Attachment 372149 Details for Bug 539201 – build.log

build.log

build.log (text/plain), 28.12 KB, created by FTBFS on 2009-11-19 17:12:54 UTC

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Creator: FTBFS

Created: 2009-11-19 17:12:54 UTC

Size: 28.12 KB

patch

obsolete

>Mock Version: 0.9.19
>ENTER do(['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/R-affyio.spec'], False, '/var/lib/mock/fedora-development-x86_64-R-affyio-1.12.0-3.fc12.src.rpm/root/', None, 21600, True, 0, 8116, 14667, None, logger=<mock.trace_decorator.getLog object at 0x2189890>)
>Executing command: ['bash', '--login', '-c', 'rpmbuild -bs --target x86_64 --nodeps builddir/build/SPECS/R-affyio.spec']
>Building target platforms: x86_64
>Building for target x86_64
>Wrote: /builddir/build/SRPMS/R-affyio-1.12.0-3.fc13.src.rpm
>Child returncode was: 0
>LEAVE do --> 
>
>ENTER do(['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/R-affyio.spec'], False, '/var/lib/mock/fedora-development-x86_64-R-affyio-1.12.0-3.fc12.src.rpm/root/', None, 21600, True, 0, 8116, 14667, None, logger=<mock.trace_decorator.getLog object at 0x2189890>)
>Executing command: ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/R-affyio.spec']
>Building target platforms: x86_64
>Building for target x86_64
>Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.MRYfp0
>+ umask 022
>+ cd /builddir/build/BUILD
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ cd /builddir/build/BUILD
>+ rm -rf affyio
>+ /bin/mkdir -p affyio
>+ cd affyio
>+ /usr/bin/gzip -dc /builddir/build/SOURCES/affyio_1.12.0.tar.gz
>+ /bin/tar -xf -
>+ STATUS=0
>+ '[' 0 -ne 0 ']'
>+ /bin/chmod -Rf a+rX,u+w,g-w,o-w .
>+ exit 0
>Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.AfZzHB
>+ umask 022
>+ cd /builddir/build/BUILD
>+ cd affyio
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ exit 0
>Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.kFJDxd
>+ umask 022
>+ cd /builddir/build/BUILD
>+ '[' /builddir/build/BUILDROOT/R-affyio-1.12.0-3.fc13.x86_64 '!=' / ']'
>+ rm -rf /builddir/build/BUILDROOT/R-affyio-1.12.0-3.fc13.x86_64
>++ dirname /builddir/build/BUILDROOT/R-affyio-1.12.0-3.fc13.x86_64
>+ mkdir -p /builddir/build/BUILDROOT
>+ mkdir /builddir/build/BUILDROOT/R-affyio-1.12.0-3.fc13.x86_64
>+ cd affyio
>+ LANG=C
>+ export LANG
>+ unset DISPLAY
>+ rm -rf /builddir/build/BUILDROOT/R-affyio-1.12.0-3.fc13.x86_64
>+ mkdir -p /builddir/build/BUILDROOT/R-affyio-1.12.0-3.fc13.x86_64/usr/lib64/R/library
>+ R CMD INSTALL affyio -l /builddir/build/BUILDROOT/R-affyio-1.12.0-3.fc13.x86_64/usr/lib64/R/library
>* 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
>configure: creating ./config.status
>config.status: creating src/Makevars
>** libs
>gcc -m64 -std=gnu99 -I/usr/include/R -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 -I/usr/local/include   -g -O2   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c fread_functions.c -o fread_functions.o
>fread_functions.c:300: warning: 'swap_uint_32' defined but not used
>gcc -m64 -std=gnu99 -I/usr/include/R -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 -I/usr/local/include   -g -O2   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c read_abatch.c -o read_abatch.o
>read_abatch.c: In function 'readfile_group':
>read_abatch.c:4339: warning: unused variable 'Current_intensity'
>read_abatch.c: In function 'checkFileCDF_group':
>read_abatch.c:4357: warning: control reaches end of non-void function
>read_abatch.c: In function 'readfile_group':
>read_abatch.c:4348: warning: control reaches end of non-void function
>gcc -m64 -std=gnu99 -I/usr/include/R -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 -I/usr/local/include   -g -O2   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c read_bpmap.c -o read_bpmap.o
>read_bpmap.c: In function 'ReadBPMAPHeader':
>read_bpmap.c:78: warning: unused variable 'version_number_int'
>gcc -m64 -std=gnu99 -I/usr/include/R -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 -I/usr/local/include   -g -O2   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c read_cdf_xda.c -o read_cdf_xda.o
>gcc -m64 -std=gnu99 -I/usr/include/R -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 -I/usr/local/include   -g -O2   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c read_cdffile2.c -o read_cdffile2.o
>read_cdffile2.c:364: warning: 'token_ends_with' defined but not used
