r-bioc-affyio →
1.32.0-1 →
armhf → 2014-06-19 06:00:35
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-02
╔══════════════════════════════════════════════════════════════════════════════╗
║ r-bioc-affyio 1.32.0-1 (armhf) 19 Jun 2014 05:50 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: r-bioc-affyio
Version: 1.32.0-1
Source Version: 1.32.0-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/r-bioc-affyio-9EYr_o/r-bioc-affyio-1.32.0' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/r-bioc-affyio-9EYr_o' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-1737c0bb-bef9-449a-a156-9ea5b0245d92' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7328 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8243 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 15.6 MB in 28s (544 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
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Checking available source versions...
Download source files with APT
──────────────────────────────
Reading package lists...
Building dependency tree...
Reading state information...
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 118 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main r-bioc-affyio 1.32.0-1 (dsc) [2064 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main r-bioc-affyio 1.32.0-1 (tar) [114 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main r-bioc-affyio 1.32.0-1 (diff) [1908 B]
Fetched 118 kB in 0s (3025 kB/s)
Download complete and in download only mode
Check arch
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-Fhga86/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 62 not upgraded.
Need to get 0 B/818 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11664 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), cdbs, zlib1g-dev, r-base-dev
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), cdbs, zlib1g-dev, r-base-dev
dpkg-deb: building package `sbuild-build-depends-r-bioc-affyio-dummy' in `/«BUILDDIR»/resolver-4l_xPz/apt_archive/sbuild-build-depends-r-bioc-affyio-dummy.deb'.
OK
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 extra packages will be installed:
bsdmainutils cdbs cpp cpp-4.9 debhelper file fontconfig fontconfig-config
fonts-dejavu-core gcc gcc-4.9 gcc-4.9-base gettext gettext-base gfortran
gfortran-4.9 groff-base intltool-debian libasan1 libasprintf0c2 libatomic1
libblas-dev libblas3 libbz2-dev libcairo2 libcroco3 libdatrie1 libdrm2
libexpat1 libffi6 libfontconfig1 libfreetype6 libgcc-4.9-dev libgcc1
libgfortran-4.9-dev libgfortran3 libgl1-mesa-glx libglapi-mesa libglib2.0-0
libgomp1 libgraphite2-3 libharfbuzz0b libice6 libjbig0 libjpeg8 libjpeg8-dev
liblapack-dev liblapack3 liblzma-dev libmagic1 libncurses5-dev
libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils
libpaper1 libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0 libpng12-0
libpng12-dev libreadline-dev libreadline6-dev libsm6 libstdc++6 libtcl8.5
libthai-data libthai0 libtiff5 libtinfo-dev libtk8.5 libubsan0 libunistring0
libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0
libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1
libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxml2 libxrender1
libxshmfence1 libxss1 libxt6 libxxf86vm1 man-db po-debconf r-base-core
r-base-dev ucf unzip x11-common xdg-utils zip zlib1g zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation devscripts cpp-doc gcc-4.9-locales dh-make
gcc-multilib manpages-dev autoconf automake1.9 libtool flex bison gdb
gcc-doc gcc-4.9-doc libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg
libasan1-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg libvtv0-dbg
libcilkrts5-dbg libquadmath-dbg gettext-doc gfortran-doc gfortran-4.9-doc
libgfortran3-dbg groff liblzma-doc ncurses-doc ttf-baekmuk
ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp
ttf-arphic-bkai00mp tcl8.5 tk8.5 less www-browser libmail-box-perl
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:
autotools-dev curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libgl1-mesa-dri libglib2.0-data shared-mime-info 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:
bsdmainutils cdbs cpp-4.9 debhelper file fontconfig fontconfig-config
fonts-dejavu-core gcc-4.9 gettext gettext-base gfortran gfortran-4.9
groff-base intltool-debian libasan1 libasprintf0c2 libblas-dev libblas3
libbz2-dev libcairo2 libcroco3 libdatrie1 libdrm2 libexpat1 libffi6
libfontconfig1 libfreetype6 libgcc-4.9-dev libgfortran-4.9-dev libgfortran3
libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgraphite2-3 libharfbuzz0b
libice6 libjbig0 libjpeg8 libjpeg8-dev liblapack-dev liblapack3 liblzma-dev
libmagic1 libncurses5-dev libpango-1.0-0 libpangocairo-1.0-0
libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre3-dev libpcrecpp0
libpipeline1 libpixman-1-0 libpng12-0 libpng12-dev libreadline-dev
libreadline6-dev libsm6 libtcl8.5 libthai-data libthai0 libtiff5
libtinfo-dev libtk8.5 libubsan0 libunistring0 libx11-6 libx11-data
libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0
libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1 libxdamage1 libxdmcp6
libxext6 libxfixes3 libxft2 libxml2 libxrender1 libxshmfence1 libxss1 libxt6
libxxf86vm1 man-db po-debconf r-base-core r-base-dev
sbuild-build-depends-r-bioc-affyio-dummy ucf unzip x11-common xdg-utils zip
zlib1g-dev
The following packages will be upgraded:
cpp gcc gcc-4.9-base libatomic1 libgcc1 libgomp1 libstdc++6 zlib1g
8 upgraded, 101 newly installed, 0 to remove and 54 not upgraded.
Need to get 59.6 MB/59.6 MB of archives.
