AffyTiling 1.16.1
Charles G. Danko
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/AffyTiling | | Last Changed Rev: 73855 / Revision: 74773 | | Last Changed Date: 2013-03-01 10:54:40 -0800 (Fri, 01 Mar 2013) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
install for i386
* installing *source* package 'AffyTiling' ...
** libs
g++ -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -imacros R_affx_constants.h -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c fusion_sdk/file/BPMAPFileData.cpp -o fusion_sdk/file/BPMAPFileData.o
In file included from fusion_sdk/file/BPMAPFileData.cpp:20:0:
fusion_sdk/file/BPMAPFileData.h:29:0: warning: ignoring #pragma warning [-Wunknown-pragmas]
fusion_sdk/file/BPMAPFileData.cpp: In member function 'bool affxbpmap::CBPMAPFileData::ReadDataSection()':
fusion_sdk/file/BPMAPFileData.cpp:370:16: warning: unused variable 'probeIn' [-Wunused-variable]
fusion_sdk/file/BPMAPFileData.cpp:371:7: warning: unused variable 'probeOut' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -imacros R_affx_constants.h -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c fusion_sdk/file/BPMAPFileWriter.cpp -o fusion_sdk/file/BPMAPFileWriter.o
In file included from fusion_sdk/file/BPMAPFileWriter.h:26:0,
from fusion_sdk/file/BPMAPFileWriter.cpp:20:
fusion_sdk/file/BPMAPFileData.h:29:0: warning: ignoring #pragma warning [-Wunknown-pragmas]
fusion_sdk/file/BPMAPFileWriter.cpp:34:0: warning: ignoring #pragma warning [-Wunknown-pragmas]
fusion_sdk/file/BPMAPFileWriter.cpp: In function 'int dna_to_byte(const string&, char*)':
fusion_sdk/file/BPMAPFileWriter.cpp:203:24: warning: variable 'n_bytes' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -imacros R_affx_constants.h -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c fusion_sdk/file/FileIO.cpp -o fusion_sdk/file/FileIO.o
fusion_sdk/file/FileIO.cpp:29:0: warning: ignoring #pragma warning [-Wunknown-pragmas]
g++ -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -imacros R_affx_constants.h -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c fusion_sdk/file/FileWriter.cpp -o fusion_sdk/file/FileWriter.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -imacros R_affx_constants.h -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c R_affx_parseBPMAP.cpp -o R_affx_parseBPMAP.o
In file included from R_affx_parseBPMAP.cpp:22:0:
fusion_sdk/file/BPMAPFileData.h:29:0: warning: ignoring #pragma warning [-Wunknown-pragmas]
In file included from D:/biocbld/BBS-2˜1.11-/R/include/R.h:44:0,
from R_affx_parseBPMAP.cpp:31:
D:/biocbld/BBS-2˜1.11-/R/include/R_ext/RS.h:45:0: warning: "ERROR" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/wingdi.h:70:0: note: this is the location of the previous definition
R_affx_parseBPMAP.cpp: In function 'SEXPREC* R_affx_parseBPMAP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
R_affx_parseBPMAP.cpp:201:74: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
R_affx_parseBPMAP.cpp:293:78: warning: embedded '\0' in format [-Wformat-contains-nul]
R_affx_parseBPMAP.cpp:295:77: warning: embedded '\0' in format [-Wformat-contains-nul]
R_affx_parseBPMAP.cpp:367:50: warning: embedded '\0' in format [-Wformat-contains-nul]
R_affx_parseBPMAP.cpp:380:39: warning: 'iIDvec' may be used uninitialized in this function [-Wuninitialized]
R_affx_parseBPMAP.cpp:376:50: warning: 'SEQ' may be used uninitialized in this function [-Wuninitialized]
R_affx_parseBPMAP.cpp:368:44: warning: 'UniqueID' may be used uninitialized in this function [-Wuninitialized]
R_affx_parseBPMAP.cpp:279:78: warning: 'nFeatures' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -imacros R_affx_constants.h -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c AnnotateProbes.cpp -o AnnotateProbes.o
AnnotateProbes.cpp: In function 'SEXPREC* AssociateRegionWithGenes(SEXP, SEXP, SEXP, SEXP, SEXP)':
AnnotateProbes.cpp:103:3: warning: 'LOWEST_INDX' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -shared -s -static-libgcc -o AffyTiling.dll tmp.def fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o R_affx_parseBPMAP.o AnnotateProbes.o -lws2_32 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.11-/R/bin/i386 -lR
rm -f fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o R_affx_parseBPMAP.o AnnotateProbes.o
installing to D:/biocbld/bbs-2.11-bioc/meat/AffyTiling.buildbin-libdir/AffyTiling/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'AffyTiling.Rnw'
** testing if installed package can be loaded
install for x64
