r-bioc-affyio →
1.44.0-1 →
armhf → 2016-11-01 12:55:32
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| r-bioc-affyio 1.44.0-1 (armhf) Tue, 01 Nov 2016 12:44:30 +0000 |
+==============================================================================+
Package: r-bioc-affyio
Version: 1.44.0-1
Source Version: 1.44.0-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-f2293e68-6363-45cc-8ef6-e436225f0711' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9422 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.4 MB]
Fetched 20.8 MB in 29s (713 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'r-bioc-affyio' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-affyio/trunk/
Need to get 110 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main r-bioc-affyio 1.44.0-1 (dsc) [2044 B]
Get:2 http://172.17.0.1/private stretch-staging/main r-bioc-affyio 1.44.0-1 (tar) [106 kB]
Get:3 http://172.17.0.1/private stretch-staging/main r-bioc-affyio 1.44.0-1 (diff) [2004 B]
Fetched 110 kB in 0s (579 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-affyio-acN81c/r-bioc-affyio-1.44.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-affyio-acN81c' 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-SgTJt1/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-SgTJt1/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-SgTJt1/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-SgTJt1/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-SgTJt1/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-SgTJt1/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-SgTJt1/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-SgTJt1/apt_archive ./ Packages [430 B]
Fetched 2078 B in 0s (3092 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
dirmngr fuse2fs gnupg-l10n kbd libffi6 libfuse2 libgnutls30 libhogweed4
libldap-2.4-2 libnettle6 libp11-kit0 libsasl2-2 libsasl2-modules
libsasl2-modules-db libssl1.0.2 libtasn1-6 manpages netbase psmisc
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 5 not upgraded.
Need to get 764 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-SgTJt1/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [764 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 764 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13408 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 9), dh-r, zlib1g-dev, r-base-dev
Filtered Build-Depends: debhelper (>= 9), dh-r, zlib1g-dev, r-base-dev
dpkg-deb: building package 'sbuild-build-depends-r-bioc-affyio-dummy' in '/<<BUILDDIR>>/resolver-SgTJt1/apt_archive/sbuild-build-depends-r-bioc-affyio-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-affyio-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-SgTJt1/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-SgTJt1/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-SgTJt1/apt_archive ./ Release.gpg [342 B]
Get:4 copy:/<<BUILDDIR>>/resolver-SgTJt1/apt_archive ./ Sources [509 B]
Get:5 copy:/<<BUILDDIR>>/resolver-SgTJt1/apt_archive ./ Packages [587 B]
Fetched 2401 B in 0s (3282 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install r-bioc-affyio 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:
dirmngr fuse2fs gnupg-l10n kbd libfuse2 libsasl2-modules manpages netbase
psmisc
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils ca-certificates cdbs
dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism file
fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base gfortran
gfortran-6 groff-base icu-devtools intltool-debian libarchive-zip-perl
libblas-common libblas-dev libblas3 libbsd0 libbz2-dev libcairo2 libcroco3
libcurl3 libdatrie1 libexpat1 libfile-stripnondeterminism-perl
libfontconfig1 libfreetype6 libgfortran-6-dev libgfortran3 libglib2.0-0
libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu-dev libicu57
libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblzma-dev
libmagic-mgc libmagic1 libncurses5-dev libnghttp2-14 libpango-1.0-0
libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3
libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev
libpng16-16 libreadline-dev librtmp1 libsigsegv2 libsm6 libssh2-1 libtcl8.6
libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtk8.6
libtool libunistring0 libx11-6 libx11-data libxau6 libxcb-render0
libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxmuu1 libxrender1
libxss1 libxt6 m4 man-db openssl po-debconf r-base-core r-base-dev ucf unzip
x11-common xauth xdg-utils zip zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation devscripts debtags dh-make gettext-doc libasprintf-dev
libgettextpo-dev gfortran-doc gfortran-6-doc libgfortran3-dbg
libcoarrays-dev groff liblapack-doc-man liblapack-doc krb5-doc krb5-user
icu-doc liblzma-doc ncurses-doc readline-doc tcl8.6 tk8.6 libtool-doc
gcj-jdk less www-browser libmail-box-perl ess r-doc-info | r-doc-pdf
r-mathlib r-base-html texlive-base texlive-latex-base
texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra
texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo
gvfs-bin
Recommended packages:
curl | wget | lynx-cur bzip2-doc libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales libpng-tools libltdl-dev xml-core
libmail-sendmail-perl r-recommended r-doc-html 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 cdbs
dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism file
fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base gfortran
gfortran-6 groff-base icu-devtools intltool-debian libarchive-zip-perl
libblas-common libblas-dev libblas3 libbsd0 libbz2-dev libcairo2 libcroco3
libcurl3 libdatrie1 libexpat1 libfile-stripnondeterminism-perl
libfontconfig1 libfreetype6 libgfortran-6-dev libgfortran3 libglib2.0-0
libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libice6 libicu-dev libicu57
libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblzma-dev
libmagic-mgc libmagic1 libncurses5-dev libnghttp2-14 libpango-1.0-0
libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3
libpcre3-dev libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev
libpng16-16 libreadline-dev librtmp1 libsigsegv2 libsm6 libssh2-1 libtcl8.6
libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtk8.6
libtool libunistring0 libx11-6 libx11-data libxau6 libxcb-render0
libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxmuu1 libxrender1
libxss1 libxt6 m4 man-db openssl po-debconf r-base-core r-base-dev
sbuild-build-depends-r-bioc-affyio-dummy ucf unzip x11-common xauth
xdg-utils zip zlib1g-dev
0 upgraded, 116 newly installed, 0 to remove and 5 not upgraded.
Need to get 78.9 MB of archives.