After this operation, 144 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libgomp1 armhf 4.9.0-6 [33.3 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main gcc-4.9-base armhf 4.9.0-6 [156 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main libstdc++6 armhf 4.9.0-6 [234 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main libatomic1 armhf 4.9.0-6 [6152 B]
Get:5 http://172.17.0.1/private/ jessie-staging/main libgcc1 armhf 1:4.9.0-6 [39.5 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main zlib1g armhf 1:1.2.8.dfsg-1+rpi1 [77.7 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.3.0-1 [21.1 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-5 [962 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.7.1-1 [964 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3.2-2 [29.2 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.18-1 [229 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-3 [836 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main libasan1 armhf 4.9.0-6 [165 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main libexpat1 armhf 2.1.0-6 [60.2 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main libpng12-0 armhf 1.2.50-1 [180 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main libfreetype6 armhf 2.5.2-1 [397 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main ucf all 3.0030 [69.7 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main fonts-dejavu-core all 2.34-1 [1047 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main fontconfig-config all 2.11.0-5 [273 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main libfontconfig1 armhf 2.11.0-5 [310 kB]
Get:22 http://172.17.0.1/private/ jessie-staging/main libdrm2 armhf 2.4.54-1 [25.9 kB]
Get:23 http://172.17.0.1/private/ jessie-staging/main libglapi-mesa armhf 10.1.4-1 [64.2 kB]
Get:24 http://172.17.0.1/private/ jessie-staging/main libxau6 armhf 1:1.0.8-1 [19.9 kB]
Get:25 http://172.17.0.1/private/ jessie-staging/main libxdmcp6 armhf 1:1.1.1-1 [24.6 kB]
Get:26 http://172.17.0.1/private/ jessie-staging/main libxcb1 armhf 1.10-3 [38.1 kB]
Get:27 http://172.17.0.1/private/ jessie-staging/main libx11-data all 2:1.6.2-2 [126 kB]
Get:28 http://172.17.0.1/private/ jessie-staging/main libx11-6 armhf 2:1.6.2-2 [657 kB]
Get:29 http://172.17.0.1/private/ jessie-staging/main libx11-xcb1 armhf 2:1.6.2-2 [163 kB]
Get:30 http://172.17.0.1/private/ jessie-staging/main libxcb-dri2-0 armhf 1.10-3 [12.1 kB]
Get:31 http://172.17.0.1/private/ jessie-staging/main libxcb-dri3-0 armhf 1.10-3 [10.6 kB]
Get:32 http://172.17.0.1/private/ jessie-staging/main libxcb-glx0 armhf 1.10-3 [23.8 kB]
Get:33 http://172.17.0.1/private/ jessie-staging/main libxcb-present0 armhf 1.10-3 [10.8 kB]
Get:34 http://172.17.0.1/private/ jessie-staging/main libxcb-sync1 armhf 1.10-3 [13.2 kB]
Get:35 http://172.17.0.1/private/ jessie-staging/main libxfixes3 armhf 1:5.0.1-1 [21.0 kB]
Get:36 http://172.17.0.1/private/ jessie-staging/main libxdamage1 armhf 1:1.1.4-1 [14.6 kB]
Get:37 http://172.17.0.1/private/ jessie-staging/main libxext6 armhf 2:1.3.2-1 [51.1 kB]
Get:38 http://172.17.0.1/private/ jessie-staging/main libxshmfence1 armhf 1.1-2 [6736 B]
Get:39 http://172.17.0.1/private/ jessie-staging/main libxxf86vm1 armhf 1:1.1.3-1 [20.0 kB]
Get:40 http://172.17.0.1/private/ jessie-staging/main libgl1-mesa-glx armhf 10.1.4-1 [134 kB]
Get:41 http://172.17.0.1/private/ jessie-staging/main libpixman-1-0 armhf 0.32.4-1 [476 kB]
Get:42 http://172.17.0.1/private/ jessie-staging/main libxcb-render0 armhf 1.10-3 [16.0 kB]
Get:43 http://172.17.0.1/private/ jessie-staging/main libxcb-shm0 armhf 1.10-3 [11.0 kB]
Get:44 http://172.17.0.1/private/ jessie-staging/main libxrender1 armhf 1:0.9.8-1 [30.4 kB]
Get:45 http://172.17.0.1/private/ jessie-staging/main libcairo2 armhf 1.12.16-2+rpi1 [894 kB]
Get:46 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.1-2 [18.1 kB]
Get:47 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.40.0-3 [2247 kB]
Get:48 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:49 http://172.17.0.1/private/ jessie-staging/main libdatrie1 armhf 0.2.8-1 [29.1 kB]
Get:50 http://172.17.0.1/private/ jessie-staging/main libgfortran3 armhf 4.9.0-6 [154 kB]
Get:51 http://172.17.0.1/private/ jessie-staging/main libgraphite2-3 armhf 1.2.4-3 [48.2 kB]
Get:52 http://172.17.0.1/private/ jessie-staging/main libharfbuzz0b armhf 0.9.28-2 [434 kB]
Get:53 http://172.17.0.1/private/ jessie-staging/main x11-common all 1:7.7+7 [287 kB]
Get:54 http://172.17.0.1/private/ jessie-staging/main libice6 armhf 2:1.0.8-2 [56.2 kB]
Get:55 http://172.17.0.1/private/ jessie-staging/main libjpeg8 armhf 8d-2 [133 kB]
Get:56 http://172.17.0.1/private/ jessie-staging/main libthai-data all 0.1.20-3 [157 kB]
Get:57 http://172.17.0.1/private/ jessie-staging/main libthai0 armhf 0.1.20-3 [41.6 kB]
Get:58 http://172.17.0.1/private/ jessie-staging/main fontconfig armhf 2.11.0-5 [401 kB]