* installing *source* package 'AffyTiling' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -imacros R_affx_constants.h -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c fusion_sdk/file/BPMAPFileData.cpp -o fusion_sdk/file/BPMAPFileData.o
In file included from fusion_sdk/file/BPMAPFileData.cpp:20:0:
fusion_sdk/file/BPMAPFileData.h:29:0: warning: ignoring #pragma warning [-Wunknown-pragmas]
fusion_sdk/file/BPMAPFileData.cpp: In member function 'bool affxbpmap::CBPMAPFileData::ReadDataSection()':
fusion_sdk/file/BPMAPFileData.cpp:370:16: warning: unused variable 'probeIn' [-Wunused-variable]
fusion_sdk/file/BPMAPFileData.cpp:371:7: warning: unused variable 'probeOut' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -imacros R_affx_constants.h -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c fusion_sdk/file/BPMAPFileWriter.cpp -o fusion_sdk/file/BPMAPFileWriter.o
In file included from fusion_sdk/file/BPMAPFileWriter.h:26:0,
from fusion_sdk/file/BPMAPFileWriter.cpp:20:
fusion_sdk/file/BPMAPFileData.h:29:0: warning: ignoring #pragma warning [-Wunknown-pragmas]
fusion_sdk/file/BPMAPFileWriter.cpp:34:0: warning: ignoring #pragma warning [-Wunknown-pragmas]
fusion_sdk/file/BPMAPFileWriter.cpp: In function 'int dna_to_byte(const string&, char*)':
fusion_sdk/file/BPMAPFileWriter.cpp:203:24: warning: variable 'n_bytes' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -imacros R_affx_constants.h -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c fusion_sdk/file/FileIO.cpp -o fusion_sdk/file/FileIO.o
fusion_sdk/file/FileIO.cpp:29:0: warning: ignoring #pragma warning [-Wunknown-pragmas]
g++ -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -imacros R_affx_constants.h -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c fusion_sdk/file/FileWriter.cpp -o fusion_sdk/file/FileWriter.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -imacros R_affx_constants.h -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c R_affx_parseBPMAP.cpp -o R_affx_parseBPMAP.o
In file included from R_affx_parseBPMAP.cpp:22:0:
fusion_sdk/file/BPMAPFileData.h:29:0: warning: ignoring #pragma warning [-Wunknown-pragmas]
In file included from D:/biocbld/BBS-2˜1.11-/R/include/R.h:44:0,
from R_affx_parseBPMAP.cpp:31:
D:/biocbld/BBS-2˜1.11-/R/include/R_ext/RS.h:45:0: warning: "ERROR" redefined [enabled by default]
c:\rtools216\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/wingdi.h:70:0: note: this is the location of the previous definition
R_affx_parseBPMAP.cpp: In function 'SEXPREC* R_affx_parseBPMAP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
R_affx_parseBPMAP.cpp:201:74: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
R_affx_parseBPMAP.cpp:293:78: warning: embedded '\0' in format [-Wformat-contains-nul]
R_affx_parseBPMAP.cpp:295:77: warning: embedded '\0' in format [-Wformat-contains-nul]
R_affx_parseBPMAP.cpp:367:50: warning: embedded '\0' in format [-Wformat-contains-nul]
R_affx_parseBPMAP.cpp:380:39: warning: 'iIDvec' may be used uninitialized in this function [-Wuninitialized]
R_affx_parseBPMAP.cpp:376:50: warning: 'SEQ' may be used uninitialized in this function [-Wuninitialized]
R_affx_parseBPMAP.cpp:368:44: warning: 'UniqueID' may be used uninitialized in this function [-Wuninitialized]
R_affx_parseBPMAP.cpp:279:78: warning: 'nFeatures' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -imacros R_affx_constants.h -I. -Ifusion_sdk/calvin_files/array/src -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src -Ifusion_sdk/calvin_files/fusion/src -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter -Ifusion_sdk/calvin_files/parameter/src -Ifusion_sdk/calvin_files/parsers/src -Ifusion_sdk/calvin_files/portability/src -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file -Ifusion_sdk/portability -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c AnnotateProbes.cpp -o AnnotateProbes.o
AnnotateProbes.cpp: In function 'SEXPREC* AssociateRegionWithGenes(SEXP, SEXP, SEXP, SEXP, SEXP)':
AnnotateProbes.cpp:103:3: warning: 'LOWEST_INDX' may be used uninitialized in this function [-Wuninitialized]
g++ -m64 -shared -s -static-libgcc -o AffyTiling.dll tmp.def fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o R_affx_parseBPMAP.o AnnotateProbes.o -lws2_32 -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.11-/R/bin/x64 -lR
rm -f fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o R_affx_parseBPMAP.o AnnotateProbes.o
installing to D:/biocbld/bbs-2.11-bioc/meat/AffyTiling.buildbin-libdir/AffyTiling/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AffyTiling' as AffyTiling_1.16.1.zip
* DONE (AffyTiling)