>gcc -m64 -std=gnu99 -I/usr/include/R -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 -I/usr/local/include   -g -O2   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c read_celfile_generic.c -o read_celfile_generic.o
>read_celfile_generic.c: In function 'read_genericcel_file_intensities':
>read_celfile_generic.c:697: warning: unused variable 'fread_err'
>read_celfile_generic.c:695: warning: unused variable 'cur_index'
>read_celfile_generic.c:694: warning: unused variable 'j'
>read_celfile_generic.c: In function 'read_genericcel_file_stddev':
>read_celfile_generic.c:747: warning: unused variable 'fread_err'
>read_celfile_generic.c:745: warning: unused variable 'cur_index'
>read_celfile_generic.c:744: warning: unused variable 'j'
>read_celfile_generic.c: In function 'read_genericcel_file_npixels':
>read_celfile_generic.c:801: warning: unused variable 'fread_err'
>read_celfile_generic.c:799: warning: unused variable 'cur_index'
>read_celfile_generic.c:798: warning: unused variable 'j'
>read_celfile_generic.c: In function 'generic_get_masks_outliers':
>read_celfile_generic.c:863: warning: unused variable 'fread_err'
>read_celfile_generic.c:861: warning: unused variable 'cur_index'
>read_celfile_generic.c:860: warning: unused variable 'j'
>read_celfile_generic.c: In function 'generic_apply_masks':
>read_celfile_generic.c:955: warning: unused variable 'fread_err'
>read_celfile_generic.c:949: warning: unused variable 'j'
>read_celfile_generic.c: In function 'gzread_genericcel_file_intensities':
>read_celfile_generic.c:1689: warning: unused variable 'fread_err'
>read_celfile_generic.c:1687: warning: unused variable 'cur_index'
>read_celfile_generic.c:1686: warning: unused variable 'j'
>read_celfile_generic.c: In function 'gzread_genericcel_file_stddev':
>read_celfile_generic.c:1740: warning: unused variable 'fread_err'
>read_celfile_generic.c:1738: warning: unused variable 'cur_index'
>read_celfile_generic.c:1737: warning: unused variable 'j'
>read_celfile_generic.c: In function 'gzread_genericcel_file_npixels':
>read_celfile_generic.c:1794: warning: unused variable 'fread_err'
>read_celfile_generic.c:1792: warning: unused variable 'cur_index'
>read_celfile_generic.c:1791: warning: unused variable 'j'
>read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers':
>read_celfile_generic.c:1859: warning: unused variable 'fread_err'
>read_celfile_generic.c:1857: warning: unused variable 'cur_index'
>read_celfile_generic.c:1856: warning: unused variable 'j'
>read_celfile_generic.c: In function 'gzgeneric_apply_masks':
>read_celfile_generic.c:1951: warning: unused variable 'fread_err'
>read_celfile_generic.c:1945: warning: unused variable 'j'
>gcc -m64 -std=gnu99 -I/usr/include/R -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 -I/usr/local/include   -g -O2   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c read_clf.c -o read_clf.o
>read_clf.c: In function 'read_clf_header':
>read_clf.c:557: warning: unused variable 'i'
>read_clf.c: At top level:
>read_clf.c:292: warning: 'token_ends_with' defined but not used
>read_clf.c:389: warning: 'IsCommentLine' defined but not used
>gcc -m64 -std=gnu99 -I/usr/include/R -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 -I/usr/local/include   -g -O2   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c read_generic.c -o read_generic.o
>read_generic.c: In function 'determine_MIMETYPE':
>read_generic.c:399: warning: control reaches end of non-void function
>gcc -m64 -std=gnu99 -I/usr/include/R -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 -I/usr/local/include   -g -O2   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c read_pgf.c -o read_pgf.o
>read_pgf.c: In function 'read_pgf_header':
>read_pgf.c:901: warning: unused variable 'i'
>read_pgf.c: In function 'insert_level0':
>read_pgf.c:1167: warning: unused variable 'temp_ptr'
>read_pgf.c: In function 'pgf_count_probeset_types':
>read_pgf.c:1265: warning: assignment from incompatible pointer type
>read_pgf.c: At top level:
>read_pgf.c:363: warning: 'token_ends_with' defined but not used
>gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o affyio.so fread_functions.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_pgf.o -lpthread -lz -lpthread -L/usr/lib64/R/lib -lR
>** R
>** preparing package for lazy loading
>** help
>*** installing help indices
>** building package indices ...
