
Setting up libx11-6:armhf (2:1.6.8-1) ...
Setting up libharfbuzz0b:armhf (2.6.4-1+rpi1) ...
Setting up libsm6:armhf (2:1.2.3-1) ...
Setting up libxmuu1:armhf (2:1.1.2-2+b3) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libpaper1:armhf (1.1.28) ...
Creating config file /etc/papersize with new version
Setting up gettext (0.19.8.1-9) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up gfortran-9 (9.2.1-17+rpi1) ...
Setting up fontconfig-config (2.13.1-2) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up libpaper-utils (1.1.28) ...
Setting up man-db (2.9.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran (4:9.2.1-3+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 intltool-debian (0.35.0+20060710.5) ...
Setting up libcurl4-openssl-dev:armhf (7.66.0-1+b1) ...
Setting up libxt6:armhf (1:1.1.5-1+b3) ...
Setting up xauth (1:1.0.10-1) ...
Setting up libxss1:armhf (1:1.2.3-1) ...
Setting up libfontconfig1:armhf (2.13.1-2) ...
Setting up fontconfig (2.13.1-2) ...
Regenerating fonts cache... done.
Setting up libxft2:armhf (2.3.2-2) ...
Setting up po-debconf (1.0.21) ...
Setting up libtk8.6:armhf (8.6.9-2) ...
Setting up libpango-1.0-0:armhf (1.42.4-7+b1) ...
Setting up libcairo2:armhf (1.16.0-4) ...
Setting up libpangoft2-1.0-0:armhf (1.42.4-7+b1) ...
Setting up libpangocairo-1.0-0:armhf (1.42.4-7+b1) ...
Setting up r-base-core (3.6.1-7) ...
Creating config file /etc/R/Renviron with new version
Setting up r-cran-futile.options (1.0.1-2) ...
Setting up r-cran-formatr (1.7-1) ...
Setting up r-bioc-genomeinfodbdata (1.2.2-1) ...
Setting up r-bioc-biocgenerics (0.32.0-1) ...
Setting up r-base-dev (3.6.1-7) ...
Setting up r-cran-lambda.r (1.2.4-1) ...
Setting up r-cran-snow (1:0.4.3-1) ...
Setting up r-cran-bitops (1.0-6-4) ...
Setting up r-bioc-zlibbioc (1.32.0+dfsg-1) ...
Setting up r-bioc-s4vectors (0.24.0-1) ...
Setting up r-cran-futile.logger (1.4.3-3) ...
Setting up r-bioc-iranges (2.20.0-1) ...
Setting up r-cran-rcurl (1.95-4.12-1) ...
Setting up r-bioc-biocparallel (1.20.0-1) ...
Setting up r-bioc-rhtslib (1.18.0+dfsg-1) ...
Setting up r-bioc-genomeinfodb (1.22.0-1) ...
Setting up r-bioc-xvector (0.26.0-1) ...
Setting up r-bioc-genomicranges (1.38.0+dfsg-1) ...
Setting up r-bioc-biostrings (2.54.0-1) ...
Setting up r-bioc-rsamtools (2.2.1-1) ...
Setting up dh-autoreconf (19) ...
Setting up dh-strip-nondeterminism (1.6.1-1) ...
Setting up debhelper (12.7.1) ...
Setting up dh-r (20190917) ...
Setting up sbuild-build-depends-r-bioc-bitseq-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-2+rpi1) ...
