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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: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch AffyTiling_1.12.0.tar.gz
StartedAt: 2012-01-09 01:03:06 -0800 (Mon, 09 Jan 2012)
EndedAt: 2012-01-09 01:03:48 -0800 (Mon, 09 Jan 2012)
EllapsedTime: 42.3 seconds
RetCode: 0
Status:  OK  
CheckDir: AffyTiling.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/AffyTiling.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AffyTiling/DESCRIPTION' ... OK
* this is package 'AffyTiling' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'AffyTiling' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

AffyTiling.Rcheck/00install.out:

* installing *source* package 'AffyTiling' ...
** libs
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/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˜1.9-B/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˜1.9-B/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˜1.9-B/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˜1.9-B/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˜1.9-B/R/include/R.h:44:0,
                 from R_affx_parseBPMAP.cpp:31:
D:/biocbld/BBS-2˜1.9-B/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˜1.9-B/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˜1.9-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-2.9-bioc/meat/AffyTiling.Rcheck/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

* DONE (AffyTiling)

AffyTiling.Rcheck/AffyTiling-Ex.timings:

nameusersystemelapsed
AnalyzeTilingCelFiles0.010.000.01
AssociateWithGenes0.080.020.10
AssociateWithInterval0.030.000.03
TilingCelFiles2Probesets000
parseBPMAP000