>* DONE (affyio)
>+ test -d affyio/src
>+ cd affyio/src
>+ rm -f fread_functions.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_pgf.o affyio.so
>+ rm -rf /builddir/build/BUILDROOT/R-affyio-1.12.0-3.fc13.x86_64/usr/lib64/R/library/R.css
>+ /usr/lib/rpm/find-debuginfo.sh --strict-build-id /builddir/build/BUILD/affyio
>extracting debug info from /builddir/build/BUILDROOT/R-affyio-1.12.0-3.fc13.x86_64/usr/lib64/R/library/affyio/libs/affyio.so
>932 blocks
>+ /usr/lib/rpm/check-buildroot
>+ /usr/lib/rpm/redhat/brp-compress
>+ /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip
>+ /usr/lib/rpm/redhat/brp-strip-comment-note /usr/bin/strip /usr/bin/objdump
>+ /usr/lib/rpm/brp-python-bytecompile
>+ /usr/lib/rpm/redhat/brp-python-hardlink
>+ /usr/lib/rpm/redhat/brp-java-repack-jars
>Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.mIFKNj
>+ umask 022
>+ cd /builddir/build/BUILD
>+ cd affyio
>+ unset DISPLAY
>+ /usr/bin/R CMD check affyio
>* checking for working pdflatex ...kpathsea: Running mktexfmt pdflatex.fmt
>fmtutil: running `pdftex -ini   -jobname=pdflatex -progname=pdflatex -translate-file=cp227.tcx *pdflatex.ini' ...
>This is pdfTeXk, Version 3.141592-1.40.3 (Web2C 7.5.6) (INITEX)
> %&-line parsing enabled.
> (/usr/share/texmf/web2c/cp227.tcx)
>entering extended mode
>(/usr/share/texmf/tex/latex/latexconfig/pdflatex.ini
>(/var/lib/texmf/tex/generic/config/pdftexconfig.tex)
>(/usr/share/texmf/tex/latex/base/latex.ltx
>(/usr/share/texmf/tex/latex/base/texsys.cfg)
>./texsys.aux found
>\@currdir set to: ./.
>Assuming \openin and \input 
>have the same search path.
>Defining UNIX/DOS style filename parser.
