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Package 494/631HostnameOS / ArchBUILDCHECKBUILD BIN
Rbowtie 0.99.2
Michael Stadler
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rbowtie
Last Changed Rev: 71993 / Revision: 72575
Last Changed Date: 2012-12-17 05:42:16 -0800 (Mon, 17 Dec 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: Rbowtie
Version: 0.99.2
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings Rbowtie_0.99.2.tar.gz
StartedAt: 2013-01-16 05:41:31 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 05:43:37 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 125.8 seconds
RetCode: 0
Status:  OK 
CheckDir: Rbowtie.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Rbowtie.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘0.99.2’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 11.8Mb
* 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
* 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 ... 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 was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/Rbowtie.Rcheck/00check.log’
for details.

Rbowtie.Rcheck/00install.out:

* installing *source* package ‘Rbowtie’ ...
** libs
** arch - 
cat ebwt_build.cpp ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp pool.h filebuf.h hit.h random_source.h assert_helpers.h qual.h range_chaser.h ebwt.h blockwise_sa.h range.h endian_swap.h mm.h spinlock.h aligner_metrics.h pat.h color_dec.h ebwt_search_backtrack.h bitpack.h ebwt_search_util.h sam.h reference.h aligner_1mm.h multikey_qsort.h range_source.h auto_array.h word_io.h sequence_io.h log.h aligner.h search_globals.h alphabet.h refmap.h binary_sa_search.h threading.h annot.h row_chaser.h ref_read.h zbox.h aligner_23mm.h color.h hit_set.h timer.h aligner_0mm.h str_util.h shmem.h ref_aligner.h formats.h tokenize.h edit.h diff_sample.h aligner_seed_mm.h bitset.h range_cache.h | md5sum | awk '{print $1}' > .bowtie-build.md5
/usr/bin/g++ -O3  -DCOMPILER_OPTIONS="\"-O3  \""  \
	-DEBWT_BUILD_HASH=`cat .bowtie-build.md5` \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_PTHREADS -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.c shmem.cpp edit.cpp ebwt.cpp  bowtie_build_main.cpp \
	 
cat ebwt_search.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 ccnt_lut.cpp ref_read.cpp alphabet.c shmem.cpp edit.cpp ebwt.cpp pool.h filebuf.h hit.h random_source.h assert_helpers.h qual.h range_chaser.h ebwt.h blockwise_sa.h range.h endian_swap.h mm.h spinlock.h aligner_metrics.h pat.h color_dec.h ebwt_search_backtrack.h bitpack.h ebwt_search_util.h sam.h reference.h aligner_1mm.h multikey_qsort.h range_source.h auto_array.h word_io.h sequence_io.h log.h aligner.h search_globals.h alphabet.h refmap.h binary_sa_search.h threading.h annot.h row_chaser.h ref_read.h zbox.h aligner_23mm.h color.h hit_set.h timer.h aligner_0mm.h str_util.h shmem.h ref_aligner.h formats.h tokenize.h edit.h diff_sample.h aligner_seed_mm.h bitset.h range_cache.h search_seeded_phase3.c search_23mm_phase2.c search_23mm_phase1.c search_23mm_phase3.c search_1mm_phase1.c search_seeded_phase2.c search_1mm_phase2.c search_seeded_phase4.c search_seeded_phase1.c | md5sum | awk '{print $1}' > .bowtie.md5
/usr/bin/g++ -O3  -DCOMPILER_OPTIONS="\"-O3  \""  \
	-DEBWT_SEARCH_HASH=`cat .bowtie.md5` \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_PTHREADS -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.c shmem.cpp edit.cpp ebwt.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 `/loc/home/biocbuild/bbs-2.12-bioc/meat/Rbowtie.Rcheck/00_pkg_src/Rbowtie/src/SpliceMap'
`"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp
`"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXXFLAGS` -c params.cpp
`"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp
`"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o
`"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o
`"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o
`"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp
`"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp
`"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-2.12-bioc/R/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o
make[1]: Leaving directory `/loc/home/biocbuild/bbs-2.12-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
   ‘Rbowtie-Overview.Rnw’ 
** testing if installed package can be loaded

* DONE (Rbowtie)

Rbowtie.Rcheck/Rbowtie-Ex.timings:

nameusersystemelapsed
Rbowtie-package0.0040.0000.006
Rbowtie0.8280.4161.256
SpliceMap0.4800.2281.607