After this operation, 239 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-SgTJt1/apt_archive ./ sbuild-build-depends-r-bioc-affyio-dummy 0.invalid.0 [786 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-8 [1087 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.12 [178 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.5-1 [975 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libexpat1 armhf 2.2.0-1 [61.7 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libpng16-16 armhf 1.6.25-2 [261 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf libfreetype6 armhf 2.6.3-3+b1 [385 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf ucf all 3.0036 [70.2 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf fontconfig-config all 2.11.0-6.7 [271 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libfontconfig1 armhf 2.11.0-6.7 [313 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf fontconfig armhf 2.11.0-6.7 [402 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf libjbig0 armhf 2.1-3.1 [27.5 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf libpaper1 armhf 1.1.24+nmu4 [21.4 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf libpcrecpp0v5 armhf 2:8.39-2 [149 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libxdmcp6 armhf 1:1.1.2-1.1 [24.9 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf libxcb1 armhf 1.12-1 [129 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libx11-data all 2:1.6.3-1 [128 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libx11-6 armhf 2:1.6.3-1 [678 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf libxext6 armhf 2:1.3.3-1 [48.1 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libxrender1 armhf 1:0.9.9-2 [28.9 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libxft2 armhf 2.3.2-1 [48.3 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf x11-common all 1:7.7+16 [251 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf libxss1 armhf 1:1.2.2-1 [16.8 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.29-1 [219 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.29-1 [104 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.29-1 [63.3 kB]
Get:31 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-1 [117 kB]
Get:32 http://172.17.0.1/private stretch-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:33 http://172.17.0.1/private stretch-staging/main armhf libkrb5support0 armhf 1.14.3+dfsg-2 [57.5 kB]
Get:34 http://172.17.0.1/private stretch-staging/main armhf libk5crypto3 armhf 1.14.3+dfsg-2 [110 kB]
Get:35 http://172.17.0.1/private stretch-staging/main armhf libkrb5-3 armhf 1.14.3+dfsg-2 [262 kB]
Get:36 http://172.17.0.1/private stretch-staging/main armhf libgssapi-krb5-2 armhf 1.14.3+dfsg-2 [131 kB]
Get:37 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-4 [7407 kB]
Get:38 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2 [805 kB]
Get:39 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:40 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.17-5 [239 kB]
Get:41 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:42 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20160430.1 [72.6 kB]
Get:43 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-4 [735 kB]
Get:44 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-1 [433 kB]
Get:45 http://172.17.0.1/private stretch-staging/main armhf openssl armhf 1.0.2j-1 [671 kB]
Get:46 http://172.17.0.1/private stretch-staging/main armhf ca-certificates all 20160104 [200 kB]
Get:47 http://172.17.0.1/private stretch-staging/main armhf cdbs all 0.4.148 [82.3 kB]
Get:48 http://172.17.0.1/private stretch-staging/main armhf dctrl-tools armhf 2.24-2 [94.4 kB]
Get:49 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:50 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 12 [15.8 kB]
Get:51 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:52 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.028-1 [14.6 kB]
Get:53 http://172.17.0.1/private stretch-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:54 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.028-1 [9020 B]
Get:55 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.0-2+rpi1 [2523 kB]
Get:56 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-2 [131 kB]
Get:57 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:58 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-1 [1433 kB]
Get:59 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:60 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:61 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.2 [826 kB]
Get:62 http://172.17.0.1/private stretch-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:63 http://172.17.0.1/private stretch-staging/main armhf unzip armhf 6.0-20 [142 kB]
Get:64 http://172.17.0.1/private stretch-staging/main armhf libpaper-utils armhf 1.1.24+nmu4 [17.2 kB]
Get:65 http://172.17.0.1/private stretch-staging/main armhf xdg-utils all 1.1.1-1 [71.1 kB]
Get:66 http://172.17.0.1/private stretch-staging/main armhf libgfortran3 armhf 6.2.0-6+rpi1 [165 kB]
Get:67 http://172.17.0.1/private stretch-staging/main armhf libblas-common armhf 3.6.1-2 [13.9 kB]
Get:68 http://172.17.0.1/private stretch-staging/main armhf libblas3 armhf 3.6.1-2 [112 kB]
Get:69 http://172.17.0.1/private stretch-staging/main armhf libpixman-1-0 armhf 0.34.0-1 [451 kB]
Get:70 http://172.17.0.1/private stretch-staging/main armhf libxcb-render0 armhf 1.12-1 [104 kB]
Get:71 http://172.17.0.1/private stretch-staging/main armhf libxcb-shm0 armhf 1.12-1 [95.9 kB]
Get:72 http://172.17.0.1/private stretch-staging/main armhf libcairo2 armhf 1.14.6-1+b1 [686 kB]
Get:73 http://172.17.0.1/private stretch-staging/main armhf libnghttp2-14 armhf 1.16.0-1 [72.5 kB]
Get:74 http://172.17.0.1/private stretch-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:75 http://172.17.0.1/private stretch-staging/main armhf libssh2-1 armhf 1.7.0-1 [125 kB]
Get:76 http://172.17.0.1/private stretch-staging/main armhf libcurl3 armhf 7.50.1-1 [251 kB]
Get:77 http://172.17.0.1/private stretch-staging/main armhf libice6 armhf 2:1.0.9-1+b1 [51.9 kB]
Get:78 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo armhf 1:1.5.1-2 [109 kB]
Get:79 http://172.17.0.1/private stretch-staging/main armhf liblapack3 armhf 3.6.1-2 [1392 kB]
Get:80 http://172.17.0.1/private stretch-staging/main armhf libthai-data all 0.1.25-2 [165 kB]
Get:81 http://172.17.0.1/private stretch-staging/main armhf libdatrie1 armhf 0.2.10-4 [32.8 kB]
Get:82 http://172.17.0.1/private stretch-staging/main armhf libthai0 armhf 0.1.25-2 [48.7 kB]
Get:83 http://172.17.0.1/private stretch-staging/main armhf libpango-1.0-0 armhf 1.40.3-2 [300 kB]
Get:84 http://172.17.0.1/private stretch-staging/main armhf libgraphite2-3 armhf 1.3.8-1 [62.5 kB]
Get:85 http://172.17.0.1/private stretch-staging/main armhf libharfbuzz0b armhf 1.2.7-1+b1 [589 kB]
Get:86 http://172.17.0.1/private stretch-staging/main armhf libpangoft2-1.0-0 armhf 1.40.3-2 [196 kB]
Get:87 http://172.17.0.1/private stretch-staging/main armhf libpangocairo-1.0-0 armhf 1.40.3-2 [186 kB]
Get:88 http://172.17.0.1/private stretch-staging/main armhf libsm6 armhf 2:1.2.2-1+b1 [31.2 kB]
Get:89 http://172.17.0.1/private stretch-staging/main armhf libtcl8.6 armhf 8.6.6+dfsg-1 [861 kB]
Get:90 http://172.17.0.1/private stretch-staging/main armhf libtiff5 armhf 4.0.6-2 [203 kB]
Get:91 http://172.17.0.1/private stretch-staging/main armhf libtk8.6 armhf 8.6.6-1 [659 kB]
Get:92 http://172.17.0.1/private stretch-staging/main armhf libxt6 armhf 1:1.1.5-1 [155 kB]
Get:93 http://172.17.0.1/private stretch-staging/main armhf r-base-core armhf 3.3.1.20161024-1 [20.8 MB]
Get:94 http://172.17.0.1/private stretch-staging/main armhf libgfortran-6-dev armhf 6.2.0-6+rpi1 [199 kB]
Get:95 http://172.17.0.1/private stretch-staging/main armhf gfortran-6 armhf 6.2.0-6+rpi1 [5405 kB]
Get:96 http://172.17.0.1/private stretch-staging/main armhf gfortran armhf 4:6.1.1-1 [1370 B]
Get:97 http://172.17.0.1/private stretch-staging/main armhf libblas-dev armhf 3.6.1-2 [18.9 kB]
Get:98 http://172.17.0.1/private stretch-staging/main armhf liblapack-dev armhf 3.6.1-2 [1379 kB]
Get:99 http://172.17.0.1/private stretch-staging/main armhf libtinfo-dev armhf 6.0+20160917-1 [65.4 kB]
Get:100 http://172.17.0.1/private stretch-staging/main armhf libncurses5-dev armhf 6.0+20160917-1 [245 kB]
Get:101 http://172.17.0.1/private stretch-staging/main armhf libreadline-dev armhf 7.0-1 [109 kB]
Get:102 http://172.17.0.1/private stretch-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.1-2 [181 kB]
Get:103 http://172.17.0.1/private stretch-staging/main armhf libjpeg-dev all 1:1.5.1-2 [56.1 kB]
Get:104 http://172.17.0.1/private stretch-staging/main armhf libpcre16-3 armhf 2:8.39-2 [235 kB]
Get:105 http://172.17.0.1/private stretch-staging/main armhf libpcre32-3 armhf 2:8.39-2 [227 kB]
Get:106 http://172.17.0.1/private stretch-staging/main armhf libpcre3-dev armhf 2:8.39-2 [568 kB]
Get:107 http://172.17.0.1/private stretch-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2+b1 [197 kB]
Get:108 http://172.17.0.1/private stretch-staging/main armhf libpng-dev armhf 1.6.25-2 [230 kB]
Get:109 http://172.17.0.1/private stretch-staging/main armhf libbz2-dev armhf 1.0.6-8 [27.8 kB]
Get:110 http://172.17.0.1/private stretch-staging/main armhf liblzma-dev armhf 5.2.2-1.2 [284 kB]
Get:111 http://172.17.0.1/private stretch-staging/main armhf icu-devtools armhf 57.1-4 [156 kB]
Get:112 http://172.17.0.1/private stretch-staging/main armhf libicu-dev armhf 57.1-4 [15.7 MB]
Get:113 http://172.17.0.1/private stretch-staging/main armhf libxmuu1 armhf 2:1.1.2-2 [23.0 kB]
Get:114 http://172.17.0.1/private stretch-staging/main armhf xauth armhf 1:1.0.9-1 [35.6 kB]
Get:115 http://172.17.0.1/private stretch-staging/main armhf r-base-dev all 3.3.1.20161024-1 [4298 B]
Get:116 http://172.17.0.1/private stretch-staging/main armhf dh-r all 20160916 [7378 B]
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Unpacking libpcre32-3:armhf (2:8.39-2) ...