Processing triggers for ca-certificates (20190110) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.33.1-2+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-17+rpi1 gcc-9_9.2.1-17+rpi1 libc6-dev_2.29-2+rpi1 libstdc++-9-dev_9.2.1-17+rpi1 libstdc++6_9.2.1-17+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.46 bash_5.0-5 binutils_2.33.1-2+rpi1 binutils-arm-linux-gnueabihf_2.33.1-2+rpi1 binutils-common_2.33.1-2+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 ca-certificates_20190110 coreutils_8.30-3 cpp_4:9.2.1-3+rpi1 cpp-9_9.2.1-17+rpi1 dash_0.5.10.2-6 dctrl-tools_2.24-3 debconf_1.5.73 debhelper_12.7.1 debianutils_4.9 dh-autoreconf_19 dh-r_20190917 dh-strip-nondeterminism_1.6.1-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-2 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 fontconfig_2.13.1-2 fontconfig-config_2.13.1-2 fonts-dejavu-core_2.37-1 g++_4:9.2.1-3+rpi1 g++-9_9.2.1-17+rpi1 gcc_4:9.2.1-3+rpi1 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1+b3 gcc-9_9.2.1-17+rpi1 gcc-9-base_9.2.1-17+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gfortran_4:9.2.1-3+rpi1 gfortran-9_9.2.1-17+rpi1 gnupg_2.2.17-3 gnupg-l10n_2.2.17-3 gnupg-utils_2.2.17-3+b1 gpg_2.2.17-3+b1 gpg-agent_2.2.17-3+b1 gpg-wks-client_2.2.17-3+b1 gpg-wks-server_2.2.17-3+b1 gpgconf_2.2.17-3+b1 gpgsm_2.2.17-3+b1 gpgv_2.2.17-3+b1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.23 icu-devtools_63.2-2 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-17+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-17+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2 libbinutils_2.33.1-2+rpi1 libblas-dev_3.8.0-8 libblas3_3.8.0-8 libblkid1_2.34-0.1 libboost-dev_1.67.0.2+b3 libboost1.67-dev_1.67.0-13 libbrotli1_1.0.7-5 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libbz2-dev_1.0.8-2 libc-bin_2.29-2+rpi1 libc-dev-bin_2.29-2+rpi1 libc6_2.29-2+rpi1 libc6-dev_2.29-2+rpi1 libcairo2_1.16.0-4 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-17+rpi1 libcom-err2_1.45.4-1 libcroco3_0.6.13-1 libcurl4_7.66.0-1+b1 libcurl4-openssl-dev_7.66.0-1+b1 libdatrie1_0.2.12-3+b1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.1-1 libfile-which-perl_1.23-1 libfontconfig1_2.13.1-2 libfreetype6_2.10.1-2 libfribidi0_1.0.7-1.1 libgcc-9-dev_9.2.1-17+rpi1 libgcc1_1:9.2.1-17+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran-9-dev_9.2.1-17+rpi1 libgfortran5_9.2.1-17+rpi1 libglib2.0-0_2.62.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.10-4 libgomp1_9.2.1-17+rpi1 libgpg-error0_1.36-7 libgraphite2-3_1.3.13-11 libgssapi-krb5-2_1.17-6+b1 libharfbuzz0b_2.6.4-1+rpi1 libhogweed5_3.5.1+really3.5.1-2 libice6_2:1.0.9-2 libicu-dev_63.2-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl19_0.20-2 libisl21_0.21-2 libjbig0_2.1-3.1+b2 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libk5crypto3_1.17-6+b1 libkeyutils1_1.6-6 libkrb5-3_1.17-6+b1 libkrb5support0_1.17-6+b1 libksba8_1.3.5-2 liblapack-dev_3.8.0-8 liblapack3_3.8.0-8 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.2-1 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncurses-dev_6.1+20191019-1 libncurses5-dev_6.1+20191019-1 libncurses6_6.1+20191019-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.39.2-1 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpango-1.0-0_1.42.4-7+b1 libpangocairo-1.0-0_1.42.4-7+b1 libpangoft2-1.0-0_1.42.4-7+b1 libpaper-utils_1.1.28 libpaper1_1.1.28 libpcre16-3_2:8.39-12 libpcre2-16-0_10.32-5 libpcre2-32-0_10.32-5 libpcre2-8-0_10.32-5 libpcre2-dev_10.32-5 libpcre2-posix0_10.32-5 libpcre3_2:8.39-12 libpcre3-dev_2:8.39-12 libpcre32-3_2:8.39-12 libpcrecpp0v5_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.1-2 libpixman-1-0_0.36.0-1 libpng-dev_1.6.37-1 libpng16-16_1.6.37-1 libpsl5_0.20.2-2 libreadline-dev_8.0-3 libreadline7_7.0-5 