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BioC 3.3: BUILD report for AffyTiling on zin2

This page was generated on 2016-10-13 12:42:01 -0700 (Thu, 13 Oct 2016).

Package 30/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AffyTiling 1.30.0
Charles G. Danko
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/AffyTiling
Last Changed Rev: 117079 / Revision: 122332
Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded [ ERROR ] skipped 
moscato2 Windows Server 2008 R2 Enterprise SP1 (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: 1.30.0
Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data AffyTiling
StartedAt: 2016-10-12 18:59:59 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 19:00:02 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 3.0 seconds
RetCode: 1
Status:  ERROR 
PackageFile: None
PackageFileSize: NA

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R 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
      -----------------------------------
* installing *source* package ‘AffyTiling’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -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_ -I/usr/local/include    -fpic  -g -O2  -Wall -O0 -c fusion_sdk/file/BPMAPFileData.cpp -o fusion_sdk/file/BPMAPFileData.o
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]
  unsigned char probeIn[PROBE_STORAGE_BUFFER_LENGTH]="";
                ^
fusion_sdk/file/BPMAPFileData.cpp:371:7: warning: unused variable ‘probeOut’ [-Wunused-variable]
  char probeOut[probeBufSize]="";
       ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -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_ -I/usr/local/include    -fpic  -g -O2  -Wall -O0 -c fusion_sdk/file/BPMAPFileWriter.cpp -o fusion_sdk/file/BPMAPFileWriter.o
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]
   unsigned short i,j,k,n_bytes;
                        ^
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -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_ -I/usr/local/include    -fpic  -g -O2  -Wall -O0 -c fusion_sdk/file/FileIO.cpp -o fusion_sdk/file/FileIO.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -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_ -I/usr/local/include    -fpic  -g -O2  -Wall -O0 -c fusion_sdk/file/FileWriter.cpp -o fusion_sdk/file/FileWriter.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG -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_ -I/usr/local/include    -fpic  -g -O2  -Wall -O0 -c R_affx_parseBPMAP.cpp -o R_affx_parseBPMAP.o
In file included from R_affx_parseBPMAP.cpp:31:0:
/home/biocbuild/bbs-3.3-bioc/R/include/S.h:41:3: error: #error S.h can not be used from C++ code: use R.h instead
 # error S.h can not be used from C++ code: use R.h instead
   ^
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:203:43: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
                 if(INTEGER(seqindices)[i] < 0 | INTEGER(seqindices)[i] > nSequences)
                                           ^
make: *** [R_affx_parseBPMAP.o] Error 1
ERROR: compilation failed for package ‘AffyTiling’
* removing ‘/tmp/RtmpFmvLFj/Rinst63033d453051/AffyTiling’
      -----------------------------------
ERROR: package installation failed