MEDIPS 1.1.2
Lukas Chavez
| Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MEDIPS | | Last Changed Rev: 50434 / Revision: 53255 | | Last Changed Date: 2010-10-25 03:13:33 -0700 (Mon, 25 Oct 2010) |
| lamb2 | Linux (openSUSE 11.2) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.4) / i386 | OK | OK | [ OK ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=MEDIPS.buildbin-libdir MEDIPS_1.1.2.tar.gz'
>>>>>>>
* installing *source* package 'MEDIPS' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c annotate.c -o annotate.o
annotate.c: In function 'annotate':
annotate.c:21: warning: suggest parentheses around comparison in operand of &
annotate.c:32: warning: suggest parentheses around comparison in operand of &
annotate.c:43: warning: suggest parentheses around comparison in operand of &
annotate.c:8: warning: unused variable 'rj'
annotate.c:8: warning: unused variable 'aj'
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c calibration.c -o calibration.o
calibration.c: In function 'calibration':
calibration.c:10: warning: suggest parentheses around comparison in operand of &
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c coupling.c -o coupling.o
coupling.c: In function 'coupling':
coupling.c:26: warning: statement with no effect
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c profile.c -o profile.o
profile.c: In function 'profile':
profile.c:42: warning: unused variable 'wie'
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:34: warning: unused variable 'items'
profile.c:11: warning: unused variable 'pvalue'
profile.c:11: warning: unused variable 'Val'
profile.c:25: warning: 'ptrgenome_norm2' may be used uninitialized in this function
profile.c:25: warning: 'ptrgenome_raw2' may be used uninitialized in this function
profile.c:13: warning: 'ptr_input' may be used uninitialized in this function
profile.c:11: warning: 'nY' may be used uninitialized in this function
profile.c:11: warning: 'Y' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c roiprofile.c -o roiprofile.o
roiprofile.c: In function 'calculate':
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:12: warning: unused variable 'Val'
roiprofile.c: In function 'roiprofile':
roiprofile.c:280: warning: suggest parentheses around comparison in operand of &
roiprofile.c:282: warning: suggest parentheses around comparison in operand of &
roiprofile.c:294: warning: suggest parentheses around comparison in operand of &
roiprofile.c:296: warning: suggest parentheses around comparison in operand of &
roiprofile.c:248: warning: unused variable 'nProtected'
roiprofile.c: In function 'calculate':
roiprofile.c:29: warning: 'ptrinput' may be used uninitialized in this function
roiprofile.c:29: warning: 'IN' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o MEDIPS.so annotate.o calibration.o coupling.o profile.o roiprofile.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/MEDIPS.buildbin-libdir/MEDIPS/libs/i386
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c annotate.c -o annotate.o
annotate.c: In function 'annotate':
annotate.c:21: warning: suggest parentheses around comparison in operand of &
annotate.c:32: warning: suggest parentheses around comparison in operand of &
annotate.c:43: warning: suggest parentheses around comparison in operand of &
annotate.c:8: warning: unused variable 'rj'
annotate.c:8: warning: unused variable 'aj'
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c calibration.c -o calibration.o
calibration.c: In function 'calibration':
calibration.c:10: warning: suggest parentheses around comparison in operand of &
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c coupling.c -o coupling.o
coupling.c: In function 'coupling':
coupling.c:26: warning: statement with no effect
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c profile.c -o profile.o
profile.c: In function 'profile':
profile.c:42: warning: unused variable 'wie'
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:34: warning: unused variable 'items'
profile.c:11: warning: unused variable 'pvalue'
profile.c:11: warning: unused variable 'Val'
profile.c:25: warning: 'ptrgenome_norm2' may be used uninitialized in this function
profile.c:25: warning: 'ptrgenome_raw2' may be used uninitialized in this function
profile.c:13: warning: 'ptr_input' may be used uninitialized in this function
profile.c:11: warning: 'nY' may be used uninitialized in this function
profile.c:11: warning: 'Y' may be used uninitialized in this function
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c roiprofile.c -o roiprofile.o
roiprofile.c: In function 'calculate':
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:12: warning: unused variable 'Val'
roiprofile.c: In function 'roiprofile':
roiprofile.c:280: warning: suggest parentheses around comparison in operand of &
roiprofile.c:282: warning: suggest parentheses around comparison in operand of &
roiprofile.c:294: warning: suggest parentheses around comparison in operand of &
roiprofile.c:296: warning: suggest parentheses around comparison in operand of &