>catcodes, registers, compatibility for TeX 2,  parameters,
>LaTeX2e <2005/12/01>
>hacks, control, par, spacing, files, font encodings, lengths,
>====================================
>Local config file fonttext.cfg used
>====================================
>(/usr/share/texmf/tex/latex/base/fonttext.cfg
>(/usr/share/texmf/tex/latex/base/fonttext.ltx
>=== Don't modify this file, use a .cfg file instead ===
>(/usr/share/texmf/tex/latex/base/omlenc.def)
>(/usr/share/texmf/tex/latex/base/t1enc.def)
>(/usr/share/texmf/tex/latex/base/ot1enc.def)
>(/usr/share/texmf/tex/latex/base/omsenc.def)
>(/usr/share/texmf/tex/latex/base/t1cmr.fd)
>(/usr/share/texmf/tex/latex/base/ot1cmr.fd)
>(/usr/share/texmf/tex/latex/base/ot1cmss.fd)
>(/usr/share/texmf/tex/latex/base/ot1cmtt.fd)))
>====================================
>Local config file fontmath.cfg used
>====================================
>(/usr/share/texmf/tex/latex/base/fontmath.cfg
>(/usr/share/texmf/tex/latex/base/fontmath.ltx
>=== Don't modify this file, use a .cfg file instead ===
>(/usr/share/texmf/tex/latex/base/omlcmm.fd)
>(/usr/share/texmf/tex/latex/base/omscmsy.fd)
>(/usr/share/texmf/tex/latex/base/omxcmex.fd)
>(/usr/share/texmf/tex/latex/base/ucmr.fd)))
>====================================
>Local config file preload.cfg used
>=====================================
>(/usr/share/texmf/tex/latex/base/preload.cfg
>(/usr/share/texmf/tex/latex/base/preload.ltx)) page nos., x-ref, environments,
>center, verbatim, math definitions, boxes, title, sectioning, contents,
>floats, footnotes, index, bibliography, output,
>===========================================
>Local configuration file hyphen.cfg used
>===========================================
>(/usr/share/texmf/tex/generic/babel/hyphen.cfg
>(/usr/share/texmf/tex/generic/hyphen/hyphen.tex)
>(/usr/share/texmf/tex/generic/hyphen/ushyphmax.tex)
>(/usr/share/texmf/tex/generic/hyphen/dumyhyph.tex)
>(/usr/share/texmf/tex/generic/hyphen/zerohyph.tex)
>(/usr/share/texmf/tex/generic/hyphen/zerohyph.tex)
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-bahyph.tex
>(/usr/share/texmf/tex/generic/hyphen/bahyph.tex))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-bghyphen.tex
>(/usr/share/texmf/tex/generic/bghyphen/bghyphen.tex
>Bulgarian hyphenation patterns
>(/usr/share/texmf/tex/generic/bghyphen/catmik.tex)
>(/usr/share/texmf/tex/generic/bghyphen/mik2t2.tex)
>(/usr/share/texmf/tex/generic/bghyphen/bghyphsi.tex)))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-copthyph.tex
>(/usr/share/texmf/tex/generic/hyphen/copthyph.tex))
>(/usr/share/texmf/tex/generic/hyphen/cyhyph.tex
>(/usr/share/texmf/tex/generic/hyphen/cathyph.tex))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-czhyph.tex
>(/usr/share/texmf/tex/generic/hyphen/czhyph.tex
>(/usr/share/texmf/tex/csplain/base/t1code.tex Font encoding set to Cork.)
>The \^, \`, \', \v, \" and \r expands to characters by Cork.
>(/usr/share/texmf/tex/csplain/base/czhyphen.tex)))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-skhyph.tex
>(/usr/share/texmf/tex/generic/hyphen/skhyph.tex
>(/usr/share/texmf/tex/csplain/base/t1code.tex Font encoding set to Cork.)
>The \^, \`, \', \v, \" and \r expands to characters by Cork.
