| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-02-27 02:34:41 -0000 (Mon, 27 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4259 |
| 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 | ||||
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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. |
| Package 1595/2169 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rbowtie2 2.5.1 (landing page) Zheng Wei
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | ERROR | ERROR | skipped | |||||||||
| Package: Rbowtie2 |
| Version: 2.5.1 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data Rbowtie2 |
| StartedAt: 2023-02-23 23:30:44 -0000 (Thu, 23 Feb 2023) |
| EndedAt: 2023-02-23 23:33:57 -0000 (Thu, 23 Feb 2023) |
| EllapsedTime: 192.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data Rbowtie2
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* checking for file ‘Rbowtie2/DESCRIPTION’ ... OK
* preparing ‘Rbowtie2’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* 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 '/tmp/RtmpBDM2rC/Rbuild1c4a2c3d597a6c/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 '/tmp/RtmpBDM2rC/Rbuild1c4a2c3d597a6c/Rbowtie2/src/adapterremoval'
(cd adapterremoval && (make clean_o -f Makefile))
make[1]: Entering directory '/tmp/RtmpBDM2rC/Rbuild1c4a2c3d597a6c/Rbowtie2/src/adapterremoval'
rm -f *.o
make[1]: Leaving directory '/tmp/RtmpBDM2rC/Rbuild1c4a2c3d597a6c/Rbowtie2/src/adapterremoval'
(cd bowtie2-2.4.4 && (make CXX="g++" -f Makefile))
make[1]: Entering directory '/tmp/RtmpBDM2rC/Rbuild1c4a2c3d597a6c/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 '/tmp/RtmpBDM2rC/Rbuild1c4a2c3d597a6c/Rbowtie2/src/bowtie2-2.4.4'
make: *** [Makefile:12: all] Error 2
ERROR: compilation failed for package ‘Rbowtie2’
* removing ‘/tmp/RtmpBDM2rC/Rinst1c4a2c71eb9b6a/Rbowtie2’
-----------------------------------
ERROR: package installation failed