Selecting previously unselected package libpcre3-dev:armhf.
Preparing to unpack .../104-libpcre3-dev_2%3a8.39-2_armhf.deb ...
Unpacking libpcre3-dev:armhf (2:8.39-2) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../105-zlib1g-dev_1%3a1.2.8.dfsg-2+b1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Selecting previously unselected package libpng-dev:armhf.
Preparing to unpack .../106-libpng-dev_1.6.25-2_armhf.deb ...
Unpacking libpng-dev:armhf (1.6.25-2) ...
Selecting previously unselected package libbz2-dev:armhf.
Preparing to unpack .../107-libbz2-dev_1.0.6-8_armhf.deb ...
Unpacking libbz2-dev:armhf (1.0.6-8) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../108-liblzma-dev_5.2.2-1.2_armhf.deb ...
Unpacking liblzma-dev:armhf (5.2.2-1.2) ...
Selecting previously unselected package icu-devtools.
Preparing to unpack .../109-icu-devtools_57.1-4_armhf.deb ...
Unpacking icu-devtools (57.1-4) ...
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Preparing to unpack .../110-libicu-dev_57.1-4_armhf.deb ...
Unpacking libicu-dev (57.1-4) ...
Selecting previously unselected package libxmuu1:armhf.
Preparing to unpack .../111-libxmuu1_2%3a1.1.2-2_armhf.deb ...
Unpacking libxmuu1:armhf (2:1.1.2-2) ...
Selecting previously unselected package xauth.
Preparing to unpack .../112-xauth_1%3a1.0.9-1_armhf.deb ...
Unpacking xauth (1:1.0.9-1) ...
Selecting previously unselected package r-base-dev.
Preparing to unpack .../113-r-base-dev_3.3.1.20161024-1_all.deb ...
Unpacking r-base-dev (3.3.1.20161024-1) ...
Selecting previously unselected package dh-r.
Preparing to unpack .../114-dh-r_20160916_all.deb ...
Unpacking dh-r (20160916) ...
Selecting previously unselected package sbuild-build-depends-r-bioc-affyio-dummy.
Preparing to unpack .../115-sbuild-build-depends-r-bioc-affyio-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-r-bioc-affyio-dummy (0.invalid.0) ...
Setting up cdbs (0.4.148) ...
Setting up libexpat1:armhf (2.2.0-1) ...
Setting up libbz2-dev:armhf (1.0.6-8) ...
Setting up libjpeg62-turbo:armhf (1:1.5.1-2) ...
Setting up libarchive-zip-perl (1.59-1) ...
Setting up libnghttp2-14:armhf (1.16.0-1) ...
Setting up libpng16-16:armhf (1.6.25-2) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libjbig0:armhf (2.1-3.1) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up fonts-dejavu-core (2.37-1) ...
Setting up libblas-common (3.6.1-2) ...
Setting up libgfortran3:armhf (6.2.0-6+rpi1) ...
Setting up groff-base (1.22.3-8) ...
Setting up libglib2.0-0:armhf (2.50.0-2+rpi1) ...
No schema files found: doing nothing.
Setting up libgfortran-6-dev:armhf (6.2.0-6+rpi1) ...
Setting up unzip (6.0-20) ...
Setting up libtinfo-dev:armhf (6.0+20160917-1) ...
Setting up dctrl-tools (2.24-2) ...
Setting up libdatrie1:armhf (0.2.10-4) ...
Setting up libtiff5:armhf (4.0.6-2) ...
Setting up gettext-base (0.19.8.1-1) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up m4 (1.4.17-5) ...
Setting up libicu57:armhf (57.1-4) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up ucf (3.0036) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2) ...
Setting up zip (3.0-11) ...
Setting up libfreetype6:armhf (2.6.3-3+b1) ...
Setting up libmagic-mgc (1:5.29-1) ...
Setting up libmagic1:armhf (1:5.29-1) ...
Setting up libgraphite2-3:armhf (1.3.8-1) ...
Setting up libcroco3:armhf (0.6.11-2) ...
Setting up libncurses5-dev:armhf (6.0+20160917-1) ...
Setting up libpixman-1-0:armhf (0.34.0-1) ...
Setting up libblas3 (3.6.1-2) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libssh2-1:armhf (1.7.0-1) ...
Processing triggers for libc-bin (2.24-5+rpi1) ...
Setting up autotools-dev (20160430.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Processing triggers for systemd (231-9) ...
Setting up openssl (1.0.2j-1) ...
Setting up libreadline-dev:armhf (7.0-1) ...
Setting up libpcrecpp0v5:armhf (2:8.39-2) ...
Setting up libpcre32-3:armhf (2:8.39-2) ...
Setting up icu-devtools (57.1-4) ...
Setting up libpcre16-3:armhf (2:8.39-2) ...
Setting up libtcl8.6:armhf (8.6.6+dfsg-1) ...
Setting up libthai-data (0.1.25-2) ...
Setting up libjpeg62-turbo-dev:armhf (1:1.5.1-2) ...
Setting up liblzma-dev:armhf (5.2.2-1.2) ...
Setting up libxdmcp6:armhf (1:1.1.2-1.1) ...
Setting up libkeyutils1:armhf (1.5.9-9) ...
Setting up bsdmainutils (9.0.12) ...
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 x11-common (1:7.7+16) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
Running in chroot, ignoring request.
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up xdg-utils (1.1.1-1) ...
Setting up ca-certificates (20160104) ...
Setting up libx11-data (2:1.6.3-1) ...
Setting up libxau6:armhf (1:1.0.8-1) ...
Setting up autopoint (0.19.8.1-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2+b1) ...
Setting up libfile-stripnondeterminism-perl (0.028-1) ...
Setting up libpaper1:armhf (1.1.24+nmu4) ...
Creating config file /etc/papersize with new version
Setting up gfortran-6 (6.2.0-6+rpi1) ...
Setting up libpaper-utils (1.1.24+nmu4) ...
Setting up libpcre3-dev:armhf (2:8.39-2) ...
Setting up fontconfig-config (2.11.0-6.7) ...
Setting up gettext (0.19.8.1-1) ...
Setting up liblapack3 (3.6.1-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up libharfbuzz0b:armhf (1.2.7-1+b1) ...
Setting up autoconf (2.69-10) ...
Setting up libthai0:armhf (0.1.25-2) ...
Setting up libicu-dev (57.1-4) ...
Setting up file (1:5.29-1) ...
Setting up libkrb5support0:armhf (1.14.3+dfsg-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libjpeg-dev (1:1.5.1-2) ...
Setting up automake (1:1.15-4) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libice6:armhf (2:1.0.9-1+b1) ...
Setting up man-db (2.7.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpng-dev:armhf (1.6.25-2) ...
Setting up libxcb1:armhf (1.12-1) ...
Setting up libtool (2.4.6-2) ...
Setting up gfortran (4:6.1.1-1) ...
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 libfontconfig1:armhf (2.11.0-6.7) ...
Setting up libsm6:armhf (2:1.2.2-1+b1) ...