libreadline8_8.0-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.4.1-2+rpi1 libselinux1_2.9-2 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsm6_2:1.2.3-1 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1-1 libss2_1.45.4-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-17+rpi1 libstdc++6_9.2.1-17+rpi1 libsub-override-perl_0.09-2 libswitch-perl_2.17-2 libsystemd0_242-7+rpi1 libtasn1-6_4.14-3 libtcl8.6_8.6.9+dfsg-2 libthai-data_0.1.28-3 libthai0_0.1.28-3 libtiff5_4.1.0-1 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtk8.6_8.6.9-2 libtool_2.4.6-11 libubsan1_9.2.1-17+rpi1 libuchardet0_0.0.6-3 libudev1_242-7+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libwebp6_0.6.1-2 libx11-6_2:1.6.8-1 libx11-data_2:1.6.8-1 libxau6_1:1.0.8-1+b2 libxcb-render0_1.13.1-2 libxcb-shm0_1.13.1-2 libxcb1_1.13.1-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxft2_2.3.2-2 libxml2_2.9.4+dfsg1-7+b2 libxmuu1_2:1.1.2-2+b3 libxrender1_1:0.9.10-1 libxss1_1:1.2.3-1 libxt6_1:1.1.5-1+b3 libzstd1_1.4.3+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-1 mawk_1.3.3-17 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_5.6 openssl_1.1.1d-2 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 pkg-config_0.29-6 po-debconf_1.0.21 r-base-core_3.6.1-7 r-base-dev_3.6.1-7 r-bioc-biocgenerics_0.32.0-1 r-bioc-biocparallel_1.20.0-1 r-bioc-biostrings_2.54.0-1 r-bioc-genomeinfodb_1.22.0-1 r-bioc-genomeinfodbdata_1.2.2-1 r-bioc-genomicranges_1.38.0+dfsg-1 r-bioc-iranges_2.20.0-1 r-bioc-rhtslib_1.18.0+dfsg-1 r-bioc-rsamtools_2.2.1-1 r-bioc-s4vectors_0.24.0-1 r-bioc-xvector_0.26.0-1 r-bioc-zlibbioc_1.32.0+dfsg-1 r-cran-bitops_1.0-6-4 r-cran-formatr_1.7-1 r-cran-futile.logger_1.4.3-3 r-cran-futile.options_1.0.1-2 r-cran-lambda.r_1.2.4-1 r-cran-rcurl_1.95-4.12-1 r-cran-snow_1:0.4.3-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-bitseq-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.96-1 tar_1.30+dfsg-6 tzdata_2019c-3 ucf_3.0038+nmu1 unzip_6.0-25 util-linux_2.34-0.1 x11-common_1:7.7+20 xauth_1:1.0.10-1 xdg-utils_1.1.3-1 xz-utils_5.2.4-1 zip_3.0-11 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Nov 11 22:51:23 2019 UTC
gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54
gpgv: issuer "daissi@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./r-bioc-bitseq_1.30.0+dfsg-1.dsc
dpkg-source: info: extracting r-bioc-bitseq in /<<BUILDDIR>>/r-bioc-bitseq-1.30.0+dfsg
dpkg-source: info: unpacking r-bioc-bitseq_1.30.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking r-bioc-bitseq_1.30.0+dfsg-1.debian.tar.xz
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-1a6f2ea4-47dd-4bff-be28-bce5c0740610
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package r-bioc-bitseq
dpkg-buildpackage: info: source version 1.30.0+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --buildsystem R
dh_auto_clean -O--buildsystem=R
dh_autoreconf_clean -O--buildsystem=R
dh_clean -O--buildsystem=R
debian/rules build-arch
dh build-arch --buildsystem R
dh_update_autotools_config -a -O--buildsystem=R
dh_autoreconf -a -O--buildsystem=R
dh_auto_configure -a -O--buildsystem=R
dh_auto_build -a -O--buildsystem=R
dh_auto_test -a -O--buildsystem=R
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --buildsystem R
dh_testroot -a -O--buildsystem=R
dh_prep -a -O--buildsystem=R
dh_auto_install -a -O--buildsystem=R
I: R Package: BitSeq Version: 1.30.0
I: Building using R version 3.6.1-7
I: R API version: r-api-3.5
I: Using built-time from d/changelog: Mon, 11 Nov 2019 23:41:37 +0100
mkdir -p /<<BUILDDIR>>/r-bioc-bitseq-1.30.0\+dfsg/debian/r-bioc-bitseq/usr/lib/R/site-library
R CMD INSTALL -l /<<BUILDDIR>>/r-bioc-bitseq-1.30.0\+dfsg/debian/r-bioc-bitseq/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 11 Nov 2019 23:41:37 +0100'"
* installing *source* package 'BitSeq' ...
