Rbowtie2.install - Githubissues

Yikun commented 1 year ago
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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Rbowtie2
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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-3.17-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-3.17-bioc/meat/Rbowtie2/src/adapterremoval'
(cd adapterremoval && (make clean_o -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie2/src/adapterremoval'
rm -f *.o
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie2/src/adapterremoval'
(cd bowtie2-2.4.4 && (make CXX="g++" -f Makefile))
make[1]: Entering directory '/home/biocbuild/bbs-3.17-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:73,
                 from bt2_search.cpp:54:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_sw.cpp:25:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_sw_driver.h:81,
                 from aligner_sw_driver.cpp:47:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from sse_util.h:27,
                 from aligner_bt.h:31,
                 from aligner_bt.cpp:20:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from sse_util.h:27,
                 from sse_util.cpp:20:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from sse_util.h:27,
                 from aligner_swsse.h:28,
                 from aligner_swsse.cpp:22:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_swsse_loc_i16.cpp:56:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_swsse_ee_i16.cpp:56:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_swsse_loc_u8.cpp:56:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from aligner_sw.h:73,
                 from aligner_swsse_ee_u8.cpp:56:
sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory
   31 | #include "simde/x86/sse2.h"
      |          ^~~~~~~~~~~~~~~~~~
compilation terminated.
make[1]: *** [Makefile:339: bowtie2-align-s] Error 1
make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie2/src/bowtie2-2.4.4'
make: *** [Makefile:12: all] Error 2
ERROR: compilation failed for package ‘Rbowtie2’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/Rbowtie2’
martin-g commented 1 year ago
Reported upstream: https://github.com/wzthu/Rbowtie2/issues/7
martin-g commented 1 year ago
Pull Request: https://github.com/wzthu/Rbowtie2/pull/8
martin-g commented 1 year ago
The PR has been merged! Leaving this issue open until we see it green in the reports.
martin-g commented 1 year ago
The report from 23.03.2023 is OK!
Yikun / BBS

Rbowtie2.install #19