>(/usr/share/texmf/tex/csplain/base/skhyphen.tex)))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-dehypht.tex
>(/usr/share/texmf/tex/generic/hyphen/dehypht.tex
>German Traditional Hyphenation Patterns `dehypht' Version 3.2a <1999/03/03>
>(Formerly known under the name `ghyph31' and `ghyphen'.)))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-dehyphn.tex
>(/usr/share/texmf/tex/generic/hyphen/dehyphn.tex
>New German Hyphenation Patterns `dehyphn' Rev.31 <2001-05-07> (WaS)))
>(/usr/share/texmf/tex/generic/hyphen/dkhyph.tex
>(/usr/share/texmf/tex/generic/hyphen/dkcommon.tex)
>(/usr/share/texmf/tex/generic/hyphen/dkspecial.tex)
>(/usr/share/texmf/tex/generic/hyphen/dkspecial.tex))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-eohyph.tex
>(/usr/share/texmf/tex/generic/hyphen/eohyph.tex
>Esperanto Hyphenation Patterns `eohyph', 1999-08-10))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-eshyph.tex
>(/usr/share/texmf/tex/generic/hyphen/eshyph.tex))
>(/usr/share/texmf/tex/generic/hyphen/cahyph.tex
>Catalan Hyphenation Patterns `cahyphen' Version 1.11 <2003/07/15>)
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-glhyph.tex
>(/usr/share/texmf/tex/generic/hyphen/glhyph.tex))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-ethyph.tex
>(/usr/share/texmf/tex/generic/hyphen/ethyph.tex
>(/usr/share/texmf/tex/generic/hyphen/cathyph.tex)))
>(/usr/share/texmf/tex/generic/hyphen/zerohyph.tex)
>(/usr/share/texmf/tex/generic/hyphen/fihyph.tex)
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-frhyph.tex
>(/usr/share/texmf/tex/generic/hyphen/frhyph.tex
>frhyph.tex - French hyphenation patterns (V2.12) <2002/12/11>))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-grphyph4.tex
>(/usr/share/texmf/tex/generic/hyphen/grphyph4.tex
>Hyphenation patterns for multi-accent (polytonic) Modern Greek))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-grmhyph4.tex
>(/usr/share/texmf/tex/generic/hyphen/grmhyph4.tex
>Hyphenation patterns for uni-accent (monotonic) Modern Greek))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-grahyph4.tex
>(/usr/share/texmf/tex/generic/hyphen/grahyph4.tex
>Hyphenation patterns for Ancient Greek))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-hrhyph.tex
>(/usr/share/texmf/tex/generic/hyphen/hrhyph.tex))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-huhyphn.tex
>(/usr/share/texmf/tex/generic/hyphen/huhyphn.tex
>Huhyphn - hungarian hyphenation patterns v20031107))
>(/usr/share/texmf/tex/generic/hyphen/iahyphen.tex)
>(/usr/share/texmf/tex/generic/hyphen/ibyhyph.tex
>Greek hyphenation patterns for Ibycus 4)
>(/usr/share/texmf/tex/generic/hyphen/inhyph.tex)
>(/usr/share/texmf/tex/generic/hyphen/icehyph.tex)
>(/usr/share/texmf/tex/generic/hyphen/ithyph.tex)
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-lahyph.tex
>(/usr/share/texmf/tex/generic/hyphen/lahyph.tex
>Latin Hyphenation Patterns `lahyph' Version 3.0b <2001/11/21>))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-mnhyph.tex
>(/usr/share/texmf/tex/generic/hyphen/mnhyph.tex
>mnhyphen.tex - Hyphenation Patterns for Xalx Mongolian, LMC Encoding))
>(/usr/share/texmf/tex/generic/hyphen/nehyph96.tex)
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-nohyphbx.tex
>(/usr/share/texmf/tex/generic/hyphen/nohyphbx.tex
>Hyphenation patterns for Norwegian))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-plhyph.tex
>(/usr/share/texmf/tex/generic/hyphen/plhyph.tex))
>(/usr/share/texmf/tex/generic/hyphen/pthyph.tex
>portuguese hiphenation 8 bits and -)
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-pyhyph.tex
>(/usr/share/texmf/tex/generic/hyphen/pyhyph.tex
>Hyphenation patterns for unaccented pinyin syllables (CJK 4.7.0)))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-rohyphen.tex
>(/usr/share/texmf/tex/generic/hyphen/rohyphen.tex
>Romanian Hyphenation Patterns: `rohyphen' 1.1 <29.10.1996>))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-ruhyphen.tex
>(/usr/share/texmf/tex/generic/ruhyphen/ruhyphen.tex
>(/usr/share/texmf/tex/generic/ruhyphen/catkoi.tex)
>(/usr/share/texmf/tex/generic/ruhyphen/koi2t2a.tex)
>(/usr/share/texmf/tex/generic/ruhyphen/ruhyphal.tex)
>(/usr/share/texmf/tex/generic/ruhyphen/cyryoal.tex)
>(/usr/share/texmf/tex/generic/ruhyphen/hypht2.tex)))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-sihyph.tex
>(/usr/share/texmf/tex/generic/hyphen/sihyph.tex
>Slovene Hyphenation Patterns `sihyph23' Version 2.3 <97/15/04>))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-sorhyph.tex
>(/usr/share/texmf/tex/generic/hyphen/sorhyph.tex
>Hyphenation patterns for Upper Sorbian, E. Werner
>Completely new revision 1997, March 22))
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-srhyphc.tex
>(/usr/share/texmf/tex/generic/hyphen/srhyphc.tex
>Serbian Cyrillic Hyphenation Patterns `srhyphc.tex' v1.0a <2003-06-09>))
>(/usr/share/texmf/tex/generic/hyphen/svhyph.tex
>Swedish hyphenation patterns, Jan Michael Rynning, 1994-03-03.)