roiprofile.c:248: warning: unused variable 'nProtected'
roiprofile.c: In function 'calculate':
roiprofile.c:29: warning: 'ptrinput' may be used uninitialized in this function
roiprofile.c:29: warning: 'IN' may be used uninitialized in this function
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o MEDIPS.so annotate.o calibration.o coupling.o profile.o roiprofile.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/MEDIPS.buildbin-libdir/MEDIPS/libs/ppc
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c annotate.c -o annotate.o
annotate.c: In function 'annotate':
annotate.c:21: warning: suggest parentheses around comparison in operand of &
annotate.c:32: warning: suggest parentheses around comparison in operand of &
annotate.c:43: warning: suggest parentheses around comparison in operand of &
annotate.c:8: warning: unused variable 'rj'
annotate.c:8: warning: unused variable 'aj'
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c calibration.c -o calibration.o
calibration.c: In function 'calibration':
calibration.c:10: warning: suggest parentheses around comparison in operand of &
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c coupling.c -o coupling.o
coupling.c: In function 'coupling':
coupling.c:26: warning: statement with no effect
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c profile.c -o profile.o
profile.c: In function 'profile':
profile.c:42: warning: unused variable 'wie'
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:221: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:227: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:263: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:269: warning: suggest parentheses around comparison in operand of &
profile.c:34: warning: unused variable 'items'
profile.c:11: warning: unused variable 'pvalue'
profile.c:11: warning: unused variable 'Val'
profile.c:25: warning: 'ptrgenome_norm2' may be used uninitialized in this function
profile.c:25: warning: 'ptrgenome_raw2' may be used uninitialized in this function
profile.c:13: warning: 'ptr_input' may be used uninitialized in this function
profile.c:11: warning: 'nY' may be used uninitialized in this function
profile.c:11: warning: 'Y' may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c roiprofile.c -o roiprofile.o
roiprofile.c: In function 'calculate':
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:181: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:186: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:221: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:226: warning: suggest parentheses around comparison in operand of &
roiprofile.c:12: warning: unused variable 'Val'
roiprofile.c: In function 'roiprofile':
roiprofile.c:280: warning: suggest parentheses around comparison in operand of &
roiprofile.c:282: warning: suggest parentheses around comparison in operand of &
roiprofile.c:294: warning: suggest parentheses around comparison in operand of &
roiprofile.c:296: warning: suggest parentheses around comparison in operand of &
roiprofile.c:248: warning: unused variable 'nProtected'
roiprofile.c: In function 'calculate':
roiprofile.c:29: warning: 'ptrinput' may be used uninitialized in this function
roiprofile.c:29: warning: 'IN' may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o MEDIPS.so annotate.o calibration.o coupling.o profile.o roiprofile.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/MEDIPS.buildbin-libdir/MEDIPS/libs/x86_64
** R
** inst
** preparing package for lazy loading
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 ...
** testing if installed package can be loaded
* DONE (MEDIPS)
>>>>>>>
>>>>>>> FIXING LINKS FOR MEDIPS.buildbin-libdir/MEDIPS/libs/i386/MEDIPS.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "MEDIPS.buildbin-libdir/MEDIPS/libs/i386/MEDIPS.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "MEDIPS.buildbin-libdir/MEDIPS/libs/i386/MEDIPS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "MEDIPS.buildbin-libdir/MEDIPS/libs/i386/MEDIPS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "MEDIPS.buildbin-libdir/MEDIPS/libs/i386/MEDIPS.so"
>>>>>>>
>>>>>>> FIXING LINKS FOR MEDIPS.buildbin-libdir/MEDIPS/libs/ppc/MEDIPS.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "MEDIPS.buildbin-libdir/MEDIPS/libs/ppc/MEDIPS.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "MEDIPS.buildbin-libdir/MEDIPS/libs/ppc/MEDIPS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "MEDIPS.buildbin-libdir/MEDIPS/libs/ppc/MEDIPS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "MEDIPS.buildbin-libdir/MEDIPS/libs/ppc/MEDIPS.so"
>>>>>>>
>>>>>>> FIXING LINKS FOR MEDIPS.buildbin-libdir/MEDIPS/libs/x86_64/MEDIPS.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "MEDIPS.buildbin-libdir/MEDIPS/libs/x86_64/MEDIPS.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "MEDIPS.buildbin-libdir/MEDIPS/libs/x86_64/MEDIPS.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "MEDIPS.buildbin-libdir/MEDIPS/libs/x86_64/MEDIPS.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "MEDIPS.buildbin-libdir/MEDIPS/libs/x86_64/MEDIPS.so"