Get:59 http://172.17.0.1/private/ jessie-staging/main libpango-1.0-0 armhf 1.36.3-1 [265 kB]
Get:60 http://172.17.0.1/private/ jessie-staging/main libpangoft2-1.0-0 armhf 1.36.3-1 [199 kB]
Get:61 http://172.17.0.1/private/ jessie-staging/main libpangocairo-1.0-0 armhf 1.36.3-1 [189 kB]
Get:62 http://172.17.0.1/private/ jessie-staging/main libpaper1 armhf 1.1.24+nmu3 [20.7 kB]
Get:63 http://172.17.0.1/private/ jessie-staging/main libpcrecpp0 armhf 1:8.31-5 [124 kB]
Get:64 http://172.17.0.1/private/ jessie-staging/main libsm6 armhf 2:1.2.1-2 [32.5 kB]
Get:65 http://172.17.0.1/private/ jessie-staging/main libtcl8.5 armhf 8.5.15-4 [649 kB]
Get:66 http://172.17.0.1/private/ jessie-staging/main libjbig0 armhf 2.0-2.1 [26.8 kB]
Get:67 http://172.17.0.1/private/ jessie-staging/main libtiff5 armhf 4.0.3-8 [192 kB]
Get:68 http://172.17.0.1/private/ jessie-staging/main libxft2 armhf 2.3.1-2 [47.7 kB]
Get:69 http://172.17.0.1/private/ jessie-staging/main libxss1 armhf 1:1.2.2-1 [16.8 kB]
Get:70 http://172.17.0.1/private/ jessie-staging/main libtk8.5 armhf 8.5.15-4 [646 kB]
Get:71 http://172.17.0.1/private/ jessie-staging/main libubsan0 armhf 4.9.0-6 [68.2 kB]
Get:72 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:73 http://172.17.0.1/private/ jessie-staging/main libxt6 armhf 1:1.1.4-1 [183 kB]
Get:74 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.18-1 [57.2 kB]
Get:75 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3.2-2 [112 kB]
Get:76 http://172.17.0.1/private/ jessie-staging/main cdbs all 0.4.123 [75.1 kB]
Get:77 http://172.17.0.1/private/ jessie-staging/main cpp-4.9 armhf 4.9.0-6 [4255 kB]
Get:78 http://172.17.0.1/private/ jessie-staging/main cpp armhf 4:4.9.0-3 [16.9 kB]
Get:79 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3.2-2 [1136 kB]
Get:80 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:81 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:82 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20140613 [692 kB]
Get:83 http://172.17.0.1/private/ jessie-staging/main libgcc-4.9-dev armhf 4.9.0-6 [348 kB]
Get:84 http://172.17.0.1/private/ jessie-staging/main gcc-4.9 armhf 4.9.0-6 [4406 kB]
Get:85 http://172.17.0.1/private/ jessie-staging/main gcc armhf 4:4.9.0-3 [5070 B]
Get:86 http://172.17.0.1/private/ jessie-staging/main libgfortran-4.9-dev armhf 4.9.0-6 [181 kB]
Get:87 http://172.17.0.1/private/ jessie-staging/main gfortran-4.9 armhf 4.9.0-6 [4480 kB]
Get:88 http://172.17.0.1/private/ jessie-staging/main gfortran armhf 4:4.9.0-3 [1264 B]
Get:89 http://172.17.0.1/private/ jessie-staging/main libblas3 armhf 1.2.20110419-7 [186 kB]
Get:90 http://172.17.0.1/private/ jessie-staging/main libblas-dev armhf 1.2.20110419-7 [201 kB]
Get:91 http://172.17.0.1/private/ jessie-staging/main libbz2-dev armhf 1.0.6-5 [33.8 kB]
Get:92 http://172.17.0.1/private/ jessie-staging/main libjpeg8-dev armhf 8d-2 [238 kB]
Get:93 http://172.17.0.1/private/ jessie-staging/main liblapack3 armhf 3.5.0-2 [2416 kB]
Get:94 http://172.17.0.1/private/ jessie-staging/main liblapack-dev armhf 3.5.0-2 [2716 kB]
Get:95 http://172.17.0.1/private/ jessie-staging/main liblzma-dev armhf 5.1.1alpha+20120614-2 [272 kB]
Get:96 http://172.17.0.1/private/ jessie-staging/main libtinfo-dev armhf 5.9+20140118-1 [64.8 kB]
Get:97 http://172.17.0.1/private/ jessie-staging/main libncurses5-dev armhf 5.9+20140118-1 [152 kB]
Get:98 http://172.17.0.1/private/ jessie-staging/main libpaper-utils armhf 1.1.24+nmu3 [17.0 kB]
Get:99 http://172.17.0.1/private/ jessie-staging/main libpcre3-dev armhf 1:8.31-5 [357 kB]
Get:100 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1+rpi1 [192 kB]
Get:101 http://172.17.0.1/private/ jessie-staging/main libpng12-dev armhf 1.2.50-1 [260 kB]
Get:102 http://172.17.0.1/private/ jessie-staging/main libreadline6-dev armhf 6.3-6 [194 kB]
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Get:104 http://172.17.0.1/private/ jessie-staging/main zip armhf 3.0-8 [326 kB]
Get:105 http://172.17.0.1/private/ jessie-staging/main unzip armhf 6.0-12 [152 kB]
Get:106 http://172.17.0.1/private/ jessie-staging/main xdg-utils all 1.1.0~rc1+git20111210-7.1 [64.6 kB]
Get:107 http://172.17.0.1/private/ jessie-staging/main r-base-core armhf 3.1.0-1 [19.4 MB]
Get:108 http://172.17.0.1/private/ jessie-staging/main r-base-dev all 3.1.0-1 [4014 B]
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Setting up libx11-data (2:1.6.2-2) ...
Setting up libx11-6:armhf (2:1.6.2-2) ...
Setting up libx11-xcb1:armhf (2:1.6.2-2) ...
Setting up libxcb-dri2-0:armhf (1.10-3) ...
Setting up libxcb-dri3-0:armhf (1.10-3) ...
Setting up libxcb-glx0:armhf (1.10-3) ...
Setting up libxcb-present0:armhf (1.10-3) ...
Setting up libxcb-sync1:armhf (1.10-3) ...
Setting up libxfixes3:armhf (1:5.0.1-1) ...
Setting up libxdamage1:armhf (1:1.1.4-1) ...
Setting up libxext6:armhf (2:1.3.2-1) ...
Setting up libxshmfence1:armhf (1.1-2) ...
Setting up libxxf86vm1:armhf (1:1.1.3-1) ...
