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BioC 3.2: BUILD report for AffyTiling on moscato1

This page was generated on 2016-04-23 10:16:50 -0700 (Sat, 23 Apr 2016).

Package 30/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AffyTiling 1.28.1
Charles G. Danko
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/AffyTiling
Last Changed Rev: 115136 / Revision: 116712
Last Changed Date: 2016-03-22 13:04:32 -0700 (Tue, 22 Mar 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  ERROR  skipped 
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded [ ERROR ] skipped  skipped 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  ERROR  skipped  skipped 

Summary

Package: AffyTiling
Version: 1.28.1
Command: chmod a+r AffyTiling -R && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data AffyTiling
StartedAt: 2016-04-22 19:33:53 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 19:35:18 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 85.7 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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###
### Running command:
###
###   chmod a+r AffyTiling -R && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data AffyTiling
###
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* checking for file 'AffyTiling/DESCRIPTION' ... OK
* preparing 'AffyTiling':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
Warning: running command '"D:/biocbld/bbs-3.2-bioc/R/bin/x64/Rcmd.exe" INSTALL -l "D:\biocbld\bbs-3.2-bioc\tmpdir\RtmpCa0Grn\Rinst1f9c68433f0c" --no-multiarch "D:/biocbld/bbs-3.2-bioc/tmpdir/RtmpCa0Grn/Rbuild1f9c14ce4eff/AffyTiling"' had status 1
      -----------------------------------
* installing *source* package 'AffyTiling' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/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/r-compiling/local/local323/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-3˜1.2-B/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/r-compiling/local/local323/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-3˜1.2-B/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/r-compiling/local/local323/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-3˜1.2-B/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/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c fusion_sdk/file/FileWriter.cpp -o fusion_sdk/file/FileWriter.o
g++ -m64 -I"D:/biocbld/BBS-3˜1.2-B/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/r-compiling/local/local323/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-3˜1.2-B/R/include/R.h:50:0,
                 from R_affx_parseBPMAP.cpp:31:
D:/biocbld/BBS-3˜1.2-B/R/include/R_ext/RS.h:45:0: warning: "ERROR" redefined [enabled by default]
c:\rtools33\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: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-3˜1.2-B/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/r-compiling/local/local323/include"     -O2 -Wall  -mtune=core2 -c AnnotateProbes.cpp -o AnnotateProbes.o
AnnotateProbes.cpp: In function 'SEXPREC* AssociateRegionWithGenes(SEXP, SEXP, SEXP, SEXP, SEXP)':
AnnotateProbes.cpp:105:3: 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/r-compiling/local/local323/lib/x64 -Ld:/RCompile/r-compiling/local/local323/lib -LD:/biocbld/BBS-3˜1.2-B/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-3.2-bioc/tmpdir/RtmpCa0Grn/Rinst1f9c68433f0c/AffyTiling/libs/x64
** R
Error in .install_package_code_files(".", instdir) : 
files in 'D:/biocbld/bbs-3.2-bioc/tmpdir/RtmpCa0Grn/Rbuild1f9c14ce4eff/AffyTiling/R' missing from 'Collate' field:
  zzz.R
ERROR: unable to collate and parse R files for package 'AffyTiling'
* removing 'D:/biocbld/bbs-3.2-bioc/tmpdir/RtmpCa0Grn/Rinst1f9c68433f0c/AffyTiling'
      -----------------------------------
ERROR: package installation failed