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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Rbowtie2.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Rbowtie2_2.12.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Rbowtie2.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘Rbowtie2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rbowtie2’ version ‘2.12.3’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘Rbowtie2’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 35.4Mb
* 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 code 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 loading without being on the library search path ... 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 ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/Rbowtie2.Rcheck/00check.log’
for details.

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