Setting up libgl1-mesa-glx:armhf (10.1.4-1) ...
Setting up libpixman-1-0:armhf (0.32.4-1) ...
Setting up libxcb-render0:armhf (1.10-3) ...
Setting up libxcb-shm0:armhf (1.10-3) ...
Setting up libxrender1:armhf (1:0.9.8-1) ...
Setting up libcairo2:armhf (1.12.16-2+rpi1) ...
Setting up libffi6:armhf (3.1-2) ...
Setting up libglib2.0-0:armhf (2.40.0-3) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-2) ...
Setting up libdatrie1:armhf (0.2.8-1) ...
Setting up libgfortran3:armhf (4.9.0-6) ...
Setting up libgraphite2-3:armhf (1.2.4-3) ...
Setting up libharfbuzz0b:armhf (0.9.28-2) ...
Setting up x11-common (1:7.7+7) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libice6:armhf (2:1.0.8-2) ...
Setting up libjpeg8:armhf (8d-2) ...
Setting up libthai-data (0.1.20-3) ...
Setting up libthai0:armhf (0.1.20-3) ...
Setting up fontconfig (2.11.0-5) ...
Regenerating fonts cache... done.
Setting up libpango-1.0-0:armhf (1.36.3-1) ...
Setting up libpangoft2-1.0-0:armhf (1.36.3-1) ...
Setting up libpangocairo-1.0-0:armhf (1.36.3-1) ...
Setting up libpaper1:armhf (1.1.24+nmu3) ...
Creating config file /etc/papersize with new version
Setting up libpcrecpp0:armhf (1:8.31-5) ...
Setting up libsm6:armhf (2:1.2.1-2) ...
Setting up libtcl8.5:armhf (8.5.15-4) ...
Setting up libjbig0:armhf (2.0-2.1) ...
Setting up libtiff5:armhf (4.0.3-8) ...
Setting up libxft2:armhf (2.3.1-2) ...
Setting up libxss1:armhf (1:1.2.2-1) ...
Setting up libtk8.5:armhf (8.5.15-4) ...
Setting up libubsan0:armhf (4.9.0-6) ...
Setting up libunistring0:armhf (0.9.3-5) ...
Setting up libxt6:armhf (1:1.1.4-1) ...
Setting up file (1:5.18-1) ...
Setting up gettext-base (0.18.3.2-2) ...
Setting up cdbs (0.4.123) ...
Setting up cpp-4.9 (4.9.0-6) ...
Setting up cpp (4:4.9.0-3) ...
Setting up gettext (0.18.3.2-2) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20140613) ...
Setting up libgcc-4.9-dev:armhf (4.9.0-6) ...
Setting up gcc-4.9 (4.9.0-6) ...
Setting up gcc (4:4.9.0-3) ...
Setting up libgfortran-4.9-dev:armhf (4.9.0-6) ...
Setting up gfortran-4.9 (4.9.0-6) ...
Setting up gfortran (4:4.9.0-3) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
Setting up libblas3 (1.2.20110419-7) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libblas-dev (1.2.20110419-7) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
Setting up libbz2-dev:armhf (1.0.6-5) ...
Setting up libjpeg8-dev:armhf (8d-2) ...
Setting up liblapack3 (3.5.0-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up liblapack-dev (3.5.0-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up liblzma-dev:armhf (5.1.1alpha+20120614-2) ...
Setting up libtinfo-dev:armhf (5.9+20140118-1) ...
Setting up libncurses5-dev:armhf (5.9+20140118-1) ...
Setting up libpaper-utils (1.1.24+nmu3) ...
Setting up libpcre3-dev:armhf (1:8.31-5) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1+rpi1) ...
Setting up libpng12-dev (1.2.50-1) ...
Setting up libreadline6-dev:armhf (6.3-6) ...
Setting up libreadline-dev:armhf (6.3-6) ...
Setting up zip (3.0-8) ...
Setting up unzip (6.0-12) ...
Setting up xdg-utils (1.1.0~rc1+git20111210-7.1) ...
Setting up r-base-core (3.1.0-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-base-dev (3.1.0-1) ...
Setting up sbuild-build-depends-r-bioc-affyio-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.18-5) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.14-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24.51.20140425-1 dpkg-dev_1.17.6+rpi1 g++-4.8_4.8.2-21 gcc-4.8_4.8.2-21 gcc-4.9_4.9.0-6 libc6-dev_2.18-5 libstdc++-4.8-dev_4.8.2-21 libstdc++6_4.9.0-6 linux-libc-dev_3.13.10-1+rpi1
Package versions: apt_1.0.1 base-files_7.2+rpi1 base-passwd_3.5.28 bash_4.3-7 binutils_2.24.51.20140425-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.7 build-essential_11.6 bzip2_1.0.6-5 cdbs_0.4.123 coreutils_8.21-1.2 cpio_2.11+dfsg-2 cpp_4:4.9.0-3 cpp-4.8_4.8.2-21 cpp-4.9_4.9.0-6 dash_0.5.7-4 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-1.2 debhelper_9.20140613 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.6+rpi1 dpkg-dev_1.17.6+rpi1 e2fslibs_1.42.9-3 e2fsprogs_1.42.9-3 fakeroot_1.18.4-2 file_1:5.18-1 findutils_4.4.2-8 fontconfig_2.11.0-5 fontconfig-config_2.11.0-5 fonts-dejavu-core_2.34-1 g++_4:4.8.2-3 g++-4.8_4.8.2-21 gcc_4:4.9.0-3 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8_4.8.2-21 gcc-4.8-base_4.8.2-21 gcc-4.9_4.9.0-6 gcc-4.9-base_4.9.0-6 gettext_0.18.3.2-2 gettext-base_0.18.3.2-2 gfortran_4:4.9.0-3 gfortran-4.9_4.9.0-6 gnupg_1.4.16-1.1 gpgv_1.4.16-1.1 grep_2.18-2 groff-base_1.22.2-5 gzip_1.6-3 hostname_3.15 init-system-helpers_1.18 initramfs-tools_0.115 initscripts_2.88dsf-53 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.2-1+rpi1 kmod_16-2 libacl1_2.2.52-1 libapt-pkg4.12_1.0.1 libasan0_4.8.2-21 libasan1_4.9.0-6 libasprintf0c2_0.18.3.2-2 libatomic1_4.9.0-6 libattr1_1:2.4.47-1 libaudit-common_1:2.3.6-1 libaudit1_1:2.3.6-1 libblas-dev_1.2.20110419-7 libblas3_1.2.20110419-7 libblkid1_2.20.1-5.7 libbz2-1.0_1.0.6-5 libbz2-dev_1.0.6-5 libc-bin_2.18-5 libc-dev-bin_2.18-5 libc6_2.18-5 libc6-dev_2.18-5 libcairo2_1.12.16-2+rpi1 libcap2_1:2.22-1.2 libcloog-isl4_0.18.2-1 libcomerr2_1.42.9-3 libcroco3_0.6.8-2 libdatrie1_0.2.8-1 libdb5.1_5.1.29-6 libdb5.3_5.3.28-3 libdbus-1-3_1.8.0-3 libdpkg-perl_1.17.6+rpi1 libdrm2_2.4.54-1 libexpat1_2.1.0-6 libffi6_3.1-2 libfontconfig1_2.11.0-5 libfreetype6_2.5.2-1 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.2-21 libgcc-4.9-dev_4.9.0-6 libgcc1_1:4.9.0-6 libgdbm3_1.8.3-12 libgfortran-4.9-dev_4.9.0-6 libgfortran3_4.9.0-6 libgl1-mesa-glx_10.1.4-1 libglapi-mesa_10.1.4-1 libglib2.0-0_2.40.0-3 libgmp10_2:6.0.0+dfsg-2 libgomp1_4.9.0-6 libgraphite2-3_1.2.4-3 libharfbuzz0b_0.9.28-2 libice6_2:1.0.8-2 libisl10_0.12.2-1 libjbig0_2.0-2.1 libjpeg8_8d-2 libjpeg8-dev_8d-2 libklibc_2.0.2-1+rpi1 libkmod2_16-2 liblapack-dev_3.5.0-2 liblapack3_3.5.0-2 liblocale-gettext-perl_1.05-8 liblzma-dev_5.1.1alpha+20120614-2 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.18-1 libmount1_2.20.1-5.7 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libncurses5-dev_5.9+20140118-1 libncursesw5_5.9+20140118-1 libpam-modules_1.1.8-3 libpam-modules-bin_1.1.8-3 libpam-runtime_1.1.8-3 libpam0g_1.1.8-3 libpango-1.0-0_1.36.3-1 libpangocairo-1.0-0_1.36.3-1 libpangoft2-1.0-0_1.36.3-1 libpaper-utils_1.1.24+nmu3 libpaper1_1.1.24+nmu3 libpcre3_1:8.31-5 libpcre3-dev_1:8.31-5 libpcrecpp0_1:8.31-5 libpipeline1_1.3.0-1 libpixman-1-0_0.32.4-1 libpng12-0_1.2.50-1 libpng12-dev_1.2.50-1 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-2 libreadline-dev_6.3-6 libreadline6_6.3-6 libreadline6-dev_6.3-6 libselinux1_2.2.2-1 libsemanage-common_2.2-1 libsemanage1_2.2-1 libsepol1_2.2-1 libslang2_2.2.4-16 libsm6_2:1.2.1-2 libss2_1.42.9-3 libstdc++-4.8-dev_4.8.2-21 libstdc++6_4.9.0-6 libtcl8.5_8.5.15-4 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b3 libtext-wrapi18n-perl_0.06-7 libthai-data_0.1.20-3 libthai0_0.1.20-3 libtiff5_4.0.3-8 libtimedate-perl_2.3000-2 libtinfo-dev_5.9+20140118-1 libtinfo5_5.9+20140118-1 libtk8.5_8.5.15-4 libubsan0_4.9.0-6 libudev1_204-8 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.7 libx11-6_2:1.6.2-2 libx11-data_2:1.6.2-2 libx11-xcb1_2:1.6.2-2 libxau6_1:1.0.8-1 libxcb-dri2-0_1.10-3 libxcb-dri3-0_1.10-3 libxcb-glx0_1.10-3 libxcb-present0_1.10-3 libxcb-render0_1.10-3 