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This page was generated on 2023-01-02 09:00:46 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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INSTALL results for Rbowtie2 on palomino5


To the developers/maintainers of the Rbowtie2 package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1589/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rbowtie2 2.5.0  (landing page)
Zheng Wei
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/Rbowtie2
git_branch: master
git_last_commit: 1327471
git_last_commit_date: 2022-11-01 11:16:15 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: Rbowtie2
Version: 2.5.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL Rbowtie2
StartedAt: 2022-12-28 15:45:23 -0500 (Wed, 28 Dec 2022)
EndedAt: 2022-12-28 15:50:10 -0500 (Wed, 28 Dec 2022)
EllapsedTime: 287.3 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL Rbowtie2
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'Rbowtie2' ...
** using staged installation
** libs
  running 'src/Makefile.win' ...
mkdir -p ../inst
(cd	adapterremoval && (/usr/bin/make -f"F:/biocbuild/bbs-3.17-bioc/R/etc/x64/Makeconf"  -fMakefile.win))
Makefile.win:46: warning: overriding recipe for target '.cc.o'
F:/biocbuild/bbs-3.17-bioc/R/etc/x64/Makeconf:262: warning: ignoring old recipe for target '.cc.o'
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c adapterset.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c alignment.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c argparse.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c debug.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c demultiplex.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c fastq.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c fastq_enc.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c fastq_io.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c linereader.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c linereader_joined.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main_adapter_id.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main_adapter_rm.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main_demultiplex.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c scheduler.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c strutils.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c threads.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c timer.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c trimmed_reads.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c userconfig.cc 
g++ -std=gnu++11  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main.cc 
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"F:/biocbuild/bbs-3.17-bioc/R/etc/x64/Makeconf" -fMakefile.win))
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="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -std=gnu++11  -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE    -DBOWTIE2 -DNDEBUG -Wall \
	-I third_party \
	-o bowtie2-build-s bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
	 -lpthread -lz
g++ -std=gnu++11  -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++\"" -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++ \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`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
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="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -std=gnu++11  -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE    -DBOWTIE2 -DNDEBUG -Wall \
	-I third_party \
	-o bowtie2-align-s bt2_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
	 -lpthread -lz
g++ -std=gnu++11  -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++\"" -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++ \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`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
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
** 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)