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Package 26/516HostnameOS / ArchBUILDCHECKBUILD BIN
AffyTiling 1.12.0
Charles G. Danko
Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/AffyTiling
Last Changed Rev: 59920 / Revision: 61898
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  ERROR 

Summary

Package: AffyTiling
Version: 1.12.0
Command: rm -rf AffyTiling.buildbin-libdir && mkdir AffyTiling.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --no-multiarch --library=AffyTiling.buildbin-libdir AffyTiling_1.12.0.tar.gz
StartedAt: 2012-01-09 06:21:04 -0800 (Mon, 09 Jan 2012)
EndedAt: 2012-01-09 06:21:18 -0800 (Mon, 09 Jan 2012)
EllapsedTime: 14.1 seconds
RetCode: 0
Status:  OK  
PackageFile: AffyTiling_1.12.0.zip
PackageFileSize: 465.9 KiB

Command output

* installing *source* package 'AffyTiling' ...
** libs
x86_64-w64-mingw32-g++  -I"D:/biocbld/bbs-2.9-bioc/R/include" -imacros R_affx_constants.h -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         -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 
fusion_sdk/file/BPMAPFileData.cpp: In member function 'bool affxbpmap::CBPMAPFileData::ReadDataSection()':
fusion_sdk/file/BPMAPFileData.cpp:370:51: warning: unused variable 'probeIn'
fusion_sdk/file/BPMAPFileData.cpp:371:28: warning: unused variable 'probeOut'
x86_64-w64-mingw32-g++  -I"D:/biocbld/bbs-2.9-bioc/R/include" -imacros R_affx_constants.h -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         -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 
fusion_sdk/file/BPMAPFileWriter.cpp:34:0: warning: ignoring #pragma warning 
x86_64-w64-mingw32-g++  -I"D:/biocbld/bbs-2.9-bioc/R/include" -imacros R_affx_constants.h -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         -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 
x86_64-w64-mingw32-g++  -I"D:/biocbld/bbs-2.9-bioc/R/include" -imacros R_affx_constants.h -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         -O2 -Wall  -mtune=core2 -c fusion_sdk/file/FileWriter.cpp -o fusion_sdk/file/FileWriter.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/bbs-2.9-bioc/R/include" -imacros R_affx_constants.h -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         -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 
In file included from D:/biocbld/bbs-2.9-bioc/R/include/R.h:44:0,
                 from R_affx_parseBPMAP.cpp:31:
D:/biocbld/bbs-2.9-bioc/R/include/R_ext/RS.h:43:0: warning: "ERROR" redefined
c:/rtools214/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/wingdi.h:63:0: note: this is the location of the previous definition
R_affx_parseBPMAP.cpp: In function 'SEXPREC* R_affx_parseBPMAP(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
R_affx_parseBPMAP.cpp:201:74: warning: suggest parentheses around comparison in operand of '|'
R_affx_parseBPMAP.cpp:293:78: warning: embedded '\0' in format
R_affx_parseBPMAP.cpp:295:77: warning: embedded '\0' in format
R_affx_parseBPMAP.cpp:367:50: warning: embedded '\0' in format
R_affx_parseBPMAP.cpp:182:6: warning: 'nFeatures' may be used uninitialized in this function
R_affx_parseBPMAP.cpp:325:20: warning: 'UniqueID' may be used uninitialized in this function
R_affx_parseBPMAP.cpp:325:42: warning: 'SEQ' may be used uninitialized in this function
R_affx_parseBPMAP.cpp:325:57: warning: 'iIDvec' may be used uninitialized in this function
x86_64-w64-mingw32-g++  -I"D:/biocbld/bbs-2.9-bioc/R/include" -imacros R_affx_constants.h -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         -O2 -Wall  -mtune=core2 -c AnnotateProbes.cpp -o AnnotateProbes.o
AnnotateProbes.cpp: In function 'SEXPREC* AssociateRegionWithGenes(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
AnnotateProbes.cpp:73:6: warning: 'LOWEST_INDX' may be used uninitialized in this function
x86_64-w64-mingw32-g++ -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:/biocbld/bbs-2.9-bioc/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-2.9-bioc/meat/AffyTiling.buildbin-libdir/AffyTiling/libs/x64
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'AffyTiling.Rnw' 
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AffyTiling' as AffyTiling_1.12.0.zip

* DONE (AffyTiling)