libxcb-shm0_1.10-3 libxcb-sync1_1.10-3 libxcb1_1.10-3 libxdamage1_1:1.1.4-1 libxdmcp6_1:1.1.1-1 libxext6_2:1.3.2-1 libxfixes3_1:5.0.1-1 libxft2_2.3.1-2 libxml2_2.9.1+dfsg1-3 libxrender1_1:0.9.8-1 libxshmfence1_1.1-2 libxss1_1:1.2.2-1 libxt6_1:1.1.4-1 libxxf86vm1_1:1.1.3-1 linux-libc-dev_3.13.10-1+rpi1 login_1:4.1.5.1-1.1 lsb-base_4.1+Debian12+rpi1 make_3.81-8.3 makedev_2.3.1-93 man-db_2.6.7.1-1 mawk_1.3.3-17 mount_2.20.1-5.7 multiarch-support_2.18-5 nano_2.2.6-1.1 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 passwd_1:4.1.5.1-1.1 patch_2.7.1-5 perl_5.18.2-2+b1 perl-base_5.18.2-2+b1 perl-modules_5.18.2-2 plymouth_0.8.8-16 po-debconf_1.0.16+nmu2 procps_1:3.3.9-2 r-base-core_3.1.0-1 r-base-dev_3.1.0-1 raspbian-archive-keyring_20120528.2 readline-common_6.3-6 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-affyio-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 sysv-rc_2.88dsf-53 sysvinit_2.88dsf-53 sysvinit-core_2.88dsf-53 sysvinit-utils_2.88dsf-53 tar_1.27.1-2 tzdata_2014b-1 ucf_3.0030 udev_204-8 unzip_6.0-12 util-linux_2.20.1-5.7 x11-common_1:7.7+7 xdg-utils_1.1.0~rc1+git20111210-7.1 xz-utils_5.1.1alpha+20120614-2 zip_3.0-8 zlib1g_1:1.2.8.dfsg-1+rpi1 zlib1g-dev_1:1.2.8.dfsg-1+rpi1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sun Jun 8 14:02:44 2014 UTC using RSA key ID D1C646D1
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./r-bioc-affyio_1.32.0-1.dsc
dpkg-source: info: extracting r-bioc-affyio in r-bioc-affyio-1.32.0
dpkg-source: info: unpacking r-bioc-affyio_1.32.0.orig.tar.gz
dpkg-source: info: unpacking r-bioc-affyio_1.32.0-1.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
LANG=en_GB.UTF-8
LC_ALL=POSIX
LOGNAME=root
MAIL=/var/mail/root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/root
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-1737c0bb-bef9-449a-a156-9ea5b0245d92
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
SHLVL=1
SSH_CLIENT=172.17.0.6 46828 22
SSH_CONNECTION=172.17.0.6 46828 172.17.2.2 22
SSH_TTY=/dev/pts/0
TERM=xterm
USER=buildd
_=/etc/init.d/buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package r-bioc-affyio
dpkg-buildpackage: source version 1.32.0-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build r-bioc-affyio-1.32.0
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
test -x debian/rules
dh_clean
if test -d src; then \
find src -regex ".*\.o" | \
xargs --no-run-if-empty -r rm; \
fi
rm -f config.log config.status
debian/rules build-arch
test -x debian/rules
mkdir -p "."
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
dh_installdirs usr/lib/R/site-library
echo "R:Depends=r-base-core (>= 3.1.0-1)" >> debian/r-bioc-affyio.substvars
if test -f /usr/bin/xvfb-run; then \
xvfb-run -a \
R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-affyio/usr/lib/R/site-library --clean \
. ; \
else \
R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-affyio/usr/lib/R/site-library \
--clean . ;\
fi
* 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 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c fread_functions.c -o fread_functions.o
fread_functions.c: In function 'gzread_int32':
fread_functions.c:414:12: warning: passing argument 1 of 'gzread' from incompatible pointer type
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' 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:439:12: warning: passing argument 1 of 'gzread' from incompatible pointer type
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' 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:458:13: warning: passing argument 1 of 'gzread' from incompatible pointer type
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' 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:476:13: warning: passing argument 1 of 'gzread' from incompatible pointer type
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' 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:497:13: warning: passing argument 1 of 'gzread' from incompatible pointer type
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' 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:513:12: warning: passing argument 1 of 'gzread' from incompatible pointer type
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' 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:529:12: warning: passing argument 1 of 'gzread' from incompatible pointer type
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' 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:547:12: warning: passing argument 1 of 'gzread' from incompatible pointer type
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' 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:575:12: warning: passing argument 1 of 'gzread' from incompatible pointer type
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' 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:600:12: warning: passing argument 1 of 'gzread' from incompatible pointer type
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' 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:620:13: warning: passing argument 1 of 'gzread' from incompatible pointer type
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' 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:636:13: warning: passing argument 1 of 'gzread' from incompatible pointer type
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' 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:656:13: warning: passing argument 1 of 'gzread' from incompatible pointer type
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' 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:673:12: warning: passing argument 1 of 'gzread' from incompatible pointer type
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' 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:690:12: warning: passing argument 1 of 'gzread' from incompatible pointer type
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' 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:706:12: warning: passing argument 1 of 'gzread' from incompatible pointer type
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' 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 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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
currentFile = open_gz_cel_file(filename);
^
read_abatch.c:1991:3: warning: passing argument 1 of 'gzAdvanceToSection' from incompatible pointer type
gzAdvanceToSection(currentFile,"[HEADER]",buffer);
^
read_abatch.c:1439:13: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){
^
read_abatch.c:1993:3: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type
gzfindStartsWith(currentFile,"Cols",buffer);
^
read_abatch.c:1416:14: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:1998:3: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type
gzfindStartsWith(currentFile,"Rows",buffer);
^
read_abatch.c:1416:14: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2003:3: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type
gzfindStartsWith(currentFile,"GridCornerUL",buffer);
^
read_abatch.c:1416:14: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2009:3: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type
gzfindStartsWith(currentFile,"GridCornerUR",buffer);
^