Setting up libk5crypto3:armhf (1.14.3+dfsg-2) ...
Setting up libxcb-render0:armhf (1.12-1) ...
Setting up po-debconf (1.0.20) ...
Setting up libblas-dev (3.6.1-2) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
Setting up libx11-6:armhf (2:1.6.3-1) ...
Setting up libxmuu1:armhf (2:1.1.2-2) ...
Setting up libxcb-shm0:armhf (1.12-1) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxrender1:armhf (1:0.9.9-2) ...
Setting up libkrb5-3:armhf (1.14.3+dfsg-2) ...
Setting up libxft2:armhf (2.3.2-1) ...
Setting up fontconfig (2.11.0-6.7) ...
Regenerating fonts cache... done.
Setting up liblapack-dev (3.6.1-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up libxext6:armhf (2:1.3.3-1) ...
Setting up libxss1:armhf (1:1.2.2-1) ...
Setting up libgssapi-krb5-2:armhf (1.14.3+dfsg-2) ...
Setting up xauth (1:1.0.9-1) ...
Setting up libpango-1.0-0:armhf (1.40.3-2) ...
Setting up libcairo2:armhf (1.14.6-1+b1) ...
Setting up libcurl3:armhf (7.50.1-1) ...
Setting up libtk8.6:armhf (8.6.6-1) ...
Setting up libpangoft2-1.0-0:armhf (1.40.3-2) ...
Setting up libpangocairo-1.0-0:armhf (1.40.3-2) ...
Setting up r-base-core (3.3.1.20161024-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-base-dev (3.3.1.20161024-1) ...
Setting up dh-autoreconf (12) ...
Setting up dh-strip-nondeterminism (0.028-1) ...
Setting up debhelper (10.2.2) ...
Setting up dh-r (20160916) ...
Setting up sbuild-build-depends-r-bioc-affyio-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-5+rpi1) ...
Processing triggers for systemd (231-9) ...
Processing triggers for ca-certificates (20160104) ...
Updating certificates in /etc/ssl/certs...
173 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.5.0-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.27-9 dpkg-dev_1.18.10 g++-6_6.2.0-6+rpi1 gcc-6_6.2.0-6+rpi1 libc6-dev_2.24-5+rpi1 libstdc++-6-dev_6.2.0-6+rpi1 libstdc++6_6.2.0-6+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.3.1 autoconf_2.69-10 automake_1:1.15-4 autopoint_0.19.8.1-1 autotools-dev_20160430.1 base-files_9.6+rpi1 base-passwd_3.5.40 bash_4.4-1 binutils_2.27-9 bsdmainutils_9.0.12 bsdutils_1:2.28.2-1 build-essential_12.2 bzip2_1.0.6-8 ca-certificates_20160104 cdbs_0.4.148 coreutils_8.25-2 cpio_2.11+dfsg-5 cpp_4:6.1.1-1 cpp-6_6.2.0-6+rpi1 dash_0.5.8-2.3 dctrl-tools_2.24-2 debconf_1.5.59 debfoster_2.7-2.1 debhelper_10.2.2 debianutils_4.8 dh-autoreconf_12 dh-r_20160916 dh-strip-nondeterminism_0.028-1 diffutils_1:3.5-1 dirmngr_2.1.15-4 dmsetup_2:1.02.133-1 dpkg_1.18.10 dpkg-dev_1.18.10 e2fslibs_1.43.3-1 e2fsprogs_1.43.3-1 fakeroot_1.21-2 file_1:5.29-1 findutils_4.6.0+git+20160703-2 fontconfig_2.11.0-6.7 fontconfig-config_2.11.0-6.7 fonts-dejavu-core_2.37-1 fuse2fs_1.43.3-1 g++_4:6.1.1-1 g++-6_6.2.0-6+rpi1 gcc_4:6.1.1-1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.3-14 gcc-6_6.2.0-6+rpi1 gcc-6-base_6.2.0-6+rpi1 gettext_0.19.8.1-1 gettext-base_0.19.8.1-1 gfortran_4:6.1.1-1 gfortran-6_6.2.0-6+rpi1 gnupg_2.1.15-4 gnupg-agent_2.1.15-4 gnupg-l10n_2.1.15-4 gpgv_2.1.15-4 grep_2.26-1 groff-base_1.22.3-8 gzip_1.6-5 hostname_3.18 icu-devtools_57.1-4 init_1.45 init-system-helpers_1.45 initscripts_2.88dsf-59.8 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 kbd_2.0.3-2 klibc-utils_2.0.4-9+rpi1 kmod_22-1.1 libacl1_2.2.52-3 libapparmor1_2.10.95-5 libapt-pkg5.0_1.3.1 libarchive-zip-perl_1.59-1 libasan3_6.2.0-6+rpi1 libassuan0_2.4.3-1 libatomic1_6.2.0-6+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-1 libaudit1_1:2.6.7-1 libblas-common_3.6.1-2 libblas-dev_3.6.1-2 libblas3_3.6.1-2 libblkid1_2.28.2-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8 libbz2-dev_1.0.6-8 libc-bin_2.24-5+rpi1 libc-dev-bin_2.24-5+rpi1 libc6_2.24-5+rpi1 libc6-dev_2.24-5+rpi1 libcairo2_1.14.6-1+b1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.2.0-6+rpi1 libcomerr2_1.43.3-1 libcroco3_0.6.11-2 libcryptsetup4_2:1.7.2-5 libcurl3_7.50.1-1 libdatrie1_0.2.10-4 libdb5.3_5.3.28-12 libdbus-1-3_1.10.12-1 libdebconfclient0_0.218 libdevmapper1.02.1_2:1.02.133-1 libdpkg-perl_1.18.10 libdrm2_2.4.71-1 libexpat1_2.2.0-1 libfakeroot_1.21-2 libfdisk1_2.28.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.028-1 libfontconfig1_2.11.0-6.7 libfreetype6_2.6.3-3+b1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-6-dev_6.2.0-6+rpi1 libgcc1_1:6.2.0-6+rpi1 libgcrypt20_1.7.3-2 libgdbm3_1.8.3-14 libgfortran-6-dev_6.2.0-6+rpi1 libgfortran3_6.2.0-6+rpi1 libglib2.0-0_2.50.0-2+rpi1 libgmp10_2:6.1.1+dfsg-1 libgnutls30_3.5.5-2 libgomp1_6.2.0-6+rpi1 libgpg-error0_1.24-1 libgraphite2-3_1.3.8-1 libgssapi-krb5-2_1.14.3+dfsg-2 libharfbuzz0b_1.2.7-1+b1 libhogweed4_3.3-1 libice6_2:1.0.9-1+b1 libicu-dev_57.1-4 libicu57_57.1-4 libidn11_1.33-1 libip4tc0_1.6.0-4 libisl15_0.17.1-1 libjbig0_2.1-3.1 libjpeg-dev_1:1.5.1-2 libjpeg62-turbo_1:1.5.1-2 libjpeg62-turbo-dev_1:1.5.1-2 libk5crypto3_1.14.3+dfsg-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libkmod2_22-1.1 libkrb5-3_1.14.3+dfsg-2 libkrb5support0_1.14.3+dfsg-2 libksba8_1.3.5-2 liblapack-dev_3.6.1-2 liblapack3_3.6.1-2 libldap-2.4-2_2.4.42+dfsg-2+rpi1+b3 liblz4-1_0.0~r131-2 liblzma-dev_5.2.2-1.2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.29-1 libmagic1_1:5.29-1 libmount1_2.28.2-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20160917-1 libncurses5-dev_6.0+20160917-1 libncursesw5_6.0+20160917-1 libnettle6_3.3-1 libnghttp2-14_1.16.0-1 libnpth0_1.2-3 libp11-kit0_0.23.2-5 libpam-modules_1.1.8-3.3 libpam-modules-bin_1.1.8-3.3 libpam-runtime_1.1.8-3.3 libpam0g_1.1.8-3.3 libpango-1.0-0_1.40.3-2 libpangocairo-1.0-0_1.40.3-2 libpangoft2-1.0-0_1.40.3-2 libpaper-utils_1.1.24+nmu4 libpaper1_1.1.24+nmu4 libpcre16-3_2:8.39-2 libpcre3_2:8.39-2 libpcre3-dev_2:8.39-2 libpcre32-3_2:8.39-2 libpcrecpp0v5_2:8.39-2 libperl5.24_5.24.1~rc3-3 libpipeline1_1.4.1-2 libpixman-1-0_0.34.0-1 libplymouth4_0.9.2-3 libpng-dev_1.6.25-2 libpng12-0_1.2.54-6 libpng16-16_1.6.25-2 libprocps6_2:3.3.12-2 libreadline-dev_7.0-1 libreadline7_7.0-1 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.26.dfsg1-15 libsasl2-modules_2.1.26.dfsg1-15 libsasl2-modules-db_2.1.26.dfsg1-15 libseccomp2_2.3.1-2 libselinux1_2.5-3 libsemanage-common_2.5-1 libsemanage1_2.5-1 libsepol1_2.5-1 libsigsegv2_2.10-5 libsm6_2:1.2.2-1+b1 libsmartcols1_2.28.2-1 libsqlite3-0_3.14.2-1 libss2_1.43.3-1 libssh2-1_1.7.0-1 libssl1.0.2_1.0.2j-1 libstdc++-6-dev_6.2.0-6+rpi1 libstdc++6_6.2.0-6+rpi1 libsystemd0_231-9 libtasn1-6_4.9-4 libtcl8.6_8.6.6+dfsg-1 libthai-data_0.1.25-2 libthai0_0.1.25-2 libtiff5_4.0.6-2 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20160917-1 libtinfo5_6.0+20160917-1 libtk8.6_8.6.6-1 libtool_2.4.6-2 libubsan0_6.2.0-6+rpi1 libudev1_231-9 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-5 libuuid1_2.28.2-1 libx11-6_2:1.6.3-1 libx11-data_2:1.6.3-1 libxau6_1:1.0.8-1 libxcb-render0_1.12-1 libxcb-shm0_1.12-1 libxcb1_1.12-1 libxdmcp6_1:1.1.2-1.1 libxext6_2:1.3.3-1 libxft2_2.3.2-1 libxml2_2.9.4+dfsg1-2 libxmuu1_2:1.1.2-2 libxrender1_1:0.9.9-2 libxss1_1:1.2.2-1 libxt6_1:1.1.5-1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.2-3.2 lsb-base_9.20160629+rpi1 m4_1.4.17-5 make_4.1-9 makedev_2.3.1-93 man-db_2.7.5-1 manpages_4.08-1 mawk_1.3.3-17 mount_2.28.2-1 multiarch-support_2.24-5+rpi1 ncurses-base_6.0+20160917-1 ncurses-bin_6.0+20160917-1 netbase_5.3 openssl_1.0.2j-1 passwd_1:4.2-3.2 patch_2.7.5-1 perl_5.24.1~rc3-3 perl-base_5.24.1~rc3-3 perl-modules-5.24_5.24.1~rc3-3 pinentry-curses_0.9.7-6 po-debconf_1.0.20 procps_2:3.3.12-2 psmisc_22.21-2.1 r-base-core_3.3.1.20161024-1 r-base-dev_3.3.1.20161024-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-affyio-dummy_0.invalid.0 sed_4.2.2-8 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_231-9 systemd-sysv_231-9 sysv-rc_2.88dsf-59.8 sysvinit-utils_2.88dsf-59.8 tar_1.29b-1 tzdata_2016h-1 ucf_3.0036 udev_231-9 unzip_6.0-20 util-linux_2.28.2-1 x11-common_1:7.7+16 xauth_1:1.0.9-1 xdg-utils_1.1.1-1 xz-utils_5.2.2-1.2 zip_3.0-11 zlib1g_1:1.2.8.dfsg-2+b1 zlib1g-dev_1:1.2.8.dfsg-2+b1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Oct 26 12:26:19 2016 UTC
gpgv: using RSA key 578A0494D1C646D1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./r-bioc-affyio_1.44.0-1.dsc
dpkg-source: info: extracting r-bioc-affyio in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-affyio_1.44.0.orig.tar.gz
dpkg-source: info: unpacking r-bioc-affyio_1.44.0-1.debian.tar.xz
dpkg-source: info: applying use_debian_packaged_zlib.patch
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=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-f2293e68-6363-45cc-8ef6-e436225f0711
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package r-bioc-affyio
