Rbowtie 1.4.5
Michael Stadler
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/Rbowtie | | Last Changed Rev: 91054 / Revision: 95116 | | Last Changed Date: 2014-06-06 08:34:15 -0700 (Fri, 06 Jun 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | ERROR | skipped | skipped |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
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### Running command:
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### /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings Rbowtie_1.4.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/Rbowtie.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rbowtie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rbowtie’ version ‘1.4.5’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Rbowtie’ can be installed ... [71s/72s] OK
* checking installed package size ... NOTE
installed size is 15.5Mb
* checking package directory ... OK
* checking ‘build’ 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
* 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 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 ... NOTE
Package unavailable to check Rd xrefs: ‘QuasR’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [2s/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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 2 notes.
See
‘/home/biocbuild/bbs-2.14-bioc/meat/Rbowtie.Rcheck/00check.log’
for details.
* installing *source* package ‘Rbowtie’ ...
** libs
** arch -
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2 -Wall -g -O2 -Wall \"" -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2 -Wall -g -O2 -Wall \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -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 \
-lpthread
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2 -Wall -g -O2 -Wall \"" -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2 -Wall -g -O2 -Wall \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -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 \
-lpthread
mkdir -p ../inst
cp bowtie ../inst/bowtie
cp bowtie-build ../inst/bowtie-build
cd SpliceMap; \
make -f Makefile; \
echo "MAKE of SpliceMap DONE"
make[1]: Entering directory `/home/biocbuild/bbs-2.14-bioc/meat/Rbowtie.Rcheck/00_pkg_src/Rbowtie/src/SpliceMap'
`"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp
`"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXXFLAGS` -c params.cpp
`"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp
`"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o
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]
`"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o
`"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o
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]
`"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp
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]
`"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp
`"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.14-bioc/R/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o
make[1]: Leaving directory `/home/biocbuild/bbs-2.14-bioc/meat/Rbowtie.Rcheck/00_pkg_src/Rbowtie/src/SpliceMap'
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
* DONE (Rbowtie)