Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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

Package 1676/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rbowtie2 2.12.0  (landing page)
Zheng Wei
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/Rbowtie2
git_branch: RELEASE_3_20
git_last_commit: 79a646a
git_last_commit_date: 2024-10-29 10:21:57 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

INSTALL results for Rbowtie2 on kunpeng2

To the developers/maintainers of the Rbowtie2 package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: Rbowtie2
Version: 2.12.0
Command: /home/biocbuild/R/R/bin/R CMD INSTALL Rbowtie2
StartedAt: 2024-11-19 20:44:03 -0000 (Tue, 19 Nov 2024)
EndedAt: 2024-11-19 20:54:09 -0000 (Tue, 19 Nov 2024)
EllapsedTime: 605.8 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL Rbowtie2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘Rbowtie2’ ...
** using staged installation
** libs
mkdir -p ../inst
(cd	adapterremoval && (make CXX="g++ -std=gnu++11" -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rbowtie2/src/adapterremoval'
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c adapterset.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c alignment.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c argparse.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c debug.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c demultiplex.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c fastq.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c fastq_enc.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c fastq_io.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c linereader.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c linereader_joined.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c main_adapter_id.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c main_adapter_rm.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c main_demultiplex.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c scheduler.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c strutils.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c threads.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c timer.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c trimmed_reads.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c userconfig.cc 
g++ -std=gnu++11 -O3 -pthread -DNDEBUG  -c main.cc 
g++ -std=gnu++11 -O3 -pthread -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
mv AdapterRemoval ../../inst/
make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rbowtie2/src/adapterremoval'
(cd	adapterremoval && (make clean_o -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rbowtie2/src/adapterremoval'
rm -f *.o
make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rbowtie2/src/adapterremoval'
(cd bowtie2-2.4.4 && (make CXX="g++" -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rbowtie2/src/bowtie2-2.4.4'
g++ -O3  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3  -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
	-Ithird_party \
	-o bowtie2-build-s bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
	 -lpthread -lz
g++ -O3  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3  -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
	-Ithird_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++ -O3  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3  -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
	-Ithird_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_sw.h:75,
                 from bt2_search.cpp:54:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
                 from aligner_sw.cpp:25:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
                 from aligner_sw_driver.h:81,
                 from aligner_sw_driver.cpp:47:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
                 from aligner_swsse_loc_i16.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
                 from aligner_swsse_ee_i16.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
                 from aligner_swsse_loc_u8.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
                 from aligner_swsse_ee_u8.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
g++ -O3  -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3  -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
	-Ithird_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_sw.h:75,
                 from bt2_search.cpp:54:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
                 from aligner_sw.cpp:25:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
                 from aligner_sw_driver.h:81,
                 from aligner_sw_driver.cpp:47:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
                 from aligner_swsse_loc_i16.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
                 from aligner_swsse_ee_i16.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
                 from aligner_swsse_loc_u8.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
In file included from aligner_sw.h:75,
                 from aligner_swsse_ee_u8.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the '< >'
make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rbowtie2/src/bowtie2-2.4.4'
(cd	bowtie2-2.4.4 && (make move -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rbowtie2/src/bowtie2-2.4.4'
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
make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rbowtie2/src/bowtie2-2.4.4'
(cd	bowtie2-2.4.4 && (make clean_dSYM -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/Rbowtie2/src/bowtie2-2.4.4'
rm -rf *.dSYM
make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/Rbowtie2/src/bowtie2-2.4.4'
g++ -shared -fPIC -o Rbowtie2.so  version_info.cpp
installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-Rbowtie2/00new/Rbowtie2/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rbowtie2)