dpkg-buildpackage: info: source version 1.44.0-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build r-bioc-affyio-1.44.0
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --buildsystem R
dh_testdir -O--buildsystem=R
dh_auto_clean -O--buildsystem=R
dh_clean -O--buildsystem=R
debian/rules build-arch
dh build-arch --buildsystem R
dh_testdir -a -O--buildsystem=R
dh_update_autotools_config -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
fakeroot debian/rules binary-arch
dh binary-arch --buildsystem R
dh_testroot -a -O--buildsystem=R
dh_prep -a -O--buildsystem=R
dh_installdirs -a -O--buildsystem=R
dh_auto_install -a -O--buildsystem=R
I: R Package: affyio Version: 1.44.0
I: Building using R version 3.3.1.20161024-1
I: R API version: r-api-3
I: Using built-time from d/changelog: Wed, 26 Oct 2016 14:17:11 +0200
mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-affyio/usr/lib/R/site-library
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-affyio/usr/lib/R/site-library --clean . "--built-timestamp='Wed, 26 Oct 2016 14:17:11 +0200'"
* installing *source* package 'affyio' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for main in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
checking for pthread_create in -lpthread... yes
checking if we can use pthreads... yes
checking if PTHREAD_STACK_MIN is defined... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fread_functions.c -o fread_functions.o
fread_functions.c: In function 'gzread_int32':
fread_functions.c:414:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types]
result = gzread(instream,destination,sizeof(int)*n);
^~~~~~~~
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^~~~~~
fread_functions.c: In function 'gzread_uint32':
fread_functions.c:439:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types]
result = gzread(instream,destination,sizeof(unsigned int)*n);
^~~~~~~~
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^~~~~~
fread_functions.c: In function 'gzread_int16':
fread_functions.c:458:20: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types]
result = gzread(instream,destination,sizeof(short)*n);
^~~~~~~~
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^~~~~~
fread_functions.c: In function 'gzread_uint16':
fread_functions.c:476:20: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types]
result = gzread(instream,destination,sizeof(unsigned short)*n);
^~~~~~~~
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^~~~~~
fread_functions.c: In function 'gzread_float32':
fread_functions.c:497:20: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types]
result = gzread(instream,destination,sizeof(float)*n);
^~~~~~~~
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^~~~~~
fread_functions.c: In function 'gzread_char':
fread_functions.c:513:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types]
result = gzread(instream,destination,sizeof(char)*n);
^~~~~~~~
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^~~~~~
fread_functions.c: In function 'gzread_uchar':
fread_functions.c:529:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types]
result = gzread(instream,destination,sizeof(unsigned char)*n);
^~~~~~~~
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^~~~~~
fread_functions.c: In function 'gzread_double64':
fread_functions.c:547:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types]
result = gzread(instream, destination,sizeof(double)*n);
^~~~~~~~
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^~~~~~
fread_functions.c: In function 'gzread_be_int32':
fread_functions.c:575:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types]
result = gzread(instream,destination,sizeof(int)*n);
^~~~~~~~
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^~~~~~
fread_functions.c: In function 'gzread_be_uint32':
fread_functions.c:600:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types]
result = gzread(instream,destination,sizeof(unsigned int)*n);
^~~~~~~~
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^~~~~~
fread_functions.c: In function 'gzread_be_int16':
fread_functions.c:620:20: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types]
result = gzread(instream,destination,sizeof(short)*n);
^~~~~~~~
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^~~~~~
fread_functions.c: In function 'gzread_be_uint16':
fread_functions.c:636:20: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types]
result = gzread(instream,destination,sizeof(unsigned short)*n);
^~~~~~~~
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^~~~~~
fread_functions.c: In function 'gzread_be_float32':
fread_functions.c:656:20: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types]
result = gzread(instream,destination,sizeof(float)*n);
^~~~~~~~
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^~~~~~
fread_functions.c: In function 'gzread_be_char':
fread_functions.c:673:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types]
result = gzread(instream,destination,sizeof(char)*n);
^~~~~~~~
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^~~~~~
fread_functions.c: In function 'gzread_be_uchar':
fread_functions.c:690:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types]
result = gzread(instream,destination,sizeof(unsigned char)*n);
^~~~~~~~
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^~~~~~
fread_functions.c: In function 'gzread_be_double64':
fread_functions.c:706:19: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types]
result = gzread(instream, destination,sizeof(double)*n);
^~~~~~~~
In file included from fread_functions.h:12:0,
from fread_functions.c:10:
/usr/include/zlib.h:1313:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^~~~~~
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init_package.c -o init_package.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_abatch.c -o read_abatch.o
read_abatch.c: In function 'gz_get_detailed_header_info':
read_abatch.c:1989:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
currentFile = open_gz_cel_file(filename);
^
read_abatch.c:1991:22: warning: passing argument 1 of 'gzAdvanceToSection' from incompatible pointer type [-Wincompatible-pointer-types]
gzAdvanceToSection(currentFile,"[HEADER]",buffer);
^~~~~~~~~~~
read_abatch.c:1439:13: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){
^~~~~~~~~~~~~~~~~~
read_abatch.c:1993:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types]
gzfindStartsWith(currentFile,"Cols",buffer);
^~~~~~~~~~~
read_abatch.c:1416:14: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^~~~~~~~~~~~~~~~
read_abatch.c:1998:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types]
gzfindStartsWith(currentFile,"Rows",buffer);
^~~~~~~~~~~
read_abatch.c:1416:14: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^~~~~~~~~~~~~~~~
read_abatch.c:2003:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types]
gzfindStartsWith(currentFile,"GridCornerUL",buffer);
^~~~~~~~~~~
read_abatch.c:1416:14: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^~~~~~~~~~~~~~~~
read_abatch.c:2009:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types]
gzfindStartsWith(currentFile,"GridCornerUR",buffer);
^~~~~~~~~~~
read_abatch.c:1416:14: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^~~~~~~~~~~~~~~~
read_abatch.c:2015:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types]
gzfindStartsWith(currentFile,"GridCornerLR",buffer);
^~~~~~~~~~~
read_abatch.c:1416:14: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^~~~~~~~~~~~~~~~
read_abatch.c:2021:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types]
gzfindStartsWith(currentFile,"GridCornerLL",buffer);
^~~~~~~~~~~
read_abatch.c:1416:14: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^~~~~~~~~~~~~~~~
read_abatch.c:2027:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types]
gzfindStartsWith(currentFile,"DatHeader",buffer);
^~~~~~~~~~~
read_abatch.c:1416:14: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^~~~~~~~~~~~~~~~
read_abatch.c:2059:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types]
gzfindStartsWith(currentFile,"Algorithm",buffer);
^~~~~~~~~~~
read_abatch.c:1416:14: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^~~~~~~~~~~~~~~~
read_abatch.c:2067:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types]
gzfindStartsWith(currentFile,"AlgorithmParameters",buffer);
^~~~~~~~~~~
read_abatch.c:1416:14: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^~~~~~~~~~~~~~~~
read_abatch.c:2072:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(currentFile);
^~~~~~~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_abatch.c: In function 'gz_get_masks_outliers':