read_abatch.c:1416:14: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2015:3: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type
gzfindStartsWith(currentFile,"GridCornerLR",buffer);
^
read_abatch.c:1416:14: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2021:3: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type
gzfindStartsWith(currentFile,"GridCornerLL",buffer);
^
read_abatch.c:1416:14: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2027:3: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type
gzfindStartsWith(currentFile,"DatHeader",buffer);
^
read_abatch.c:1416:14: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2059:3: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type
gzfindStartsWith(currentFile,"Algorithm",buffer);
^
read_abatch.c:1416:14: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2067:3: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type
gzfindStartsWith(currentFile,"AlgorithmParameters",buffer);
^
read_abatch.c:1416:14: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2072:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
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' 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
currentFile = open_gz_cel_file(filename);
^
read_abatch.c:2104:3: warning: passing argument 1 of 'gzAdvanceToSection' from incompatible pointer type
gzAdvanceToSection(currentFile,"[MASKS]",buffer);
^
read_abatch.c:1439:13: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){
^
read_abatch.c:2105:3: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type
gzfindStartsWith(currentFile,"NumberCells=",buffer);
^
read_abatch.c:1416:14: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2109:3: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type
gzfindStartsWith(currentFile,"CellHeader=",buffer);
^
read_abatch.c:1416:14: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2118:5: warning: passing argument 3 of 'ReadgzFileLine' from incompatible pointer type
ReadgzFileLine(buffer, BUF_SIZE, currentFile);
^
read_abatch.c:1354:13: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void ReadgzFileLine(char *buffer, int buffersize, gzFile currentFile){
^
read_abatch.c:2133:3: warning: passing argument 1 of 'gzAdvanceToSection' from incompatible pointer type
gzAdvanceToSection(currentFile,"[OUTLIERS]",buffer);
^
read_abatch.c:1439:13: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void gzAdvanceToSection(gzFile my_file,char *sectiontitle, char *buffer){
^
read_abatch.c:2134:3: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type
gzfindStartsWith(currentFile,"NumberCells=",buffer);
^
read_abatch.c:1416:14: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2138:3: warning: passing argument 1 of 'gzfindStartsWith' from incompatible pointer type
gzfindStartsWith(currentFile,"CellHeader=",buffer);
^
read_abatch.c:1416:14: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void gzfindStartsWith(gzFile my_file,char *starts, char *buffer){
^
read_abatch.c:2146:5: warning: passing argument 3 of 'ReadgzFileLine' from incompatible pointer type
ReadgzFileLine(buffer, BUF_SIZE, currentFile);
^
read_abatch.c:1354:13: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
static void ReadgzFileLine(char *buffer, int buffersize, gzFile currentFile){
^
read_abatch.c:2158:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
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' 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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_abatch.c:3148:5: warning: passing argument 1 of 'gzclose' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3153:5: warning: passing argument 1 of 'gzclose' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3159:5: warning: passing argument 1 of 'gzclose' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3164:5: warning: passing argument 1 of 'gzclose' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3169:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
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' 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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_abatch.c:3247:8: warning: passing argument 1 of 'gzread' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
read_abatch.c:3289:5: warning: passing argument 1 of 'gzclose' from incompatible pointer type
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' 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:3591:2: warning: passing argument 1 of 'gzclose' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3597:2: warning: passing argument 1 of 'gzclose' from incompatible pointer type
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' but argument is of type 'struct FILE *'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3607:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
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' 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:3644:2: warning: passing argument 1 of 'gzclose' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3654:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
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' 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:3692:2: warning: passing argument 1 of 'gzclose' from incompatible pointer type
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' but argument is of type 'struct FILE *'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_abatch.c:3702:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
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' 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:3735:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' but argument is of type 'struct FILE *'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_abatch.c:3748:5: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_abatch.c:3761:5: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_abatch.c:3764:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
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' 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:3797:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_abatch.c:3827:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
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' 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 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1074:5: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c:1080:5: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c:1089:4: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_celfile_generic.c:1094:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' 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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1151:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' 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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1633:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' 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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1701:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' 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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1745:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' 