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BioC 2.12: CHECK report for AffyTiling on moscato2

This page was generated on 2013-10-09 09:38:39 -0700 (Wed, 09 Oct 2013).

Package 27/671HostnameOS / ArchBUILDCHECKBUILD BIN
AffyTiling 1.18.0
Charles G. Danko
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/AffyTiling
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: AffyTiling
Version: 1.18.0
Command: rm -rf AffyTiling.buildbin-libdir && mkdir AffyTiling.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=AffyTiling.buildbin-libdir AffyTiling_1.18.0.tar.gz >AffyTiling-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=AffyTiling.buildbin-libdir --install="check:AffyTiling-install.out" --force-multiarch --no-vignettes --timings AffyTiling_1.18.0.tar.gz && mv AffyTiling.buildbin-libdir/* AffyTiling.Rcheck/ && rmdir AffyTiling.buildbin-libdir
StartedAt: 2013-10-09 00:55:26 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 00:57:06 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 100.1 seconds
RetCode: 0
Status:  OK  
CheckDir: AffyTiling.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/AffyTiling.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AffyTiling/DESCRIPTION' ... OK
* this is package 'AffyTiling' version '1.18.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'AffyTiling' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
Foreign function call with 'PACKAGE' argument in a different package:
  .Call("rma_c_complete", ..., PACKAGE = "affy")
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'E:/biocbld/bbs-2.12-bioc/meat/AffyTiling.buildbin-libdir/AffyTiling/libs/i386/AffyTiling.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'E:/biocbld/bbs-2.12-bioc/meat/AffyTiling.buildbin-libdir/AffyTiling/libs/x64/AffyTiling.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [2s] OK
** running examples for arch 'x64' ... [2s] 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

NOTE: There were 2 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/AffyTiling.Rcheck/00check.log'
for details.

AffyTiling.Rcheck/00install.out:


install for i386

* installing *source* package 'AffyTiling' ...
** libs
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/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/CRANpkg/extralibs64/local/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++ -m32 -I"E:/biocbld/BBS-2˜1.12-/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/CRANpkg/extralibs64/local/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++ -m32 -I"E:/biocbld/BBS-2˜1.12-/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/CRANpkg/extralibs64/local/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++ -m32 -I"E:/biocbld/BBS-2˜1.12-/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/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c fusion_sdk/file/FileWriter.cpp -o fusion_sdk/file/FileWriter.o
g++ -m32 -I"E:/biocbld/BBS-2˜1.12-/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/CRANpkg/extralibs64/local/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 E:/biocbld/BBS-2˜1.12-/R/include/R.h:44:0,
                 from R_affx_parseBPMAP.cpp:31:
E:/biocbld/BBS-2˜1.12-/R/include/R_ext/RS.h:45:0: warning: "ERROR" redefined [enabled by default]
c:\rtools31\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:293:78: warning: embedded '\0' in format [-Wformat-contains-nul]
R_affx_parseBPMAP.cpp:295:77: warning: embedded '\0' in format [-Wformat-contains-nul]
R_affx_parseBPMAP.cpp:367:50: warning: embedded '\0' in format [-Wformat-contains-nul]
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++ -m32 -I"E:/biocbld/BBS-2˜1.12-/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/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c AnnotateProbes.cpp -o AnnotateProbes.o
AnnotateProbes.cpp: In function 'SEXPREC* AssociateRegionWithGenes(SEXP, SEXP, SEXP, SEXP, SEXP)':
AnnotateProbes.cpp:103:3: warning: 'LOWEST_INDX' may be used uninitialized in this function [-Wuninitialized]
g++ -m32 -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/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/R/bin/i386 -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 E:/biocbld/bbs-2.12-bioc/meat/AffyTiling.buildbin-libdir/AffyTiling/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'AffyTiling' ...
** libs
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/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/CRANpkg/extralibs64/local/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"E:/biocbld/BBS-2˜1.12-/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/CRANpkg/extralibs64/local/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"E:/biocbld/BBS-2˜1.12-/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/CRANpkg/extralibs64/local/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"E:/biocbld/BBS-2˜1.12-/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/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c fusion_sdk/file/FileWriter.cpp -o fusion_sdk/file/FileWriter.o
g++ -m64 -I"E:/biocbld/BBS-2˜1.12-/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/CRANpkg/extralibs64/local/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 E:/biocbld/BBS-2˜1.12-/R/include/R.h:44:0,
                 from R_affx_parseBPMAP.cpp:31:
E:/biocbld/BBS-2˜1.12-/R/include/R_ext/RS.h:45:0: warning: "ERROR" redefined [enabled by default]
c:\rtools31\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:293:78: warning: embedded '\0' in format [-Wformat-contains-nul]
R_affx_parseBPMAP.cpp:295:77: warning: embedded '\0' in format [-Wformat-contains-nul]
R_affx_parseBPMAP.cpp:367:50: warning: embedded '\0' in format [-Wformat-contains-nul]
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"E:/biocbld/BBS-2˜1.12-/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/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c AnnotateProbes.cpp -o AnnotateProbes.o
AnnotateProbes.cpp: In function 'SEXPREC* AssociateRegionWithGenes(SEXP, SEXP, SEXP, SEXP, SEXP)':
AnnotateProbes.cpp:103:3: 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/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.12-/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 E:/biocbld/bbs-2.12-bioc/meat/AffyTiling.buildbin-libdir/AffyTiling/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AffyTiling' as AffyTiling_1.18.0.zip
* DONE (AffyTiling)