Multiple platform build/check report for BioC 3.20 - INSTALL results for Rbowtie2 on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4739
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4482
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4510
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4462
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 nebbiolo2

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.

raw results

Summary

Package: Rbowtie2

Version: 2.12.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Rbowtie2

StartedAt: 2024-11-28 15:19:48 -0500 (Thu, 28 Nov 2024)

EndedAt: 2024-11-28 15:25:12 -0500 (Thu, 28 Nov 2024)

EllapsedTime: 324.3 seconds

RetCode: 0

Status: OK

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Rbowtie2
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/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 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
	-I third_party \
	-o bowtie2-build-s bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
	 -lpthread -lz
g++ -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${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 \
	-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++ -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -DPOPCNT_CAPABILITY -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 \
	-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
bt2_search.cpp: In function ‘int read_dir(const char*, int*)’:
bt2_search.cpp:4590:67: warning: pointer ‘dir’ may be used after ‘int closedir(DIR*)’ [-Wuse-after-free]
 4590 |                 cerr << "read_dir: could not close directory " << dir << endl;
      |                                                                   ^~~
bt2_search.cpp:4588:20: note: call to ‘int closedir(DIR*)’ here
 4588 |         if(closedir(dir) != 0) {
      |            ~~~~~~~~^~~~~
In file included from /usr/include/c++/13/istream:41,
                 from /usr/include/c++/13/fstream:40,
                 from bt2_search.cpp:22:
In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits<char>]’,
    inlined from ‘int read_dir(const char*, int*)’ at bt2_search.cpp:4590:53,
    inlined from ‘void steal_threads(int, int, EList<int>&, EList<T*>&) [with T = std::thread]’ at bt2_search.cpp:4606:27,
    inlined from ‘void thread_monitor(int, int, EList<int>&, EList<T*>&) [with T = std::thread]’ at bt2_search.cpp:4627:16,
    inlined from ‘void multiseedSearch(Scoring&, const PatternParams&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)’ at bt2_search.cpp:4747:18:
/usr/include/c++/13/ostream:293:25: warning: pointer may be used after ‘int closedir(DIR*)’ [-Wuse-after-free]
  293 |       { return _M_insert(__p); }
      |                ~~~~~~~~~^~~~~
In function ‘int read_dir(const char*, int*)’,
    inlined from ‘void steal_threads(int, int, EList<int>&, EList<T*>&) [with T = std::thread]’ at bt2_search.cpp:4606:27,
    inlined from ‘void thread_monitor(int, int, EList<int>&, EList<T*>&) [with T = std::thread]’ at bt2_search.cpp:4627:16,
    inlined from ‘void multiseedSearch(Scoring&, const PatternParams&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)’ at bt2_search.cpp:4747:18:
bt2_search.cpp:4588:20: note: call to ‘int closedir(DIR*)’ here
 4588 |         if(closedir(dir) != 0) {
      |            ~~~~~~~~^~~~~
In file included from aligner_seed2.cpp:22:
In member function ‘void DescentOutgoing::update(DescentEdge)’,
    inlined from ‘size_t Descent::recalcOutgoing(const Read&, const Scoring&, TAlScore, TAlScore, DescentRedundancyChecker&, EFactory<DescentPos>&, const EList<DescentRoot>&, const EList<DescentConfig>&, PerReadMetrics&)’ at aligner_seed2.cpp:647:17:
aligner_seed2.h:1019:31: warning: ‘edge.DescentEdge::nex’ may be used uninitialized [-Wmaybe-uninitialized]
 1019 |                         best1 = e;
      |                         ~~~~~~^~~
aligner_seed2.cpp: 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.cpp:585:21: note: ‘edge.DescentEdge::nex’ was declared here
  585 |         DescentEdge edge;
      |                     ^~~~
g++ -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -DPOPCNT_CAPABILITY -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 \
	-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
bt2_search.cpp: In function ‘int read_dir(const char*, int*)’:
bt2_search.cpp:4590:67: warning: pointer ‘dir’ may be used after ‘int closedir(DIR*)’ [-Wuse-after-free]
 4590 |                 cerr << "read_dir: could not close directory " << dir << endl;
      |                                                                   ^~~
bt2_search.cpp:4588:20: note: call to ‘int closedir(DIR*)’ here
 4588 |         if(closedir(dir) != 0) {
      |            ~~~~~~~~^~~~~
In file included from /usr/include/c++/13/istream:41,
                 from /usr/include/c++/13/fstream:40,
                 from bt2_search.cpp:22:
In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(const void*) [with _CharT = char; _Traits = std::char_traits<char>]’,
    inlined from ‘int read_dir(const char*, int*)’ at bt2_search.cpp:4590:53,
    inlined from ‘void steal_threads(int, int, EList<int>&, EList<T*>&) [with T = std::thread]’ at bt2_search.cpp:4606:27,
    inlined from ‘void thread_monitor(int, int, EList<int>&, EList<T*>&) [with T = std::thread]’ at bt2_search.cpp:4627:16,
    inlined from ‘void multiseedSearch(Scoring&, const PatternParams&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)’ at bt2_search.cpp:4747:18:
/usr/include/c++/13/ostream:293:25: warning: pointer may be used after ‘int closedir(DIR*)’ [-Wuse-after-free]
  293 |       { return _M_insert(__p); }
      |                ~~~~~~~~~^~~~~
In function ‘int read_dir(const char*, int*)’,
    inlined from ‘void steal_threads(int, int, EList<int>&, EList<T*>&) [with T = std::thread]’ at bt2_search.cpp:4606:27,
    inlined from ‘void thread_monitor(int, int, EList<int>&, EList<T*>&) [with T = std::thread]’ at bt2_search.cpp:4627:16,
    inlined from ‘void multiseedSearch(Scoring&, const PatternParams&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)’ at bt2_search.cpp:4747:18:
bt2_search.cpp:4588:20: note: call to ‘int closedir(DIR*)’ here
 4588 |         if(closedir(dir) != 0) {
      |            ~~~~~~~~^~~~~
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/bbs-3.20-bioc/R/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)