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-tkhyph.tex
>(/usr/share/texmf/tex/generic/hyphen/tkhyph.tex
>(/usr/share/texmf/tex/generic/hyphen/cathyph.tex)))
>(/usr/share/texmf/tex/generic/hyphen/ukhyphen.tex)
>(/usr/share/texmf/tex/generic/xu-hyphen/xu-ukrhyph.tex
>(/usr/share/texmf/tex/generic/ukrhyph/ukrhyph.tex
>Ukrainian hyphenation patterns in t2a encoding
>(/usr/share/texmf/tex/generic/ukrhyph/catlcy.tex)
>(/usr/share/texmf/tex/generic/ukrhyph/lcy2t2a.tex)
>(/usr/share/texmf/tex/generic/ukrhyph/ukrhypmp.tex)
>(/usr/share/texmf/tex/generic/ruhyphen/hypht2.tex))))
>=================================
>Applying patch file ltpatch.ltx
>=================================
>(/usr/share/texmf/tex/latex/base/ltpatch.ltx)
> ) )
>Beginning to dump on file pdflatex.fmt
> (format=pdflatex 2009.11.18)
>5927 strings of total length 82929
>47930 memory locations dumped; current usage is 144&43637
>3390 multiletter control sequences
>\font\nullfont=nullfont
>\font\OMX/cmex/m/n/10=cmex10
>\font\tenln=line10
>\font\tenlnw=linew10
>\font\tencirc=lcircle10
>\font\tencircw=lcirclew10
>\font\OT1/cmr/m/n/5=cmr5
>\font\OT1/cmr/m/n/7=cmr7
>\font\OT1/cmr/m/n/10=cmr10
>\font\OML/cmm/m/it/5=cmmi5
>\font\OML/cmm/m/it/7=cmmi7
>\font\OML/cmm/m/it/10=cmmi10
>\font\OMS/cmsy/m/n/5=cmsy5
>\font\OMS/cmsy/m/n/7=cmsy7
>\font\OMS/cmsy/m/n/10=cmsy10
>3633 words of font info for 14 preloaded fonts
>645 hyphenation exceptions
>Hyphenation trie of length 172735 has 4897 ops out of 35111
>  138 for language 47
>  224 for language 46
>  13 for language 45
>  127 for language 44
>  62 for language 43
>  110 for language 42
>  71 for language 41
>  119 for language 40
>  68 for language 39
>  2 for language 38
>  7 for language 37
>  194 for language 36
>  756 for language 35
>  265 for language 34
>  21 for language 33
>  26 for language 32
>  35 for language 31
>  147 for language 30
>  21 for language 29
>  98 for language 28
>  38 for language 27
>  117 for language 26
>  19 for language 25
>  98 for language 24
>  18 for language 23
>  50 for language 22
>  88 for language 21
>  31 for language 20
>  45 for language 18
>  18 for language 17
>  21 for language 16
>  158 for language 15
>  145 for language 14
>  60 for language 13
>  235 for language 12
>  207 for language 11
>  248 for language 10
>  63 for language 9
>  143 for language 8
>  14 for language 7
>  12 for language 6
>  5 for language 5
>  2 for language 2
>  377 for language 1
>  181 for language 0
>No pages of output.
>Transcript written on pdflatex.log.
>fmtutil: /builddir/.texlive2007/texmf-var/web2c/pdftex/pdflatex.fmt installed.