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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1790:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1802:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' 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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1844:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1848:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1861:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' 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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:1910:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1915:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1920:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1939:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:1960:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' 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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_celfile_generic.c:2012:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:2017:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:2022:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:2038:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' but argument is of type 'struct gzFile_s **'
ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
^
read_celfile_generic.c:2056:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' 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 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c read_generic.c -o read_generic.o
read_generic.c: In function 'gzread_ASTRING_fw':
read_generic.c:927:2: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:973:2: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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
if ((infile = gzopen(cur_file_name, "rb")) == NULL)
^
read_generic.c:1540:7: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:627:5: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c:633:5: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c:642:4: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
read_multichannel_celfile_generic.c:647:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' 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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:701:5: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:704:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' 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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:741:5: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:751:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' 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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:793:5: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:807:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' 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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:849:5: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:856:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:867:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' 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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:912:5: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:919:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:923:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:936:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' 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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:981:5: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:989:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:994:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:999:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:1018:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:1039:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' 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
if ((infile = gzopen(filename, "rb")) == NULL)
^
read_multichannel_celfile_generic.c:1090:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:1095:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:1100:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:1116:3: warning: passing argument 1 of 'gzseek' from incompatible pointer type
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' 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:1134:3: warning: passing argument 1 of 'gzclose' from incompatible pointer type
gzclose(infile);
^
In file included from read_multichannel_celfile_generic.c:43:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' 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 -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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
my_pgf->probesets->current= my_pgf->probesets->current->next;
^
gcc -std=gnu99 -shared -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)
rm -vf /«PKGBUILDDIR»/debian/r-bioc-affyio/usr/lib/R/site-library/R.css \
/«PKGBUILDDIR»/debian/r-bioc-affyio/usr/lib/R/site-library/affyio/COPYING \
/«PKGBUILDDIR»/debian/r-bioc-affyio/usr/lib/R/site-library/affyio/LICENSE.txt
if test -f debian/overrides; then \
install -d /«PKGBUILDDIR»/debian/r-bioc-affyio/usr/share/lintian/overrides ; \
install -m 0644 debian/overrides \
/«PKGBUILDDIR»/debian/r-bioc-affyio/usr/share/lintian/overrides/r-bioc-affyio; \
fi
Adding cdbs dependencies to debian/r-bioc-affyio.substvars
dh_installdirs -pr-bioc-affyio
rm -rf debian/r-bioc-affyio/usr/lib/R/site-library/affyio/LICENSE
dh_installdocs -pr-bioc-affyio
dh_installexamples -pr-bioc-affyio
dh_installman -pr-bioc-affyio
dh_installinfo -pr-bioc-affyio
dh_installmenu -pr-bioc-affyio
dh_installcron -pr-bioc-affyio
dh_installinit -pr-bioc-affyio
dh_installdebconf -pr-bioc-affyio
dh_installemacsen -pr-bioc-affyio
dh_installcatalogs -pr-bioc-affyio
dh_installpam -pr-bioc-affyio
dh_installlogrotate -pr-bioc-affyio
dh_installlogcheck -pr-bioc-affyio
dh_installchangelogs -pr-bioc-affyio
dh_installudev -pr-bioc-affyio
dh_lintian -pr-bioc-affyio
dh_bugfiles -pr-bioc-affyio
dh_install -pr-bioc-affyio
dh_link -pr-bioc-affyio
dh_installmime -pr-bioc-affyio
dh_installgsettings -pr-bioc-affyio
dh_strip -pr-bioc-affyio
dh_compress -pr-bioc-affyio
dh_fixperms -pr-bioc-affyio
dh_makeshlibs -pr-bioc-affyio
dh_installdeb -pr-bioc-affyio
dh_perl -pr-bioc-affyio
dh_shlibdeps -pr-bioc-affyio
dh_gencontrol -pr-bioc-affyio
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -pr-bioc-affyio
dh_builddeb -pr-bioc-affyio
dpkg-deb: building package `r-bioc-affyio' in `../r-bioc-affyio_1.32.0-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-bioc-affyio_1.32.0-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build r-bioc-affyio-1.32.0
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140619-0600
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
r-bioc-affyio_1.32.0-1_armhf.changes:
─────────────────────────────────────
Format: 1.8
Date: Sun, 08 Jun 2014 15:57:01 +0200
Source: r-bioc-affyio
Binary: r-bioc-affyio
Architecture: armhf
Version: 1.32.0-1
Distribution: jessie-staging
Urgency: low
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 (1.32.0-1) unstable; urgency=low
.
