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This page was generated on 2023-04-12 11:05:47 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

INSTALL results for Rbowtie2 on palomino4


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 1605/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rbowtie2 2.4.2  (landing page)
Zheng Wei
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/Rbowtie2
git_branch: RELEASE_3_16
git_last_commit: e55c9b7
git_last_commit_date: 2023-02-24 03:54:22 -0400 (Fri, 24 Feb 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Rbowtie2
Version: 2.4.2
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL Rbowtie2
StartedAt: 2023-04-10 16:12:12 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 16:17:22 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 310.6 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL Rbowtie2
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.16-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-3.16-bioc/R/etc/x64/Makeconf"  -fMakefile.win))
Makefile.win:46: warning: overriding recipe for target '.cc.o'
F:/biocbuild/bbs-3.16-bioc/R/etc/x64/Makeconf:258: warning: ignoring old recipe for target '.cc.o'
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c adapterset.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c alignment.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c argparse.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c debug.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c demultiplex.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c fastq.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c fastq_enc.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c fastq_io.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c linereader.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c linereader_joined.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main_adapter_id.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main_adapter_rm.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main_demultiplex.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c scheduler.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c strutils.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c threads.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c timer.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c trimmed_reads.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c userconfig.cc 
g++ -std=gnu++14  -std=gnu++11 -O3  -D_REENTRANT -lpthread -DNDEBUG  -c main.cc 
g++ -std=gnu++14  -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-3.16-bioc/R/etc/x64/Makeconf" -fMakefile.win))
g++ -std=gnu++14  -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="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -std=gnu++14  -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE    -DBOWTIE2 -DNDEBUG -Wall \
	-I third_party \
	-o bowtie2-build-s bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
	 -lpthread -lz
g++ -std=gnu++14  -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++\"" -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++ \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -std=gnu++14  -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++14  -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="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -std=gnu++14  -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE    -DBOWTIE2 -DNDEBUG -Wall \
	-I third_party \
	-o bowtie2-align-s bt2_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
	 -lpthread -lz
g++ -std=gnu++14  -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++\"" -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 -static-libgcc -static-libstdc++ \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -std=gnu++14  -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)