ArrayExpressHTS 1.3.0
Angela Goncalves , Andrew Tikhonov
| Snapshot Date: 2011-06-15 19:55:29 -0700 (Wed, 15 Jun 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ArrayExpressHTS | | Last Changed Rev: 55212 / Revision: 56217 | | Last Changed Date: 2011-05-03 06:23:29 -0700 (Tue, 03 May 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | N O T S U P P O R T E D |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | N O T S U P P O R T E D |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | N O T S U P P O R T E D |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=ArrayExpressHTS.buildbin-libdir ArrayExpressHTS_1.3.0.tar.gz'
>>>>>>>
* installing *source* package ‘ArrayExpressHTS’ ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c addXS.c -o addXS.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c fltbam.c -o fltbam.o
In file included from hashtable_itr.h:6,
from fltbam.c:4:
hashtable_private.h:35: warning: ISO C does not allow extra ‘;’ outside of a function
fltbam.c: In function ‘equalkeys’:
fltbam.c:40: warning: pointer targets in passing argument 1 of ‘strcmp’ differ in signedness
fltbam.c:40: warning: pointer targets in passing argument 2 of ‘strcmp’ differ in signedness
fltbam.c: In function ‘fltbam’:
fltbam.c:125: warning: pointer targets in passing argument 1 of ‘strcpy’ differ in signedness
fltbam.c:126: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
fltbam.c: At top level:
hashtable_itr.h:46: warning: inline function ‘hashtable_iterator_value’ declared but never defined
hashtable_itr.h:32: warning: inline function ‘hashtable_iterator_key’ declared but never defined
hashtable_itr.h:46: warning: inline function ‘hashtable_iterator_value’ declared but never defined
hashtable_itr.h:32: warning: inline function ‘hashtable_iterator_key’ declared but never defined
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c functions.c -o functions.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c hashtable.c -o hashtable.o
In file included from hashtable.c:2:
hashtable_private.h:35: warning: ISO C does not allow extra ‘;’ outside of a function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c hashtable_itr.c -o hashtable_itr.o
In file included from hashtable_itr.c:4:
hashtable_private.h:35: warning: ISO C does not allow extra ‘;’ outside of a function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c hashtable_utility.c -o hashtable_utility.o
In file included from hashtable_utility.c:4:
hashtable_private.h:35: warning: ISO C does not allow extra ‘;’ outside of a function
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ArrayExpressHTS.so addXS.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o -L/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/usrlib/i386 -lbam -lbcf -ltabix -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/i386
*** arch - ppc
Error in system.file("usretc", .Platform[["r_arch"]], "Rsamtools.mk", :
no file found
Calls: cat -> system.file
Execution halted
Error in system.file("usretc", .Platform[["r_arch"]], "Rsamtools.mk", :
no file found
Calls: cat -> system.file
Execution halted
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c addXS.c -o addXS.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c fltbam.c -o fltbam.o
In file included from hashtable_itr.h:6,
from fltbam.c:4:
hashtable_private.h:35: warning: ISO C does not allow extra ‘;’ outside of a function
fltbam.c: In function ‘equalkeys’:
fltbam.c:40: warning: pointer targets in passing argument 1 of ‘strcmp’ differ in signedness
fltbam.c:40: warning: pointer targets in passing argument 2 of ‘strcmp’ differ in signedness
fltbam.c: In function ‘fltbam’:
fltbam.c:125: warning: pointer targets in passing argument 1 of ‘strcpy’ differ in signedness
fltbam.c:126: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
fltbam.c: At top level:
hashtable_itr.h:46: warning: inline function ‘hashtable_iterator_value’ declared but never defined
hashtable_itr.h:32: warning: inline function ‘hashtable_iterator_key’ declared but never defined
hashtable_itr.h:46: warning: inline function ‘hashtable_iterator_value’ declared but never defined
hashtable_itr.h:32: warning: inline function ‘hashtable_iterator_key’ declared but never defined
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c functions.c -o functions.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c hashtable.c -o hashtable.o
In file included from hashtable.c:2:
hashtable_private.h:35: warning: ISO C does not allow extra ‘;’ outside of a function
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c hashtable_itr.c -o hashtable_itr.o
In file included from hashtable_itr.c:4:
hashtable_private.h:35: warning: ISO C does not allow extra ‘;’ outside of a function