** using staged installation
configure: Version def: -DBS_VERSION=\"1.30.0\"
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 we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking for g++ -std=gnu++11 option to support OpenMP... -fopenmp
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/Makevars.win
** libs
make[1]: Entering directory '/<<BUILDDIR>>/r-bioc-bitseq-1.30.0+dfsg/src'
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++/9/vector:72,
from ArgumentParser.h:6,
from ArgumentParser.cpp:5:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CollapsedSampler.cpp -o CollapsedSampler.o
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c FileHeader.cpp -o FileHeader.o
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c GibbsParameters.cpp -o GibbsParameters.o
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c GibbsSampler.cpp -o GibbsSampler.o
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MyTimer.cpp -o MyTimer.o
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PosteriorSamples.cpp -o PosteriorSamples.o
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++/9/vector:72,
from ReadDistribution.h:4,
from ReadDistribution.cpp:7:
/usr/include/c++/9/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++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from ReadDistribution.h:4,
from ReadDistribution.cpp:7:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void ReadDistribution::updateMismatchFreq(bam1_t*)':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:60,
from ReadDistribution.h:5,
from ReadDistribution.cpp:7:
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const 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++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from ReadDistribution.h:5,
from ReadDistribution.cpp:7:
/usr/include/c++/9/bits/stl_map.h: In member function 'double ReadDistribution::getWeightNorm(long int, ns_rD::readT, long int)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In member function 'bool ReadDistribution::observed(ns_rD::fragmentP)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long int, std::pair<const long int, double>, std::_Select1st<std::pair<const long int, double> >, std::less<long int>, std::allocator<std::pair<const long int, double> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:67,
from ReadDistribution.h:4,
from ReadDistribution.cpp:7:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'ReadDistribution::ReadDistribution()':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++/9/vector:72,
from Sampler.h:4,
from Sampler.cpp:5:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from Sampler.h:4,
from Sampler.cpp:5:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void Sampler::appendFile()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SimpleSparse.cpp -o SimpleSparse.o
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++/9/vector:72,
from TagAlignments.h:5,
from TagAlignments.cpp:3:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from TagAlignments.h:5,
from TagAlignments.cpp:3:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void TagAlignments::pushAlignmentL(long int, double)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++/9/algorithm:62,
from TranscriptExpression.cpp:1:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from TranscriptExpression.cpp:1:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >; _Distance = int; _Tp = trExpInfoT; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from TranscriptExpression.cpp:1:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In member function 'void TranscriptExpression::doSort(bool)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trExpInfoT*, std::vector<trExpInfoT> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++/9/vector:72,
from TranscriptInfo.h:4,
from TranscriptInfo.cpp:4:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const transcriptT&}; _Tp = transcriptT; _Alloc = std::allocator<transcriptT>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<transcriptT>::iterator' {aka '__gnu_cxx::__normal_iterator<transcriptT*, std::vector<transcriptT> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from TranscriptInfo.h:4,
from TranscriptInfo.cpp:4:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<transcriptT*, std::vector<transcriptT> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'bool TranscriptInfo::readInfo(std::string)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<transcriptT*, std::vector<transcriptT> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++/9/vector:72,
from TranscriptSequence.h:6,
from TranscriptSequence.cpp:6:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const trSeqInfoT&}; _Tp = trSeqInfoT; _Alloc = std::allocator<trSeqInfoT>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<trSeqInfoT>::iterator' {aka '__gnu_cxx::__normal_iterator<trSeqInfoT*, std::vector<trSeqInfoT> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from TranscriptSequence.h:6,
from TranscriptSequence.cpp:6:
/usr/include/c++/9/bits/stl_vector.h: In member function 'bool TranscriptSequence::readSequence(std::string, refFormatT)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<trSeqInfoT*, std::vector<trSeqInfoT> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++/9/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++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<boost::random::gamma_distribution<double>::param_type>::iterator' {aka '__gnu_cxx::__normal_iterator<boost::random::gamma_distribution<double>::param_type*, std::vector<boost::random::gamma_distribution<double>::param_type> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void VariationalBayes::generateSamples(long int, const string&, const std::vector<double>*, std::ofstream*)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<boost::random::gamma_distribution<double>::param_type*, std::vector<boost::random::gamma_distribution<double>::param_type> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
