Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:07:10 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for Rbowtie2 on tokay2


To the developers/maintainers of the Rbowtie2 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rbowtie2.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1538/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rbowtie2 2.0.0  (landing page)
Zheng Wei
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/Rbowtie2
git_branch: RELEASE_3_14
git_last_commit: 67ee493
git_last_commit_date: 2021-10-26 12:37:39 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Rbowtie2
Version: 2.0.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:Rbowtie2.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Rbowtie2_2.0.0.tar.gz
StartedAt: 2022-04-13 01:17:13 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 01:18:06 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 52.9 seconds
RetCode: 0
Status:   OK  
CheckDir: Rbowtie2.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:Rbowtie2.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Rbowtie2_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Rbowtie2.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rbowtie2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rbowtie2' version '2.0.0'
* package encoding: UTF-8
* 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 'Rbowtie2' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 72.8Mb
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
bowtie2_samtools 4.70   0.11    7.36
bowtie2-build    0.01   0.06    5.25
* 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-3.14-bioc/meat/Rbowtie2.Rcheck/00check.log'
for details.

Installation output

Rbowtie2.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch Rbowtie2
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
* installing *source* package 'Rbowtie2' ...
** using staged installation
** libs
  running 'src/Makefile.win' ...
mkdir -p ../inst
(cd	adapterremoval && (/usr/bin/make -f"C:/Users/biocbuild/bbs-3.14-bioc/R/etc/x64/Makeconf"  -fMakefile.win))
Makefile.win:46: warning: overriding recipe for target '.cc.o'
C:/Users/biocbuild/bbs-3.14-bioc/R/etc/x64/Makeconf:243: warning: ignoring old recipe for target '.cc.o'
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c adapterset.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c alignment.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c argparse.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c debug.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c demultiplex.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c fastq.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c fastq_enc.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c fastq_io.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c linereader.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c linereader_joined.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main_adapter_id.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main_adapter_rm.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main_demultiplex.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c scheduler.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c strutils.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c threads.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c timer.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c trimmed_reads.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c userconfig.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main.cc 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG   -o AdapterRemoval adapterset.o alignment.o argparse.o debug.o demultiplex.o fastq.o fastq_enc.o fastq_io.o linereader.o linereader_joined.o main_adapter_id.o main_adapter_rm.o main_demultiplex.o scheduler.o strutils.o threads.o timer.o trimmed_reads.o userconfig.o main.o
cp AdapterRemoval ../../inst/
(cd bowtie2-2.4.4 && (/usr/bin/make -f"C:/Users/biocbuild/bbs-3.14-bioc/R/etc/x64/Makeconf" -fMakefile.win))
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++\"" -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++ \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE    -DBOWTIE2 -DNDEBUG -Wall \
	 -I third_party \
	-o bowtie2-build-s bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
	 -lpthread -lz
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++\"" -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++ \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE    -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
	 -I third_party \
	-o bowtie2-build-l bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
	 -lpthread -lz
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++\"" -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++ \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE    -DBOWTIE2 -DNDEBUG -Wall \
	 -I third_party \
	-o bowtie2-align-s bt2_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
	 -lpthread -lz
In file included from aligner_seed2.cpp:22:
aligner_seed2.h: In member function 'size_t Descent::recalcOutgoing(const Read&, const Scoring&, TAlScore, TAlScore, DescentRedundancyChecker&, EFactory<DescentPos>&, const EList<DescentRoot>&, const EList<DescentConfig>&, PerReadMetrics&)':
aligner_seed2.h:1019:10: warning: 'edge.DescentEdge::nex' may be used uninitialized in this function [-Wmaybe-uninitialized]
    best1 = e;
    ~~~~~~^~~
aligner_seed2.cpp:585:14: note: 'edge.DescentEdge::nex' was declared here
  DescentEdge edge;
              ^~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++\"" -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++ \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE    -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
	 -I third_party \
	-o bowtie2-align-l bt2_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
	 -lpthread -lz
In file included from aligner_seed2.cpp:22:
aligner_seed2.h: In member function 'size_t Descent::recalcOutgoing(const Read&, const Scoring&, TAlScore, TAlScore, DescentRedundancyChecker&, EFactory<DescentPos>&, const EList<DescentRoot>&, const EList<DescentConfig>&, PerReadMetrics&)':
aligner_seed2.h:1019:10: warning: 'edge.DescentEdge::nex' may be used uninitialized in this function [-Wmaybe-uninitialized]
    best1 = e;
    ~~~~~~^~~
aligner_seed2.cpp:585:14: note: 'edge.DescentEdge::nex' was declared here
  DescentEdge edge;
              ^~~~
echo "@echo off" > bowtie2.bat
echo "perl %~dp0/bowtie2 %*" >> bowtie2.bat
echo "@echo off" > bowtie2-build.bat
echo "python3 %~dp0/bowtie2-build %*" >> bowtie2-build.bat
(cd	bowtie2-2.4.4 && (/usr/bin/make move -fMakefile.win))
mv bowtie2-align-s ../../inst
mv bowtie2-build-s ../../inst
mv bowtie2-align-l ../../inst
mv bowtie2-build-l ../../inst
cp bowtie2 ../../inst
cp bowtie2-build ../../inst
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Rbowtie2'
    finding HTML links ... done
    adapterremoval_usage                    html  
    adapterremoval_version                  html  
    bowtie2-build                           html  
    bowtie2                                 html  
    bowtie2_build_usage                     html  
    bowtie2_samtools                        html  
    bowtie2_usage                           html  
    bowtie2_version                         html  
    checkFileCreateable                     html  
    checkFileExist                          html  
    checkIndexType                          html  
    checkPathExist                          html  
    checkSamtoolsExists                     html  
    dot-callbinary                          html  
    identify_adapters                       html  
    remove_adapters                         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 (Rbowtie2)
Making 'packages.html' ... done

Tests output

Example timings

Rbowtie2.Rcheck/Rbowtie2-Ex.timings

nameusersystemelapsed
adapterremoval_usage0.000.060.31
adapterremoval_version0.000.000.13
bowtie2-build0.010.065.25
bowtie20.050.003.33
bowtie2_build_usage0.000.020.25
bowtie2_samtools4.700.117.36
bowtie2_usage0.000.030.50
bowtie2_version0.000.000.44
identify_adapters0.000.000.23
remove_adapters0.000.000.46