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BioC 2.12: CHECK report for Rbowtie on moscato2

This page was generated on 2013-10-09 09:39:15 -0700 (Wed, 09 Oct 2013).

Package 525/671HostnameOS / ArchBUILDCHECKBUILD BIN
Rbowtie 1.0.3
Michael Stadler
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/Rbowtie
Last Changed Rev: 76239 / Revision: 81334
Last Changed Date: 2013-05-05 00:59:16 -0700 (Sun, 05 May 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: Rbowtie
Version: 1.0.3
Command: rm -rf Rbowtie.buildbin-libdir && mkdir Rbowtie.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=Rbowtie.buildbin-libdir Rbowtie_1.0.3.tar.gz >Rbowtie-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=Rbowtie.buildbin-libdir --install="check:Rbowtie-install.out" --force-multiarch --no-vignettes --timings Rbowtie_1.0.3.tar.gz && mv Rbowtie.buildbin-libdir/* Rbowtie.Rcheck/ && rmdir Rbowtie.buildbin-libdir
StartedAt: 2013-10-09 03:46:30 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 03:50:52 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 261.6 seconds
RetCode: 0
Status:  OK  
CheckDir: Rbowtie.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/Rbowtie.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 'Rbowtie/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rbowtie' version '1.0.3'
* 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 'Rbowtie' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 13.1Mb
* 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 ... 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... [11s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
SpliceMap 0.22   0.11    6.03
** running examples for arch 'x64' ... [10s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
SpliceMap 0.24   0.14    5.61
* 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 was 1 note.
See
  'E:/biocbld/bbs-2.12-bioc/meat/Rbowtie.Rcheck/00check.log'
for details.

Rbowtie.Rcheck/00install.out:


install for i386

* installing *source* package 'Rbowtie' ...
** libs
  running 'src/Makefile.win' ...
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -static-libgcc -static-libstdc++  \""  -static-libgcc -static-libstdc++    \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`R CMD config CXX -v 2>&1 | grep \" version \"`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2   -DNDEBUG -Wall \
	-I SeqAn-1.1 \
	-o bowtie-build ebwt_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp  bowtie_build_main.cpp \
	 
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -static-libgcc -static-libstdc++  \""  -static-libgcc -static-libstdc++   \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`R CMD config CXX -v 2>&1 | grep \" version \"`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2   -DNDEBUG -Wall \
	-I SeqAn-1.1 \
	-o bowtie ebwt_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
	 
mkdir -p ../inst
cp bowtie ../inst/bowtie
cp bowtie-build ../inst/bowtie-build
cd SpliceMap; \
make -f Makefile.win; \
echo "MAKE of SpliceMap DONE"	
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp  -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -c params.cpp -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o -static-libgcc
runSpliceMap_QuasR.cpp: In function 'int main(int, char* const*)':
runSpliceMap_QuasR.cpp:108:31: warning: variable 'chr_file_list_it' set but not used [-Wunused-but-set-variable]
runSpliceMap_QuasR.cpp: In function 'void processbowtie(std::string&, std::string&)':
runSpliceMap_QuasR.cpp:1327:9: warning: variable 'min_mismatch' set but not used [-Wunused-but-set-variable]
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o -static-libgcc
amalgamateSAM.cpp: In function 'int extractId(const string&)':
amalgamateSAM.cpp:19:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
amalgamateSAM.cpp:19:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
amalgamateSAM.cpp: In function 'void update_jun_coverage(std::map<std::basic_string<char>, std::map<int, std::map<int, jun_store_ij> > >&, std::string, bool)':
amalgamateSAM.cpp:695:17: warning: variable 'front_clip' set but not used [-Wunused-but-set-variable]
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp -static-libgcc
getSpliceMapUnmapped.cpp: In function 'int extractNextId(const string&)':
getSpliceMapUnmapped.cpp:88:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
getSpliceMapUnmapped.cpp:88:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o -static-libgcc
MAKE of SpliceMap DONE
mkdir -p ../inst
cp SpliceMap/SpliceMap ../inst/SpliceMap
cp SpliceMap/amalgamateSAM ../inst/amalgamateSAM
cp SpliceMap/getSpliceMapUnmapped ../inst/getSpliceMapUnmapped
cp SpliceMap/fuseReorder ../inst/fuseReorder
cp SpliceMap/runSpliceMap_QuasR ../inst/runSpliceMap_QuasR
cp SpliceMap/sortsam ../inst/sortsam
** R
** 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 'Rbowtie' ...
** libs
  running 'src/Makefile.win' ...
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -static-libgcc -static-libstdc++  \""  -static-libgcc -static-libstdc++    \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`R CMD config CXX -v 2>&1 | grep \" version \"`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2   -DNDEBUG -Wall \
	-I SeqAn-1.1 \
	-o bowtie-build ebwt_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp  bowtie_build_main.cpp \
	 
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -static-libgcc -static-libstdc++  \""  -static-libgcc -static-libstdc++   \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`R CMD config CXX -v 2>&1 | grep \" version \"`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2   -DNDEBUG -Wall \
	-I SeqAn-1.1 \
	-o bowtie ebwt_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
	 
mkdir -p ../inst
cp bowtie ../inst/bowtie
cp bowtie-build ../inst/bowtie-build
cd SpliceMap; \
make -f Makefile.win; \
echo "MAKE of SpliceMap DONE"	
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp  -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -c params.cpp -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o -static-libgcc
runSpliceMap_QuasR.cpp: In function 'int main(int, char* const*)':
runSpliceMap_QuasR.cpp:108:31: warning: variable 'chr_file_list_it' set but not used [-Wunused-but-set-variable]
runSpliceMap_QuasR.cpp: In function 'void processbowtie(std::string&, std::string&)':
runSpliceMap_QuasR.cpp:1327:9: warning: variable 'min_mismatch' set but not used [-Wunused-but-set-variable]
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o -static-libgcc
amalgamateSAM.cpp: In function 'int extractId(const string&)':
amalgamateSAM.cpp:19:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
amalgamateSAM.cpp:19:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
amalgamateSAM.cpp: In function 'void update_jun_coverage(std::map<std::basic_string<char>, std::map<int, std::map<int, jun_store_ij> > >&, std::string, bool)':
amalgamateSAM.cpp:695:17: warning: variable 'front_clip' set but not used [-Wunused-but-set-variable]
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp -static-libgcc
getSpliceMapUnmapped.cpp: In function 'int extractNextId(const string&)':
getSpliceMapUnmapped.cpp:88:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
getSpliceMapUnmapped.cpp:88:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp -static-libgcc
`"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXX` `"E:/biocbld/BBS-2˜1.12-/R/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o -static-libgcc
MAKE of SpliceMap DONE
mkdir -p ../inst
cp SpliceMap/SpliceMap ../inst/SpliceMap
cp SpliceMap/amalgamateSAM ../inst/amalgamateSAM
cp SpliceMap/getSpliceMapUnmapped ../inst/getSpliceMapUnmapped
cp SpliceMap/fuseReorder ../inst/fuseReorder
cp SpliceMap/runSpliceMap_QuasR ../inst/runSpliceMap_QuasR
cp SpliceMap/sortsam ../inst/sortsam
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Rbowtie' as Rbowtie_1.0.3.zip
* DONE (Rbowtie)