gcc -std=gnu99 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bam_plbuf.c -o bam_plbuf.o
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c common.cpp -o common.o
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++/9/algorithm:62,
from estimateExpression.cpp:1:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from estimateExpression.cpp:1:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from estimateExpression.cpp:1:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void MCMC(TagAlignments*, gibbsParameters&, ArgumentParser&)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++/9/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++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<ns_params::paramT>::iterator' {aka '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from estimateHyperPar.cpp:6:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from estimateHyperPar.cpp:6:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Distance = int; _Tp = ns_params::paramT; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from estimateHyperPar.cpp:6:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/stl_vector.h: In function 'int estimateHyperPar(int*, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from estimateHyperPar.cpp:6:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1428 | { return _M_erase(begin() + (__position - cbegin())); }
| ^
/usr/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1428 | { return _M_erase(begin() + (__position - cbegin())); }
| ^
/usr/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1428 | { return _M_erase(begin() + (__position - cbegin())); }
| ^
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++/9/algorithm:62,
from lowess.cpp:17:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from lowess.cpp:17:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from lowess.cpp:17:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++/9/vector:72,
from ArgumentParser.h:6,
from misc.h:6,
from misc.cpp:5:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ns_params::paramT&}; _Tp = ns_params::paramT; _Alloc = std::allocator<ns_params::paramT>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<ns_params::paramT>::iterator' {aka '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from misc.cpp:1:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: 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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from misc.cpp:1:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from misc.cpp:1:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void ns_misc::computeCI(double, std::vector<double>*, double*, double*)':
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from misc.cpp:1:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >; _Distance = int; _Tp = ns_params::paramT; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from misc.cpp:1:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from ArgumentParser.h:6,
from misc.h:6,
from misc.cpp:5:
/usr/include/c++/9/bits/stl_vector.h: In function 'bool ns_params::readParams(const string&, std::vector<ns_params::paramT>*, std::ofstream*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from misc.cpp:1:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_params::paramT*, std::vector<ns_params::paramT> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -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++/9/vector:72,
from ArgumentParser.h:6,
from parseAlignment.cpp:7:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {ns_parseAlignment::TagAlignment}; _Tp = ns_parseAlignment::TagAlignment; _Alloc = std::allocator<ns_parseAlignment::TagAlignment>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<ns_parseAlignment::TagAlignment>::iterator' {aka '__gnu_cxx::__normal_iterator<ns_parseAlignment::TagAlignment*, std::vector<ns_parseAlignment::TagAlignment> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'int parseAlignment(int*, char**)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ns_parseAlignment::TagAlignment*, std::vector<ns_parseAlignment::TagAlignment> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
gcc -std=gnu99 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sam.c -o sam.o
g++ -std=gnu++11 -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=\"1.30.0\" -DSUPPORT_OPENMP=1 -DBIOC_BUILD=1 -I"/usr/lib/R/site-library/Rhtslib/include" -I. -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jEdEmw/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c transposeFiles.cpp -o transposeFiles.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-z,relro -o BitSeq.so ArgumentParser.o CollapsedSampler.o FileHeader.o GibbsParameters.o GibbsSampler.o MyTimer.o PosteriorSamples.o R_init_BitSeq.o ReadDistribution.o Sampler.o SimpleSparse.o TagAlignments.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o VariationalBayes.o bam_plbuf.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o estimateVBExpression.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o misc.o parseAlignment.o sam.o transposeFiles.o /usr/lib/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -fopenmp -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/<<BUILDDIR>>/r-bioc-bitseq-1.30.0+dfsg/src'
make[1]: Entering directory '/<<BUILDDIR>>/r-bioc-bitseq-1.30.0+dfsg/src'
make[1]: Leaving directory '/<<BUILDDIR>>/r-bioc-bitseq-1.30.0+dfsg/src'
installing to /<<BUILDDIR>>/r-bioc-bitseq-1.30.0+dfsg/debian/r-bioc-bitseq/usr/lib/R/site-library/00LOCK-r-bioc-bitseq-1.30.0+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-1.30.0\+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 292.
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 293.
Use of uninitialized value $dep_line in split at /usr/share/perl5/Dpkg/Deps.pm line 296.