read_abatch.c:2100:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
currentFile = open_gz_cel_file(filename);
^
read_abatch.c:2104:22: warning: passing argument 1 of 'gzAdvanceToSection' from incompatible pointer type [-Wincompatible-pointer-types]
gzAdvanceToSection(currentFile,"[MASKS]",buffer);
^~~~~~~~~~~
read_abatch.c:1439:13: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){
^~~~~~~~~~~~~~~~~~
read_abatch.c:2105:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types]
gzfindStartsWith(currentFile,"NumberCells=",buffer);
^~~~~~~~~~~
read_abatch.c:1416:14: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^~~~~~~~~~~~~~~~
read_abatch.c:2109:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types]
gzfindStartsWith(currentFile,"CellHeader=",buffer);
^~~~~~~~~~~
read_abatch.c:1416:14: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^~~~~~~~~~~~~~~~
read_abatch.c:2118:38: warning: passing argument 3 of 'ReadgzFileLine' from incompatible pointer type [-Wincompatible-pointer-types]
ReadgzFileLine(buffer, BUF_SIZE, currentFile);
^~~~~~~~~~~
read_abatch.c:1354:13: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void ReadgzFileLine(char *buffer, int buffersize, gzFile currentFile){
^~~~~~~~~~~~~~
read_abatch.c:2133:22: warning: passing argument 1 of 'gzAdvanceToSection' from incompatible pointer type [-Wincompatible-pointer-types]
gzAdvanceToSection(currentFile,"[OUTLIERS]",buffer);
^~~~~~~~~~~
read_abatch.c:1439:13: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){
^~~~~~~~~~~~~~~~~~
read_abatch.c:2134:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types]
gzfindStartsWith(currentFile,"NumberCells=",buffer);
^~~~~~~~~~~
read_abatch.c:1416:14: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^~~~~~~~~~~~~~~~
read_abatch.c:2138:20: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type [-Wincompatible-pointer-types]
gzfindStartsWith(currentFile,"CellHeader=",buffer);
^~~~~~~~~~~
read_abatch.c:1416:14: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^~~~~~~~~~~~~~~~
read_abatch.c:2146:38: warning: passing argument 3 of 'ReadgzFileLine' from incompatible pointer type [-Wincompatible-pointer-types]
ReadgzFileLine(buffer, BUF_SIZE, currentFile);
^~~~~~~~~~~
read_abatch.c:1354:13: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
static void ReadgzFileLine(char *buffer, int buffersize, gzFile currentFile){
^~~~~~~~~~~~~~
read_abatch.c:2158:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(currentFile);
^~~~~~~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_abatch.c: In function 'isgzBinaryCelFile':
read_abatch.c:3141:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_abatch.c:3148:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_abatch.c:3153:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_abatch.c:3159:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_abatch.c:3164:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_abatch.c:3169:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_abatch.c: In function 'gzread_binary_header':
read_abatch.c:3192:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_abatch.c:3247:15: warning: passing argument 1 of 'gzread' from incompatible pointer type [-Wincompatible-pointer-types]
if (!gzread(infile,this_header->header,sizeof(char)*this_header->header_len)){
^~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1313:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^~~~~~
read_abatch.c:3289:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_abatch.c: In function 'gzread_binarycel_file_intensities':
read_abatch.c:3591:10: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(my_header->gzinfile);
^~~~~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_abatch.c:3597:10: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(my_header->infile);
^~~~~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'FILE * {aka struct _IO_FILE *}'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_abatch.c:3607:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(my_header->gzinfile);
^~~~~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_abatch.c: In function 'gzread_binarycel_file_stddev':
read_abatch.c:3644:10: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(my_header->gzinfile);
^~~~~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_abatch.c:3654:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(my_header->gzinfile);
^~~~~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_abatch.c: In function 'gzread_binarycel_file_npixels':
read_abatch.c:3692:10: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(my_header->infile);
^~~~~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'FILE * {aka struct _IO_FILE *}'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_abatch.c:3702:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(my_header->gzinfile);
^~~~~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_abatch.c: In function 'gz_binary_apply_masks':
read_abatch.c:3735:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(my_header->infile,my_header->n_cells*sizeofrecords,SEEK_CUR);
^~~~~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'FILE * {aka struct _IO_FILE *}'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_abatch.c:3748:12: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(my_header->gzinfile,my_header->n_masks*sizeof(cur_loc),SEEK_CUR);
^~~~~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_abatch.c:3761:12: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(my_header->gzinfile,my_header->n_outliers*sizeof(cur_loc),SEEK_CUR);
^~~~~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_abatch.c:3764:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(my_header->gzinfile);
^~~~~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_abatch.c: In function 'gzbinary_get_masks_outliers':
read_abatch.c:3797:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(my_header->gzinfile,my_header->n_cells*sizeofrecords,SEEK_CUR);
^~~~~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_abatch.c:3827:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(my_header->gzinfile);
^~~~~~~~~
In file included from fread_functions.h:12:0,
from read_abatch.c:164:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_bpmap.c -o read_bpmap.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_cdf_xda.c -o read_cdf_xda.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_cdffile2.c -o read_cdffile2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_celfile_generic.c -o read_celfile_generic.o
read_celfile_generic.c: In function 'isgzGenericCelFile':
read_celfile_generic.c:1067:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1074:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_celfile_generic.c:1080:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_celfile_generic.c:1089:12: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_celfile_generic.c:1094:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_celfile_generic.c: In function 'gzgeneric_get_header_info':
read_celfile_generic.c:1115:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1151:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_celfile_generic.c: In function 'gzgeneric_get_detailed_header_info':
read_celfile_generic.c:1175:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1633:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_celfile_generic.c: In function 'check_gzgeneric_cel_file':
read_celfile_generic.c:1661:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1701:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_celfile_generic.c: In function 'gzread_genericcel_file_intensities':
read_celfile_generic.c:1726:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1745:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_celfile_generic.c: In function 'gzread_genericcel_file_stddev':
read_celfile_generic.c:1777:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1790:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_celfile_generic.c:1802:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_celfile_generic.c: In function 'gzread_genericcel_file_npixels':
read_celfile_generic.c:1831:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1844:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_celfile_generic.c:1848:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_celfile_generic.c:1861:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers':
