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Package 18/353HostnameOS / ArchBUILDCHECKBUILD BIN
AffyTiling 1.4.0
Charles G. Danko
Snapshot Date: 2009-12-13 23:30:35 -0800 (Sun, 13 Dec 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/AffyTiling
Last Changed Rev: 43061 / Revision: 43539
Last Changed Date: 2009-11-17 05:31:51 -0800 (Tue, 17 Nov 2009)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
Package: AffyTiling
Version: 1.4.0
Command: E:\biocbld\bbs-2.5-bioc\R\bin\R.exe CMD check --no-vignettes AffyTiling_1.4.0.tar.gz
StartedAt: 2009-12-14 03:40:36 -0800 (Mon, 14 Dec 2009)
EndedAt: 2009-12-14 03:41:20 -0800 (Mon, 14 Dec 2009)
EllapsedTime: 44.5 seconds
RetCode: 0
Status: OK
CheckDir: AffyTiling.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.5-bioc/meat/AffyTiling.Rcheck'
* using R version 2.10.0 (2009-10-26)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AffyTiling/DESCRIPTION' ... OK
* this is package 'AffyTiling' version '1.4.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'AffyTiling' can be installed ... 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 name space can be loaded with stated dependencies ... 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 ... NOTE
AnalyzeTilingCelFiles: no visible global function definition for
  'normalize.quantiles'
* 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 data for non-ASCII characters ... 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 ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

AffyTiling.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package 'AffyTiling' ...
** libs
  making DLL ...
g++ -I"e:/biocbld/bbs-2.5-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  -c fusion_sdk/file/BPMAPFileData.cpp -o fusion_sdk/file/BPMAPFileData.o
In file included from fusion_sdk/file/BPMAPFileData.cpp:20:
fusion_sdk/file/BPMAPFileData.h:29: warning: ignoring #pragma warning 
fusion_sdk/file/BPMAPFileData.cpp: In member function 'bool affxbpmap::CBPMAPFileData::ReadDataSection()':
fusion_sdk/file/BPMAPFileData.cpp:370: warning: unused variable 'probeIn'
fusion_sdk/file/BPMAPFileData.cpp:371: warning: unused variable 'probeOut'
g++ -I"e:/biocbld/bbs-2.5-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  -c fusion_sdk/file/BPMAPFileWriter.cpp -o fusion_sdk/file/BPMAPFileWriter.o
In file included from fusion_sdk/file/BPMAPFileWriter.h:26,
                 from fusion_sdk/file/BPMAPFileWriter.cpp:20:
fusion_sdk/file/BPMAPFileData.h:29: warning: ignoring #pragma warning 
fusion_sdk/file/BPMAPFileWriter.cpp:34: warning: ignoring #pragma warning 
g++ -I"e:/biocbld/bbs-2.5-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  -c fusion_sdk/file/FileIO.cpp -o fusion_sdk/file/FileIO.o
fusion_sdk/file/FileIO.cpp:29: warning: ignoring #pragma warning 
g++ -I"e:/biocbld/bbs-2.5-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  -c fusion_sdk/file/FileWriter.cpp -o fusion_sdk/file/FileWriter.o
g++ -I"e:/biocbld/bbs-2.5-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  -c R_affx_parseBPMAP.cpp -o R_affx_parseBPMAP.o
In file included from R_affx_parseBPMAP.cpp:22:
fusion_sdk/file/BPMAPFileData.h:29: warning: ignoring #pragma warning 
In file included from e:/biocbld/bbs-2.5-bioc/R/include/R.h:50,
                 from R_affx_parseBPMAP.cpp:31:
e:/biocbld/bbs-2.5-bioc/R/include/R_ext/RS.h:43:1: warning: "ERROR" redefined
In file included from c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include/windows.h:52,
                 from fusion_sdk/file/BPMAPFileData.h:30,
                 from R_affx_parseBPMAP.cpp:22:
c:\rtools\mingw\bin\../lib/gcc/mingw32/4.2.1-sjlj/../../../../include/wingdi.h:313:1: warning: 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:293: warning: embedded '\0' in format
R_affx_parseBPMAP.cpp:295: warning: embedded '\0' in format
R_affx_parseBPMAP.cpp:367: warning: embedded '\0' in format
R_affx_parseBPMAP.cpp:182: warning: 'nFeatures' may be used uninitialized in this function
R_affx_parseBPMAP.cpp:325: warning: 'UniqueID' may be used uninitialized in this function
R_affx_parseBPMAP.cpp:325: warning: 'SEQ' may be used uninitialized in this function
R_affx_parseBPMAP.cpp:325: warning: 'iIDvec' may be used uninitialized in this function
g++ -I"e:/biocbld/bbs-2.5-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  -c AnnotateProbes.cpp -o AnnotateProbes.o
AnnotateProbes.cpp: In function 'SEXPREC* AssociateRegionWithGenes(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
AnnotateProbes.cpp:73: warning: 'LOWEST_INDX' may be used uninitialized in this function
g++ -shared -s -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 -Le:/biocbld/bbs-2.5-bioc/R/bin -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
  ... done
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

** help
*** installing help indices
** building package indices ...
** MD5 sums
* DONE (AffyTiling)