| Back to Build/check report for BioC 3.13 on Apple's new arm64 arch |
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This page was generated on 2021-01-31 03:53:36 -0500 (Sun, 31 Jan 2021).
| These are experimental builds on Apple's new arm64 arch. See here for more information. |
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To the developers/maintainers of the Rbowtie package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1429/1938 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rbowtie 1.31.6 Michael Stadler
| taxco | macOS 11.0.1 Big Sur / arm64 | OK | NA | NA | |||||||||
| Package: Rbowtie |
| Version: 1.31.6 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rbowtie |
| StartedAt: 2021-01-30 16:05:15 -0500 (Sat, 30 Jan 2021) |
| EndedAt: 2021-01-30 16:07:37 -0500 (Sat, 30 Jan 2021) |
| EllapsedTime: 142.1 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rbowtie
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library’
* installing *source* package ‘Rbowtie’ ...
** using staged installation
** libs
** arch -
clang++ -O3 -DCOMPILER_OPTIONS="\"-O3 -stdlib=libc++ -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 \"" -stdlib=libc++ -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2021-01-30T16:05:16\"" -DCOMPILER_VERSION="\"`clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \
-I third_party \
-o bowtie-build-s ebwt_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp bowtie_build_main.cpp \
-L/opt/R/arm64/lib -lz -lpthread
In file included from ebwt_build.cpp:10:
In file included from ./ebwt.h:25:
In file included from ./blockwise_sa.h:16:
In file included from ./binary_sa_search.h:12:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
1 warning generated.
clang++ -O3 -DCOMPILER_OPTIONS="\"-O3 -stdlib=libc++ -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 \"" -stdlib=libc++ -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2021-01-30T16:05:37\"" -DCOMPILER_VERSION="\"`clang++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \
-I third_party \
-o bowtie-align-s ebwt_search.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp hit.cpp bowtie_main.cpp \
-L/opt/R/arm64/lib -lz -lpthread
In file included from ebwt_search.cpp:17:
In file included from ./aligner.h:15:
In file included from ./aligner_metrics.h:11:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
1 warning generated.
In file included from pat.cpp:10:
In file included from ./pat.h:22:
In file included from ./read.h:29:
In file included from ./hit_set.h:20:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
In file included from pat.cpp:10:
In file included from ./pat.h:22:
In file included from ./read.h:29:
In file included from ./hit_set.h:20:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
pat.cpp:382:3: note: in instantiation of function template specialization 'itoa10<unsigned long long>' requested here
itoa10<TReadId>(static_cast<TReadId>(i), nametmp_);
^
2 warnings generated.
In file included from ebwt_search_util.cpp:1:
In file included from ./ebwt_search_util.h:9:
In file included from ./hit.h:20:
In file included from ./hit_set.h:20:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
1 warning generated.
In file included from sam.cpp:8:
In file included from ./hit.h:20:
In file included from ./hit_set.h:20:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
In file included from sam.cpp:8:
In file included from ./hit.h:20:
In file included from ./hit_set.h:20:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./sstring.h:2154:2: note: in instantiation of function template specialization 'itoa10<unsigned int>' requested here
itoa10<A>(static_cast<A>(i), buf);
^
sam.cpp:42:17: note: in instantiation of function template specialization 'operator<<<char, 25, 2, 0, unsigned int>' requested here
o << "\tLN:" << (plen[i]) << '\n';
^
2 warnings generated.
In file included from hit.cpp:2:
In file included from ./hit.h:20:
In file included from ./hit_set.h:20:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./read.h:331:5: note: in instantiation of function template specialization 'itoa10<unsigned long>' requested here
itoa10(ops[i].n, buf); o.append(buf);
^
In file included from hit.cpp:2:
In file included from ./hit.h:20:
In file included from ./hit_set.h:20:
In file included from ./sstring.h:29:
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
if (value <= 0 && value != 0) *out++ = '-';
~~~~~~~~~~~^~~~~~~~~~~~~
./sstring.h:2154:2: note: in instantiation of function template specialization 'itoa10<unsigned int>' requested here
itoa10<A>(static_cast<A>(i), buf);
^
hit.cpp:109:8: note: in instantiation of function template specialization 'operator<<<char, 25, 2, 0, unsigned int>' requested here
o << h.h.first;
^
2 warnings generated.
mkdir -p ../inst
cp bowtie-align-s ../inst/bowtie
cp bowtie-build-s ../inst/bowtie-build
cd SpliceMap; \
make -f Makefile; \
echo "MAKE of SpliceMap DONE"
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c params.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o
runSpliceMap_QuasR.cpp:108:31: warning: unused variable 'chr_file_list_it' [-Wunused-variable]
vector<string>::iterator chr_file_list_it = chr_file_list.begin();
^
1 warning generated.
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp
`"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXX` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config LDFLAGS` `"/Library/Frameworks/R.framework/Resources/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o
MAKE of SpliceMap DONE
mkdir -p ../inst
cp SpliceMap/SpliceMap ../inst/SpliceMap
cp SpliceMap/amalgamateSAM ../inst/amalgamateSAM
cp SpliceMap/getSpliceMapUnmapped ../inst/getSpliceMapUnmapped
cp SpliceMap/fuseReorder ../inst/fuseReorder
cp SpliceMap/runSpliceMap_QuasR ../inst/runSpliceMap_QuasR
cp SpliceMap/sortsam ../inst/sortsam
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rbowtie)