read_celfile_generic.c:1896:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1910:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_celfile_generic.c:1915:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_celfile_generic.c:1920:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_celfile_generic.c:1939:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_celfile_generic.c:1960:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_celfile_generic.c: In function 'gzgeneric_apply_masks':
read_celfile_generic.c:1991:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:2012:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_celfile_generic.c:2017:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_celfile_generic.c:2022:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_celfile_generic.c:2038:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_celfile_generic.c:2056:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_clf.c -o read_clf.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_generic.c -o read_generic.o
read_generic.c: In function 'gzread_ASTRING_fw':
read_generic.c:927:9: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(instream, length-destination->len, SEEK_CUR);
^~~~~~~~
In file included from fread_functions.h:12:0,
from read_generic.c:50:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_generic.c: In function 'gzread_AWSTRING_fw':
read_generic.c:973:9: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(instream, length-2*destination->len, SEEK_CUR);
^~~~~~~~
In file included from fread_functions.h:12:0,
from read_generic.c:50:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_generic.c: In function 'gzRead_Generic':
read_generic.c:1508:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(cur_file_name, "rb")) == NULL)
^
read_generic.c:1540:14: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from fread_functions.h:12:0,
from read_generic.c:50:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_multichannel_celfile_generic.c -o read_multichannel_celfile_generic.o
read_multichannel_celfile_generic.c: In function 'isgzGenericMultiChannelCelFile':
read_multichannel_celfile_generic.c:620:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:627:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_multichannel_celfile_generic.c:633:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_multichannel_celfile_generic.c:642:12: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_multichannel_celfile_generic.c:647:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_multichannel_celfile_generic.c: In function 'gzmultichannel_determine_number_channels':
read_multichannel_celfile_generic.c:677:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:701:12: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile,next_group,SEEK_SET);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_multichannel_celfile_generic.c:704:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_multichannel_celfile_generic.c: In function 'gzmultichannel_determine_channel_name':
read_multichannel_celfile_generic.c:729:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:741:12: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile,next_group,SEEK_SET);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_multichannel_celfile_generic.c:751:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_intensities_multichannel':
read_multichannel_celfile_generic.c:778:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:793:12: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile,next_group,SEEK_SET);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_multichannel_celfile_generic.c:807:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_stddev_multichannel':
read_multichannel_celfile_generic.c:834:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:849:12: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile,next_group,SEEK_SET);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_multichannel_celfile_generic.c:856:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_multichannel_celfile_generic.c:867:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_multichannel_celfile_generic.c: In function 'gzread_genericcel_file_npixels_multichannel':
read_multichannel_celfile_generic.c:896:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:912:12: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile,next_group,SEEK_SET);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_multichannel_celfile_generic.c:919:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_multichannel_celfile_generic.c:923:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_multichannel_celfile_generic.c:936:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_multichannel_celfile_generic.c: In function 'gzgeneric_get_masks_outliers_multichannel':
read_multichannel_celfile_generic.c:965:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:981:12: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile,next_group,SEEK_SET);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_multichannel_celfile_generic.c:989:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_multichannel_celfile_generic.c:994:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_multichannel_celfile_generic.c:999:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_multichannel_celfile_generic.c:1018:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_multichannel_celfile_generic.c:1039:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
read_multichannel_celfile_generic.c: In function 'gzgeneric_apply_masks_multichannel':
read_multichannel_celfile_generic.c:1069:15: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:1090:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_multichannel_celfile_generic.c:1095:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_multichannel_celfile_generic.c:1100:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_multichannel_celfile_generic.c:1116:10: warning: passing argument 1 of 'gzseek' from incompatible pointer type [-Wincompatible-pointer-types]
gzseek(infile, my_data_set.file_pos_last, SEEK_SET);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1726:28: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^~~~~~
read_multichannel_celfile_generic.c:1134:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
gzclose(infile);
^~~~~~
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^~~~~~~
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 -DUSE_PTHREADS=1 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fpic -g -O2 -fdebug-prefix-map=/build/r-base-KhISWV/r-base-3.3.1.20161024=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_pgf.c -o read_pgf.o
read_pgf.c: In function 'pgf_count_probeset_types':
read_pgf.c:1265:28: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
my_pgf->probesets->current= my_pgf->probesets->current->next;
^
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o affyio.so fread_functions.o init_package.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_clf.o read_generic.o read_multichannel_celfile_generic.o read_pgf.o -lpthread -lz -lpthread -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
installing to /<<PKGBUILDDIR>>/debian/r-bioc-affyio/usr/lib/R/site-library/affyio/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (affyio)
W: Ignoring specified R dependency: R (>= 2.6.0)
dh_install -a -O--buildsystem=R
dh_installdocs -a -O--buildsystem=R
dh_installchangelogs -a -O--buildsystem=R
dh_installexamples -a -O--buildsystem=R
dh_installman -a -O--buildsystem=R
dh_installcatalogs -a -O--buildsystem=R
dh_installcron -a -O--buildsystem=R
dh_installdebconf -a -O--buildsystem=R
dh_installemacsen -a -O--buildsystem=R
dh_installifupdown -a -O--buildsystem=R
dh_installinfo -a -O--buildsystem=R
dh_installinit -a -O--buildsystem=R
dh_installmenu -a -O--buildsystem=R
dh_installmime -a -O--buildsystem=R
dh_installmodules -a -O--buildsystem=R
dh_installlogcheck -a -O--buildsystem=R
dh_installlogrotate -a -O--buildsystem=R
dh_installpam -a -O--buildsystem=R
dh_installppp -a -O--buildsystem=R
dh_installudev -a -O--buildsystem=R
dh_installgsettings -a -O--buildsystem=R
dh_bugfiles -a -O--buildsystem=R
dh_ucf -a -O--buildsystem=R
dh_lintian -a -O--buildsystem=R
dh_gconf -a -O--buildsystem=R
dh_icons -a -O--buildsystem=R
dh_perl -a -O--buildsystem=R
dh_usrlocal -a -O--buildsystem=R
dh_link -a -O--buildsystem=R
dh_installwm -a -O--buildsystem=R
dh_installxfonts -a -O--buildsystem=R
dh_strip_nondeterminism -a -O--buildsystem=R
dh_compress -a -O--buildsystem=R
dh_fixperms -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
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -a -O--buildsystem=R
dh_builddeb -a -O--buildsystem=R
dpkg-deb: building package 'r-bioc-affyio-dbgsym' in '../r-bioc-affyio-dbgsym_1.44.0-1_armhf.deb'.