> OK
>* using log directory '/builddir/build/BUILD/affyio/affyio.Rcheck'
>* using R version 2.10.0 (2009-10-26)
>* using session charset: UTF-8
>* checking for file 'affyio/DESCRIPTION' ... OK
>* this is package 'affyio' version '1.12.0'
>* checking package name space information ... OK
>* checking package dependencies ... OK
>* checking if this is a source package ... OK
>* checking for executable files ... OK
>* checking whether package 'affyio' can be installed ... OK
>* checking package directory ... OK
>* checking for portable file names ... OK
>* checking for sufficient/correct file permissions ... OK
>* checking DESCRIPTION meta-information ... OK
>* checking top-level files ... OK
>* checking index information ... OK
>* checking package subdirectories ... OK
>* checking R files for non-ASCII characters ... OK
>* checking R files for syntax errors ... OK
>* checking whether the package can be loaded ... OK
>* checking whether the package can be loaded with stated dependencies ... OK
>* checking whether the name space can be loaded with stated dependencies ... OK
>* checking for unstated dependencies in R code ... OK
>* checking S3 generic/method consistency ... OK
>* checking replacement functions ... OK
>* checking foreign function calls ... OK
>* checking R code for possible problems ... OK
>* checking Rd files ... OK
>* checking Rd metadata ... OK
>* checking Rd cross-references ... WARNING
>Warning: unable to access index for repository http://cran.r-project.org/src/contrib
>Warning: unable to access index for repository http://www.omegahat.org/R/src/contrib
>Warning: unable to access index for repository http://www.bioconductor.org/packages/2.5/bioc/src/contrib
>Warning: unable to access index for repository http://www.bioconductor.org/packages/2.5/data/annotation/src/contrib
>Warning: unable to access index for repository http://www.bioconductor.org/packages/2.5/data/experiment/src/contrib
>Unknown package(s) âmakecdfenvâ in Rd xrefs
>* checking for missing documentation entries ... OK
>* checking for code/documentation mismatches ... OK
>* checking Rd \usage sections ... OK
>* checking line endings in C/C++/Fortran sources/headers ... OK
>* checking line endings in Makefiles ... OK
>* checking for portable compilation flags in Makevars ... OK
>* checking for portable use of $BLAS_LIBS ... OK
>* checking examples ... NONE
>* checking PDF version of manual ... OK
>WARNING: There was 1 warning, see
>  /builddir/build/BUILD/affyio/affyio.Rcheck/00check.log
>for details
>+ exit 0
>Processing files: R-affyio-1.12.0-3.fc13.x86_64
>error: File not found: /builddir/build/BUILDROOT/R-affyio-1.12.0-3.fc13.x86_64/usr/lib64/R/library/affyio/man
>error: File not found: /builddir/build/BUILDROOT/R-affyio-1.12.0-3.fc13.x86_64/usr/lib64/R/library/affyio/latex
>error: File not found: /builddir/build/BUILDROOT/R-affyio-1.12.0-3.fc13.x86_64/usr/lib64/R/library/affyio/CONTENTS
>RPM build errors:
>    File not found: /builddir/build/BUILDROOT/R-affyio-1.12.0-3.fc13.x86_64/usr/lib64/R/library/affyio/man
>    File not found: /builddir/build/BUILDROOT/R-affyio-1.12.0-3.fc13.x86_64/usr/lib64/R/library/affyio/latex
>    File not found: /builddir/build/BUILDROOT/R-affyio-1.12.0-3.fc13.x86_64/usr/lib64/R/library/affyio/CONTENTS
>Child returncode was: 1
>EXCEPTION: Command failed. See logs for output.
> # ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/R-affyio.spec']
>Traceback (most recent call last):
>  File "/usr/lib/python2.6/site-packages/mock/trace_decorator.py", line 70, in trace
>    result = func(*args, **kw)
>  File "/usr/lib/python2.6/site-packages/mock/util.py", line 324, in do
>    raise mock.exception.Error, ("Command failed. See logs for output.\n # %s" % (command,), child.returncode)
>Error: Command failed. See logs for output.
> # ['bash', '--login', '-c', 'rpmbuild -bb --target x86_64 --nodeps builddir/build/SPECS/R-affyio.spec']
>LEAVE do --> EXCEPTION RAISED
>

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Attachments on bug 539201: 372145 | 372146 | 372147 | 372148 | 372149 | 372150