Michael Stadler
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/Rbowtie |
| Branch: RELEASE_3_9 |
| Last Commit: 512cdaa |
| Last Changed Date: 2019-05-02 11:53:40 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:27:21 -0400 (Wed, 16 Oct 2019).
| Package 1319/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rbowtie 1.24.0 Michael Stadler
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Rbowtie |
| Version: 1.24.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:Rbowtie.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Rbowtie_1.24.0.tar.gz |
| StartedAt: 2019-10-16 06:22:15 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:22:51 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 35.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rbowtie.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:Rbowtie.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Rbowtie_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rbowtie.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-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 '1.24.0'
* 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 'Rbowtie' can be installed ... OK
* checking installed package size ... NOTE
installed size is 15.0Mb
* 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 ... 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 GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
SpliceMap 0.03 0.07 10.17
* 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
* DONE
Status: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rbowtie.Rcheck/00check.log'
for details.
Rbowtie.Rcheck/00install.out
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch Rbowtie
###
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* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
* installing *source* package 'Rbowtie' ...
** using staged installation
** libs
running 'src/Makefile.win' ...
C:/Rtools/mingw_64/bin//g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64 -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY \"" -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY \
-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 -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \
-isystem ./SeqAn-1.1 -I third_party -I third_party \
-o bowtie-build-s ebwt_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp bowtie_build_main.cpp \
-lz
In file included from ebwt.h:31:0,
from ebwt_build.cpp:11:
hit.h: In member function 'void HitSink::maybeFlush(size_t)':
hit.h:580:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(ptCounts_[threadId] >= perThreadBufSize_) {
^
In file included from ebwt.h:39:0,
from ebwt_build.cpp:11:
reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const':
reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
uint64_t origBufOff = bufOff;
^
In file included from ebwt.h:27:0,
from ebwt_build.cpp:11:
blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = seqan::String, seqan::Alloc >; TIndexOffU = unsigned int]':
ebwt_build.cpp:673:1: required from here
blockwise_sa.h:305:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < length(_sampleSuffs) + 1; i++) {
^
blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = seqan::String, seqan::Packed<> >; TIndexOffU = unsigned int]':
ebwt_build.cpp:673:1: required from here
blockwise_sa.h:305:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
C:/Rtools/mingw_64/bin//g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64 -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY \"" -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY \
-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 -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \
-isystem ./SeqAn-1.1 -I third_party -I third_party \
-o bowtie-align-s 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 sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
-lz
In file included from ebwt.h:31:0,
from ebwt_search.cpp:21:
hit.h: In member function 'void HitSink::maybeFlush(size_t)':
hit.h:580:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(ptCounts_[threadId] >= perThreadBufSize_) {
^
In file included from ebwt.h:39:0,
from ebwt_search.cpp:21:
reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const':
reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
uint64_t origBufOff = bufOff;
^
pat.cpp: In member function 'std::pair PatternSourcePerThread::nextReadPair()':
pat.cpp:109:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
bool this_is_last = buf_.cur_buf_ == last_batch_size_-1;
^
pat.cpp: In member function 'virtual bool FastaPatternSource::parse(Read&, Read&, TReadId) const':
pat.cpp:711:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(size_t i = 0; i < seqoff - trim3; i++) {
^
pat.cpp: In member function 'virtual bool FastaContinuousPatternSource::parse(Read&, Read&, TReadId) const':
pat.cpp:888:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(size_t i = 0; i < seqoff; i++) {
^
In file included from ebwt_search_util.h:9:0,
from ebwt_search_util.cpp:1:
hit.h: In member function 'void HitSink::maybeFlush(size_t)':
hit.h:580:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(ptCounts_[threadId] >= perThreadBufSize_) {
^
In file included from sam.cpp:12:0:
hit.h: In member function 'void HitSink::maybeFlush(size_t)':
hit.h:580:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(ptCounts_[threadId] >= perThreadBufSize_) {
^
In file included from hit.cpp:1:0:
hit.h: In member function 'void HitSink::maybeFlush(size_t)':
hit.h:580:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(ptCounts_[threadId] >= perThreadBufSize_) {
^
mkdir -p ../inst
cp bowtie-align-s ../inst/bowtie
cp bowtie-build-s ../inst/bowtie-build
cd SpliceMap; \
make -f Makefile.win; \
echo "MAKE of SpliceMap DONE"
`"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp -static-libgcc
`"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -c params.cpp -static-libgcc
`"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp -static-libgcc
`"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/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:537:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (line.length() > head_clip_length) {
^
runSpliceMap_QuasR.cpp:595:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (line.length() > head_clip_length) {
^
runSpliceMap_QuasR.cpp:716:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (line.length() > head_clip_length) {
^
runSpliceMap_QuasR.cpp:841:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (line.length() > head_clip_length) {
^
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]
int min_mismatch;
^
`"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o -static-libgcc
sortsam.cpp: In function 'int main(int, char* const*)':
sortsam.cpp:189:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (nmloc == string::npos) { // unaligned, no NM tag
^
sortsam.cpp:194:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (nmloc2 == string::npos) {
^
sortsam.cpp:231:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (nmloc == string::npos) { // unaligned, no NM tag
^
sortsam.cpp:236:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (nmloc2 == string::npos) {
^
`"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/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:19:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(start_pos != string::npos && end_pos != string::npos)
^
amalgamateSAM.cpp:19:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(start_pos != string::npos && end_pos != string::npos)
^
amalgamateSAM.cpp: In function 'void update_jun_coverage(std::map, std::map > >&, std::string, bool)':
amalgamateSAM.cpp:695:17: warning: variable 'front_clip' set but not used [-Wunused-but-set-variable]
uint_fast32_t front_clip = 0;
^
`"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp -static-libgcc
getSpliceMapUnmapped.cpp: In function 'int extractNextId(const string&)':
getSpliceMapUnmapped.cpp:88:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(start_pos != string::npos && end_pos != string::npos)
^
getSpliceMapUnmapped.cpp:88:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(start_pos != string::npos && end_pos != string::npos)
^
`"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp -static-libgcc
`"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/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
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Rbowtie'
finding HTML links ... done
Rbowtie-package html
Rbowtie html
SpliceMap html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rbowtie)
Making 'packages.html' ... done
Rbowtie.Rcheck/Rbowtie-Ex.timings
| name | user | system | elapsed | |
| Rbowtie-package | 0 | 0 | 0 | |
| Rbowtie | 0.00 | 0.00 | 2.83 | |
| SpliceMap | 0.03 | 0.07 | 10.17 | |