Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (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 1676/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rbowtie2 2.12.0 (landing page) Zheng Wei
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | ERROR | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: Rbowtie2 |
Version: 2.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rbowtie2 |
StartedAt: 2024-11-19 15:15:07 -0500 (Tue, 19 Nov 2024) |
EndedAt: 2024-11-19 15:19:25 -0500 (Tue, 19 Nov 2024) |
EllapsedTime: 258.7 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rbowtie2 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘Rbowtie2’ ... ** using staged installation ** libs mkdir -p ../inst (cd adapterremoval && (make CXX="g++ -std=gnu++11" -f Makefile)) 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/ (cd adapterremoval && (make clean_o -f Makefile)) rm -f *.o (cd bowtie2-2.4.4 && (make CXX="g++" -f Makefile)) 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="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -I third_party \ -o bowtie2-build-s bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \ -lpthread -lz In file included from bt2_build.cpp:28: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_idx.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_io.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_util.cpp:26: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. g++ -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${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 In file included from bt2_build.cpp:28: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_idx.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_io.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_util.cpp:26: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. 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 In file included from bt2_search.cpp:41: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_idx.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_io.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_util.cpp:26: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from aligner_seed.cpp:23: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:103: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from aligner_sw_driver.cpp:47: In file included from ./aligner_sw_driver.h:84: In file included from ./group_walk.h:86: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ aligner_sw_driver.cpp:1074:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable] int64_t pastedRefoff = (int64_t)wr.toff - rdoff; ^ aligner_sw_driver.cpp:1769:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable] int64_t pastedRefoff = (int64_t)wr.toff - rdoff; ^ 3 warnings generated. In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:103: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. 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 In file included from bt2_search.cpp:41: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_idx.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_io.cpp:25: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from bt2_util.cpp:26: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from aligner_seed.cpp:23: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:103: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. In file included from aligner_sw_driver.cpp:47: In file included from ./aligner_sw_driver.h:84: In file included from ./group_walk.h:86: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ aligner_sw_driver.cpp:1074:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable] int64_t pastedRefoff = (int64_t)wr.toff - rdoff; ^ aligner_sw_driver.cpp:1769:13: warning: variable 'pastedRefoff' set but not used [-Wunused-but-set-variable] int64_t pastedRefoff = (int64_t)wr.toff - rdoff; ^ 3 warnings generated. In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:103: ./bt2_idx.h:2625:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable] TIndexOffU patoff = 0; ^ 1 warning generated. (cd bowtie2-2.4.4 && (make move -f Makefile)) 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 (cd bowtie2-2.4.4 && (make clean_dSYM -f Makefile)) rm -rf *.dSYM g++ -shared -fPIC -o Rbowtie2.so version_info.cpp installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)