* New upstream version
* debian/{control,copyright}: Fixed homepage
Checksums-Sha1:
9034c500dc44a64223a20b5c7abc49bc3b3e501c 62682 r-bioc-affyio_1.32.0-1_armhf.deb
Checksums-Sha256:
a45e01211c10766c4c3f53b68b9a572a558c37f9198c6b91b00a57a986bc179a 62682 r-bioc-affyio_1.32.0-1_armhf.deb
Files:
00ddaa79f7c74ebcbf30e43e05b6167b 62682 gnu-r optional r-bioc-affyio_1.32.0-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
r-bioc-affyio_1.32.0-1_armhf.deb
────────────────────────────────
new debian package, version 2.0.
size 62682 bytes: control archive=1306 bytes.
587 bytes, 13 lines control
1780 bytes, 23 lines md5sums
Package: r-bioc-affyio
Version: 1.32.0-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 172
Depends: r-base-core (>= 3.1.0-1), libc6 (>= 2.4), zlib1g (>= 1:1.1.4)
Section: gnu-r
Priority: optional
Homepage: http://bioconductor.org/packages/release/bioc/html/affyio.html
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 2014-06-19 05:59 ./
drwxr-xr-x root/root 0 2014-06-19 05:59 ./usr/
drwxr-xr-x root/root 0 2014-06-19 05:58 ./usr/lib/
drwxr-xr-x root/root 0 2014-06-19 05:58 ./usr/lib/R/
drwxr-xr-x root/root 0 2014-06-19 05:59 ./usr/lib/R/site-library/
drwxr-xr-x root/root 0 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/
-rw-r--r-- root/root 46 2014-06-19 05:58 ./usr/lib/R/site-library/affyio/NAMESPACE
-rw-r--r-- root/root 562 2014-06-19 05:58 ./usr/lib/R/site-library/affyio/DESCRIPTION
drwxr-xr-x root/root 0 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/Meta/
-rw-r--r-- root/root 691 2014-06-19 05:58 ./usr/lib/R/site-library/affyio/Meta/package.rds
-rw-r--r-- root/root 448 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/Meta/Rd.rds
-rw-r--r-- root/root 460 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/Meta/hsearch.rds
-rw-r--r-- root/root 215 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/Meta/links.rds
-rw-r--r-- root/root 205 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/Meta/nsInfo.rds
drwxr-xr-x root/root 0 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/libs/
-rw-r--r-- root/root 153620 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/libs/affyio.so
drwxr-xr-x root/root 0 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/R/
-rw-r--r-- root/root 1056 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/R/affyio
-rw-r--r-- root/root 2866 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/R/affyio.rdb
-rw-r--r-- root/root 367 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/R/affyio.rdx
drwxr-xr-x root/root 0 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/help/
-rw-r--r-- root/root 200 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/help/paths.rds
-rw-r--r-- root/root 9022 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/help/affyio.rdb
-rw-r--r-- root/root 312 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/help/affyio.rdx
-rw-r--r-- root/root 261 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/help/AnIndex
-rw-r--r-- root/root 162 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/help/aliases.rds
drwxr-xr-x root/root 0 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/html/
-rw-r--r-- root/root 1545 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/html/00Index.html
-rw-r--r-- root/root 1179 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/html/R.css
-rw-r--r-- root/root 322 2014-06-19 05:59 ./usr/lib/R/site-library/affyio/INDEX
drwxr-xr-x root/root 0 2014-06-19 05:59 ./usr/share/
drwxr-xr-x root/root 0 2014-06-19 05:59 ./usr/share/doc/
drwxr-xr-x root/root 0 2014-06-19 05:59 ./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 560 2013-10-18 08:57 ./usr/share/doc/r-bioc-affyio/copyright
-rw-r--r-- root/root 241 2014-06-08 14:00 ./usr/share/doc/r-bioc-affyio/changelog.Debian.gz
-rw-r--r-- root/root 162 2014-04-11 22:32 ./usr/share/doc/r-bioc-affyio/changelog.gz
┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
└──────────────────────────────────────────────────────────────────────────────┘
┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
└──────────────────────────────────────────────────────────────────────────────┘
Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 1244
Build-Time: 108
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 402
Job: r-bioc-affyio_1.32.0-1
Machine Architecture: armhf
Package: r-bioc-affyio
Package-Time: 559
Source-Version: 1.32.0-1
Space: 1244
Status: successful
Version: 1.32.0-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20140619-0600
Build needed 00:09:19, 1244k disc space