dpkg-deb: building package 'r-bioc-affyio' in '../r-bioc-affyio_1.44.0-1_armhf.deb'.
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-bioc-affyio_1.44.0-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build r-bioc-affyio-1.44.0
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2016-11-01T12:55:13Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
r-bioc-affyio_1.44.0-1_armhf.changes:
-------------------------------------
Format: 1.8
Date: Wed, 26 Oct 2016 14:17:11 +0200
Source: r-bioc-affyio
Binary: r-bioc-affyio
Architecture: armhf
Version: 1.44.0-1
Distribution: stretch-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
r-bioc-affyio - BioConductor tools for parsing Affymetrix data files
Changes:
r-bioc-affyio (1.44.0-1) unstable; urgency=medium
.
* New upstream version
* Convert to dh-r
* Generic BioConductor homepage
Checksums-Sha1:
ecc1a8b050f79c90699d520718f9fed13b1fa550 159974 r-bioc-affyio-dbgsym_1.44.0-1_armhf.deb
6f47e3631471d65d97ac5a0a4ac91d2d51428377 66508 r-bioc-affyio_1.44.0-1_armhf.deb
Checksums-Sha256:
de8aa055185975aac7cde2f7b1e5d2741bd37d44cda0bcb3d31e4064e4b5434c 159974 r-bioc-affyio-dbgsym_1.44.0-1_armhf.deb
71f7a4d75b0f069eabd012ba53c6a2fc88cffcd26b739b0296d3c3268550e74f 66508 r-bioc-affyio_1.44.0-1_armhf.deb
Files:
5d4d6ef273249d0c957063c5b0a45de7 159974 debug extra r-bioc-affyio-dbgsym_1.44.0-1_armhf.deb
8dfd3e9330820e623e8189cdf9684bd8 66508 gnu-r optional r-bioc-affyio_1.44.0-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
r-bioc-affyio-dbgsym_1.44.0-1_armhf.deb
---------------------------------------
new debian package, version 2.0.
size 159974 bytes: control archive=493 bytes.
445 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: r-bioc-affyio-dbgsym
Source: r-bioc-affyio
Version: 1.44.0-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 180
Depends: r-bioc-affyio (= 1.44.0-1)
Section: debug
Priority: extra
Homepage: https://bioconductor.org/packages/affyio/
Description: Debug symbols for r-bioc-affyio
Auto-Built-Package: debug-symbols
Build-Ids: 8d2e1456e50745249e398b84784dda3b7e29c445
drwxr-xr-x root/root 0 2016-10-26 12:17 ./
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/lib/
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/lib/debug/.build-id/8d/
-rw-r--r-- root/root 173476 2016-10-26 12:17 ./usr/lib/debug/.build-id/8d/2e1456e50745249e398b84784dda3b7e29c445.debug
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/share/
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/share/doc/
lrwxrwxrwx root/root 0 2016-10-26 12:17 ./usr/share/doc/r-bioc-affyio-dbgsym -> r-bioc-affyio
r-bioc-affyio_1.44.0-1_armhf.deb
--------------------------------
new debian package, version 2.0.
size 66508 bytes: control archive=1236 bytes.
584 bytes, 13 lines control
1780 bytes, 23 lines md5sums
Package: r-bioc-affyio
Version: 1.44.0-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 208
Depends: r-base-core (>= 3.3.1.20161024-1), r-api-3, libc6 (>= 2.4), zlib1g (>= 1:1.1.4)
Section: gnu-r
Priority: optional
Homepage: https://bioconductor.org/packages/affyio/
Description: BioConductor tools for parsing Affymetrix data files
This BioConductor package provides routines for parsing Affymetrix data
files based upon file format information. Primary focus is on accessing
the CEL and CDF file formats.
drwxr-xr-x root/root 0 2016-10-26 12:17 ./
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/lib/
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/lib/R/
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/lib/R/site-library/
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/
-rw-r--r-- root/root 635 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/DESCRIPTION
-rw-r--r-- root/root 375 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/INDEX
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/Meta/
-rw-r--r-- root/root 484 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/Meta/Rd.rds
-rw-r--r-- root/root 496 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/Meta/hsearch.rds
-rw-r--r-- root/root 229 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/Meta/links.rds
-rw-r--r-- root/root 206 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/Meta/nsInfo.rds
-rw-r--r-- root/root 744 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/Meta/package.rds
-rw-r--r-- root/root 46 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/NAMESPACE
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/R/
-rw-r--r-- root/root 1056 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/R/affyio
-rw-r--r-- root/root 3307 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/R/affyio.rdb
-rw-r--r-- root/root 382 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/R/affyio.rdx
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/help/
-rw-r--r-- root/root 297 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/help/AnIndex
-rw-r--r-- root/root 10726 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/help/affyio.rdb
-rw-r--r-- root/root 335 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/help/affyio.rdx
-rw-r--r-- root/root 172 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/help/aliases.rds
-rw-r--r-- root/root 211 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/help/paths.rds
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/html/
-rw-r--r-- root/root 1785 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/html/00Index.html
-rw-r--r-- root/root 1335 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/html/R.css
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/libs/
-rw-r--r-- root/root 157820 2016-10-26 12:17 ./usr/lib/R/site-library/affyio/libs/affyio.so
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/share/
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/share/doc/
drwxr-xr-x root/root 0 2016-10-26 12:17 ./usr/share/doc/r-bioc-affyio/
-rw-r--r-- root/root 285 2013-09-12 08:59 ./usr/share/doc/r-bioc-affyio/README.test
-rw-r--r-- root/root 410 2016-10-26 12:17 ./usr/share/doc/r-bioc-affyio/changelog.Debian.gz
-rw-r--r-- root/root 193 2016-10-17 20:23 ./usr/share/doc/r-bioc-affyio/changelog.gz
-rw-r--r-- root/root 535 2016-10-26 12:16 ./usr/share/doc/r-bioc-affyio/copyright
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 1600
Build-Time: 123
Distribution: stretch-staging
Host Architecture: armhf
Install-Time: 467
Job: r-bioc-affyio_1.44.0-1
Machine Architecture: armhf
Package: r-bioc-affyio
Package-Time: 643
Source-Version: 1.44.0-1
Space: 1600
Status: successful
Version: 1.44.0-1
--------------------------------------------------------------------------------
Finished at 2016-11-01T12:55:13Z
Build needed 00:10:43, 1600k disc space