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/ppc -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c hashtable_utility.c -o hashtable_utility.o
In file included from hashtable_utility.c:4:
hashtable_private.h:35: warning: ISO C does not allow extra ‘;’ outside of a function
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ArrayExpressHTS.so addXS.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/ppc
*** arch - x86_64
Error in system.file("usretc", .Platform[["r_arch"]], "Rsamtools.mk", :
no file found
Calls: cat -> system.file
Execution halted
Error in system.file("usretc", .Platform[["r_arch"]], "Rsamtools.mk", :
no file found
Calls: cat -> system.file
Execution halted
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c addXS.c -o addXS.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c fltbam.c -o fltbam.o
In file included from hashtable_itr.h:6,
from fltbam.c:4:
hashtable_private.h:35: warning: ISO C does not allow extra ‘;’ outside of a function
fltbam.c: In function ‘equalkeys’:
fltbam.c:40: warning: pointer targets in passing argument 1 of ‘strcmp’ differ in signedness
fltbam.c:40: warning: pointer targets in passing argument 2 of ‘strcmp’ differ in signedness
fltbam.c: In function ‘fltbam’:
fltbam.c:125: warning: pointer targets in passing argument 1 of ‘strcpy’ differ in signedness
fltbam.c:126: warning: pointer targets in passing argument 1 of ‘strlen’ differ in signedness
fltbam.c: At top level:
hashtable_itr.h:46: warning: inline function ‘hashtable_iterator_value’ declared but never defined
hashtable_itr.h:32: warning: inline function ‘hashtable_iterator_key’ declared but never defined
hashtable_itr.h:46: warning: inline function ‘hashtable_iterator_value’ declared but never defined
hashtable_itr.h:32: warning: inline function ‘hashtable_iterator_key’ declared but never defined
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c functions.c -o functions.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c hashtable.c -o hashtable.o
In file included from hashtable.c:2:
hashtable_private.h:35: warning: ISO C does not allow extra ‘;’ outside of a function
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c hashtable_itr.c -o hashtable_itr.o
In file included from hashtable_itr.c:4:
hashtable_private.h:35: warning: ISO C does not allow extra ‘;’ outside of a function
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/x86_64 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rsamtools/include" -fPIC -g -O2 -Wall -pedantic -c hashtable_utility.c -o hashtable_utility.o
In file included from hashtable_utility.c:4:
hashtable_private.h:35: warning: ISO C does not allow extra ‘;’ outside of a function
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o ArrayExpressHTS.so addXS.o fltbam.o functions.o hashtable.o hashtable_itr.o hashtable_utility.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/x86_64
** R
** inst
** preparing package for lazy loading
Loading required package: MASS
Loading required package: lpSolve
Loading required package: IRanges
Attaching package: ‘IRanges’
The following object(s) are masked from ‘package:base’:
Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union
Loading required package: GenomicRanges
Loading required package: Biostrings
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘ArrayExpressHTS.Rnw’
** testing if installed package can be loaded
Thu Jun 16 05:47:54 2011 [AEHTS] [TRACE] --> initDefaultEnvironment
* DONE (ArrayExpressHTS)
>>>>>>>
>>>>>>> FIXING LINKS FOR ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/i386/ArrayExpressHTS.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/i386/ArrayExpressHTS.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/i386/ArrayExpressHTS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/i386/ArrayExpressHTS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/i386/ArrayExpressHTS.so"
>>>>>>>
>>>>>>> FIXING LINKS FOR ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/ppc/ArrayExpressHTS.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/ppc/ArrayExpressHTS.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/ppc/ArrayExpressHTS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/ppc/ArrayExpressHTS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/ppc/ArrayExpressHTS.so"
>>>>>>>
>>>>>>> FIXING LINKS FOR ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgcc_s.1.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libgfortran.2.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.5.2.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libreadline.dylib" "ArrayExpressHTS.buildbin-libdir/ArrayExpressHTS/libs/x86_64/ArrayExpressHTS.so"