I: Using r-bioc-rsamtools for Depends:Rsamtools (>= 1.99.3)
I: Using r-bioc-edger for Suggests:edgeR
W: Cannot find a debian package for Suggests:DESeq
W: Cannot find a debian package for Suggests:BiocStyle
I: Using r-bioc-s4vectors for Imports:S4Vectors
I: Using r-bioc-iranges for Imports:IRanges
I: BioConductor API version: r-api-bioc-3.10
dh_installdocs -a -O--buildsystem=R
dh_installchangelogs -a -O--buildsystem=R
dh_installinit -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_1.30.0+dfsg-1_armhf.deb'.
dpkg-deb: building package 'r-bioc-bitseq-dbgsym' in '../r-bioc-bitseq-dbgsym_1.30.0+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-bioc-bitseq_1.30.0+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 2019-11-18T11:27:02Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
r-bioc-bitseq_1.30.0+dfsg-1_armhf.changes:
------------------------------------------
Format: 1.8
Date: Mon, 11 Nov 2019 23:41:37 +0100
Source: r-bioc-bitseq
Binary: r-bioc-bitseq r-bioc-bitseq-dbgsym
Architecture: armhf
Version: 1.30.0+dfsg-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Dylan Aïssi <daissi@debian.org>
Description:
r-bioc-bitseq - transcript expression inference and analysis for RNA-seq data
Changes:
r-bioc-bitseq (1.30.0+dfsg-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
* Fixed debian/watch for BioConductor
* debhelper-compat 12
* Standards-Version: 4.4.1
* Add libcurl4-openssl-dev to Build-Depends
Checksums-Sha1:
c8e44a54024344e61b7f580c98ea899ec1be587b 2997316 r-bioc-bitseq-dbgsym_1.30.0+dfsg-1_armhf.deb
5f5a882166352cfaa5e8c55e7f74df1f112b8c67 8434 r-bioc-bitseq_1.30.0+dfsg-1_armhf.buildinfo
cbf972d80304c712f067ff884a90c2d3442aeddb 1078696 r-bioc-bitseq_1.30.0+dfsg-1_armhf.deb
Checksums-Sha256:
9126d9e7ad783b316876f0e9d5806abe9e11dcd2c24d2dbcdd77180465ca001c 2997316 r-bioc-bitseq-dbgsym_1.30.0+dfsg-1_armhf.deb
5604ba5cad93a2d55faae557f7c1c0a340123aab610c46623ef7108b4d16d8be 8434 r-bioc-bitseq_1.30.0+dfsg-1_armhf.buildinfo
5f2c29ccd81dc41d292891200950a2a2c2df097eb0febc9a14921a06bca5610e 1078696 r-bioc-bitseq_1.30.0+dfsg-1_armhf.deb
Files:
ee36d40c58cd32d83cb55624d04c108d 2997316 debug optional r-bioc-bitseq-dbgsym_1.30.0+dfsg-1_armhf.deb
3e7f5d8f311642222678cfbe092f974a 8434 gnu-r optional r-bioc-bitseq_1.30.0+dfsg-1_armhf.buildinfo
d013543f893af8f57b7602f7be8ff3d4 1078696 gnu-r optional r-bioc-bitseq_1.30.0+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
r-bioc-bitseq-dbgsym_1.30.0+dfsg-1_armhf.deb
--------------------------------------------
new Debian package, version 2.0.
size 2997316 bytes: control archive=540 bytes.
401 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: r-bioc-bitseq-dbgsym
Source: r-bioc-bitseq
Version: 1.30.0+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 3051
Depends: r-bioc-bitseq (= 1.30.0+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for r-bioc-bitseq
Build-Ids: 7236ff39e1ba59d01feec83a324d522e017d8f79
drwxr-xr-x root/root 0 2019-11-11 22:41 ./
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/lib/
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/lib/debug/.build-id/72/
-rw-r--r-- root/root 3113904 2019-11-11 22:41 ./usr/lib/debug/.build-id/72/36ff39e1ba59d01feec83a324d522e017d8f79.debug
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/share/
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-11-11 22:41 ./usr/share/doc/r-bioc-bitseq-dbgsym -> r-bioc-bitseq
r-bioc-bitseq_1.30.0+dfsg-1_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 1078696 bytes: control archive=1904 bytes.
1213 bytes, 22 lines control
2861 bytes, 36 lines md5sums
Package: r-bioc-bitseq
Version: 1.30.0+dfsg-1
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 5836
Depends: r-base-core (>= 3.6.1-7), r-api-3.5, r-api-bioc-3.10, r-bioc-rsamtools (>= 1.99.3), r-bioc-s4vectors, r-bioc-iranges, libc6 (>= 2.29), libcurl4 (>= 7.18.0), libgcc1 (>= 1:3.5), libgomp1 (>= 6), libstdc++6 (>= 5.2)
Suggests: r-bioc-edger
Section: gnu-r
Priority: optional
Homepage: https://bioconductor.org/packages/BitSeq/
Description: transcript expression inference and analysis for RNA-seq data
The BitSeq package is targeted for transcript expression
analysis and differential expression analysis of RNA-seq data
in two stage process. In the first stage it uses Bayesian
inference methodology to infer expression of individual
transcripts from individual RNA-seq experiments. The second
stage of BitSeq embraces the differential expression analysis
of transcript expression. Providing expression estimates from
replicates of multiple conditions, Log-Normal model of the
estimates is used for inferring the condition mean transcript
expression and ranking the transcripts based on the likelihood
of differential expression.
drwxr-xr-x root/root 0 2019-11-11 22:41 ./
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/lib/
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/lib/R/
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/lib/R/site-library/
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/
-rw-r--r-- root/root 697 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/CITATION
-rw-r--r-- root/root 1738 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/DESCRIPTION
-rw-r--r-- root/root 1159 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/INDEX
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/Meta/
-rw-r--r-- root/root 864 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/Meta/Rd.rds
-rw-r--r-- root/root 132 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/Meta/features.rds
-rw-r--r-- root/root 918 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/Meta/hsearch.rds
-rw-r--r-- root/root 394 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/Meta/links.rds
-rw-r--r-- root/root 384 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/Meta/nsInfo.rds
-rw-r--r-- root/root 1331 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/Meta/package.rds
-rw-r--r-- root/root 240 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/Meta/vignette.rds
-rw-r--r-- root/root 383 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/NAMESPACE
-rw-r--r-- root/root 4127 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/NEWS
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/R/
-rw-r--r-- root/root 1056 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/R/BitSeq
-rw-r--r-- root/root 41263 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/R/BitSeq.rdb
-rw-r--r-- root/root 646 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/R/BitSeq.rdx
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/doc/
-rw-r--r-- root/root 6584 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/doc/BitSeq.R
-rw-r--r-- root/root 17960 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/doc/BitSeq.Rnw
-rw-r--r-- root/root 216087 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/doc/BitSeq.pdf
-rw-r--r-- root/root 1316 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/doc/index.html
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/extdata/
-rw-r--r-- root/root 4070127 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/extdata/data-c0b0.sam
-rw-r--r-- root/root 176210 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/extdata/data-c0b1.rpkm
-rw-r--r-- root/root 176210 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/extdata/data-c1b0.rpkm
-rw-r--r-- root/root 176210 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/extdata/data-c1b1.rpkm
-rw-r--r-- root/root 87197 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/extdata/ensSelect1.fasta
-rw-r--r-- root/root 2009 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/extdata/ensSelect1.tr
-rw-r--r-- root/root 636 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/extdata/parameters1.txt
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/help/
-rw-r--r-- root/root 655 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/help/AnIndex
-rw-r--r-- root/root 42559 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/help/BitSeq.rdb
-rw-r--r-- root/root 483 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/help/BitSeq.rdx
-rw-r--r-- root/root 308 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/help/aliases.rds
-rw-r--r-- root/root 290 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/help/paths.rds
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/html/
-rw-r--r-- root/root 4296 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/html/00Index.html
-rw-r--r-- root/root 1335 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/html/R.css
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/libs/
-rw-r--r-- root/root 890332 2019-11-11 22:41 ./usr/lib/R/site-library/BitSeq/libs/BitSeq.so
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/share/
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-11-11 22:41 ./usr/share/doc/r-bioc-bitseq/
-rw-r--r-- root/root 424 2019-11-11 22:41 ./usr/share/doc/r-bioc-bitseq/changelog.Debian.gz
-rw-r--r-- root/root 10115 2019-11-11 22:41 ./usr/share/doc/r-bioc-bitseq/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 18604
Build-Time: 755
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 1070
Job: r-bioc-bitseq_1.30.0+dfsg-1
Machine Architecture: armhf
Package: r-bioc-bitseq
Package-Time: 1880
Source-Version: 1.30.0+dfsg-1
Space: 18604
Status: successful
Version: 1.30.0+dfsg-1
--------------------------------------------------------------------------------
Finished at 2019-11-18T11:27:02Z
Build needed 00:31:20, 18604k disc space