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This page was generated on 2023-03-01 07:38:48 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the Rbowtie package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rbowtie.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 1595/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Rbowtie 1.39.1 (landing page) Michael Stadler
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
Package: Rbowtie |
Version: 1.39.1 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Rbowtie.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Rbowtie_1.39.1.tar.gz |
StartedAt: 2023-02-28 12:27:54 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 12:28:23 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 29.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Rbowtie.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Rbowtie.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Rbowtie_1.39.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘Rbowtie/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Rbowtie’ version ‘1.39.1’ * 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 ‘Rbowtie’ can be installed ... OK * checking installed package size ... NOTE installed size is 18.3Mb * 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 R 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 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 ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘Rbowtie-Overview.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie.Rcheck/00check.log’ for details.
Rbowtie.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Rbowtie ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘Rbowtie’ ... ** using staged installation ** libs g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -g -O2 -Wall -g -O2 -Wall \"" -Wl,--hash-style=both -g -O2 -Wall -g -O2 -Wall \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2023-02-27T09:37:14\"" -DCOMPILER_VERSION="\"`g++ -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/usr/local/lib -lz -lpthread In file included from ebwt_build.cpp:8: In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’, inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’ at multikey_qsort.h:584:31: ds.h:497:17: warning: ‘tmp2’ may be used uninitialized [-Wmaybe-uninitialized] 497 | list_[cur_++] = el; | ^~~~~ In file included from diff_sample.h:14, from blockwise_sa.h:17, from ebwt.h:25, from ebwt_build.cpp:10: multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’: multikey_qsort.h:583:36: note: ‘tmp2’ declared here 583 | QSortRange tmp2; | ^~~~ In file included from ebwt_build.cpp:8: In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’, inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’ at multikey_qsort.h:593:31: ds.h:497:17: warning: ‘tmp3’ may be used uninitialized [-Wmaybe-uninitialized] 497 | list_[cur_++] = el; | ^~~~~ In file included from diff_sample.h:14, from blockwise_sa.h:17, from ebwt.h:25, from ebwt_build.cpp:10: multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’: multikey_qsort.h:592:36: note: ‘tmp3’ declared here 592 | QSortRange tmp3; | ^~~~ In file included from ebwt_build.cpp:8: In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’, inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’ at multikey_qsort.h:601:31: ds.h:497:17: warning: ‘tmp4’ may be used uninitialized [-Wmaybe-uninitialized] 497 | list_[cur_++] = el; | ^~~~~ In file included from diff_sample.h:14, from blockwise_sa.h:17, from ebwt.h:25, from ebwt_build.cpp:10: multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’: multikey_qsort.h:600:36: note: ‘tmp4’ declared here 600 | QSortRange tmp4; | ^~~~ In file included from ebwt_build.cpp:8: In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’, inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’ at multikey_qsort.h:584:31: ds.h:497:17: warning: ‘tmp2’ may be used uninitialized [-Wmaybe-uninitialized] 497 | list_[cur_++] = el; | ^~~~~ In file included from diff_sample.h:14, from blockwise_sa.h:17, from ebwt.h:25, from ebwt_build.cpp:10: multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’: multikey_qsort.h:583:36: note: ‘tmp2’ declared here 583 | QSortRange tmp2; | ^~~~ In file included from ebwt_build.cpp:8: In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’, inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’ at multikey_qsort.h:593:31: ds.h:497:17: warning: ‘tmp3’ may be used uninitialized [-Wmaybe-uninitialized] 497 | list_[cur_++] = el; | ^~~~~ In file included from diff_sample.h:14, from blockwise_sa.h:17, from ebwt.h:25, from ebwt_build.cpp:10: multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’: multikey_qsort.h:592:36: note: ‘tmp3’ declared here 592 | QSortRange tmp3; | ^~~~ In file included from ebwt_build.cpp:8: In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’, inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’ at multikey_qsort.h:601:31: ds.h:497:17: warning: ‘tmp4’ may be used uninitialized [-Wmaybe-uninitialized] 497 | list_[cur_++] = el; | ^~~~~ In file included from diff_sample.h:14, from blockwise_sa.h:17, from ebwt.h:25, from ebwt_build.cpp:10: multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’: multikey_qsort.h:600:36: note: ‘tmp4’ declared here 600 | QSortRange tmp4; | ^~~~ g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -g -O2 -Wall -g -O2 -Wall \"" -Wl,--hash-style=both -g -O2 -Wall -g -O2 -Wall \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2023-02-27T09:37:38\"" -DCOMPILER_VERSION="\"`g++ -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/usr/local/lib -lz -lpthread 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" make[1]: Entering directory '/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie/src/SpliceMap' `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXXFLAGS` -c params.cpp `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o runSpliceMap_QuasR.cpp: In function ‘int main(int, char* const*)’: runSpliceMap_QuasR.cpp:108:38: warning: variable ‘chr_file_list_it’ set but not used [-Wunused-but-set-variable] 108 | vector<string>::iterator chr_file_list_it = chr_file_list.begin(); | ^~~~~~~~~~~~~~~~ runSpliceMap_QuasR.cpp:537:47: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 537 | if (line.length() > head_clip_length) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ runSpliceMap_QuasR.cpp:595:47: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 595 | if (line.length() > head_clip_length) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ runSpliceMap_QuasR.cpp:716:47: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 716 | if (line.length() > head_clip_length) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ runSpliceMap_QuasR.cpp:841:43: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 841 | if (line.length() > head_clip_length) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ runSpliceMap_QuasR.cpp: In function ‘void processbowtie(std::string&, std::string&)’: runSpliceMap_QuasR.cpp:1327:9: warning: variable ‘min_mismatch’ set but not used [-Wunused-but-set-variable] 1327 | int min_mismatch; | ^~~~~~~~~~~~ `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o sortsam.cpp: In function ‘int main(int, char* const*)’: sortsam.cpp:189:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 189 | if (nmloc == string::npos) { // unaligned, no NM tag | ~~~~~~^~~~~~~~~~~~~~~ sortsam.cpp:194:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 194 | if (nmloc2 == string::npos) { | ~~~~~~~^~~~~~~~~~~~~~~ sortsam.cpp:231:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 231 | if (nmloc == string::npos) { // unaligned, no NM tag | ~~~~~~^~~~~~~~~~~~~~~ sortsam.cpp:236:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 236 | if (nmloc2 == string::npos) { | ~~~~~~~^~~~~~~~~~~~~~~ `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o amalgamateSAM.cpp: In function ‘int extractId(const string&)’: amalgamateSAM.cpp:19:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 19 | if(start_pos != string::npos && end_pos != string::npos) | ~~~~~~~~~~^~~~~~~~~~~~~~~ amalgamateSAM.cpp:19:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 19 | if(start_pos != string::npos && end_pos != string::npos) | ~~~~~~~~^~~~~~~~~~~~~~~ amalgamateSAM.cpp: In function ‘void update_jun_coverage(std::map<std::__cxx11::basic_string<char>, std::map<int, std::map<int, jun_store_ij> > >&, std::string, bool)’: amalgamateSAM.cpp:695:31: warning: variable ‘front_clip’ set but not used [-Wunused-but-set-variable] 695 | uint_fast32_t front_clip = 0; | ^~~~~~~~~~ `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp getSpliceMapUnmapped.cpp: In function ‘int extractNextId(const string&)’: getSpliceMapUnmapped.cpp:88:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 88 | if(start_pos != string::npos && end_pos != string::npos) | ~~~~~~~~~~^~~~~~~~~~~~~~~ getSpliceMapUnmapped.cpp:88:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 88 | if(start_pos != string::npos && end_pos != string::npos) | ~~~~~~~~^~~~~~~~~~~~~~~ `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.17-bioc/R/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o make[1]: Leaving directory '/home/biocbuild/bbs-3.17-bioc/meat/Rbowtie/src/SpliceMap' 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)
Rbowtie.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(Rbowtie) > > test_check("Rbowtie") *** Warning *** 'bowtie2-build-s' was run directly. It is recommended that you run the wrapper script 'bowtie-build' instead. [1] "Usage: bowtie2-build-s [options]* <reference_in> <ebwt_outfile_base>" [2] " reference_in comma-separated list of files with ref sequences" [3] " ebwt_outfile_base write Ebwt data to files with this dir/basename" [4] "Options:" [5] " -f reference files are Fasta (default)" [6] " -c reference sequences given on cmd line (as <seq_in>)" [7] " -a/--noauto disable automatic -p/--bmax/--dcv memory-fitting" [8] " -p/--packed use packed strings internally; slower, uses less mem" [9] " --bmax <int> max bucket sz for blockwise suffix-array builder" [10] " --bmaxdivn <int> max bucket sz as divisor of ref len (default: 4)" [11] " --dcv <int> diff-cover period for blockwise (default: 1024)" [12] " --nodc disable diff-cover (algorithm becomes quadratic)" [13] " -r/--noref don't build .3/.4.ebwt (packed reference) portion" [14] " -3/--justref just build .3/.4.ebwt (packed reference) portion" [15] " -o/--offrate <int> SA is sampled every 2^offRate BWT chars (default: 5)" [16] " -t/--ftabchars <int> # of chars consumed in initial lookup (default: 10)" [17] " --threads <int> # of threads" [18] " --ntoa convert Ns in reference to As" [19] " --seed <int> seed for random number generator" [20] " -q/--quiet verbose output (for debugging)" [21] " -h/--help print detailed description of tool and its options" [22] " --usage print this usage message" [23] " --version print version information and quit" *** Warning *** bowtie-align-s was run directly. It is recommended that you run the wrapper script 'bowtie' instead. [1] "Usage: " [2] "bowtie-align-s [options]* -x <ebwt> {-1 <m1> -2 <m2> | --12 <r> | --interleaved <i> | <s>} [<hit>]" [3] "" [4] " <ebwt> Index filename prefix (minus trailing .X.ebwt)." [5] " <m1> Comma-separated list of files containing upstream mates (or the" [6] " sequences themselves, if -c is set) paired with mates in <m2>" [7] " <m2> Comma-separated list of files containing downstream mates (or the" [8] " sequences themselves if -c is set) paired with mates in <m1>" [9] " <r> Comma-separated list of files containing Crossbow-style reads. Can be" [10] " a mixture of paired and unpaired. Specify \"-\" for stdin." [11] " <i> Files with interleaved paired-end FASTQ reads." [12] " <s> Comma-separated list of files containing unpaired reads, or the" [13] " sequences themselves, if -c is set. Specify \"-\" for stdin." [14] " <hit> File to write hits to (default: stdout)" [15] "Input:" [16] " -q query input files are FASTQ .fq/.fastq (default)" [17] " -f query input files are (multi-)FASTA .fa/.mfa" [18] " -F k:<int>,i:<int> query input files are continuous FASTA where reads" [19] " are substrings (k-mers) extracted from a FASTA file <s>" [20] " and aligned at offsets 1, 1+i, 1+2i ... end of reference" [21] " -r query input files are raw one-sequence-per-line" [22] " -c query sequences given on cmd line (as <mates>, <singles>)" [23] " -Q/--quals <file> QV file(s) corresponding to CSFASTA inputs; use with -f -C" [24] " --Q1/--Q2 <file> same as -Q, but for mate files 1 and 2 respectively" [25] " -s/--skip <int> skip the first <int> reads/pairs in the input" [26] " -u/--qupto <int> stop after first <int> reads/pairs (excl. skipped reads)" [27] " -5/--trim5 <int> trim <int> bases from 5' (left) end of reads" [28] " -3/--trim3 <int> trim <int> bases from 3' (right) end of reads" [29] " --phred33-quals input quals are Phred+33 (default)" [30] " --phred64-quals input quals are Phred+64 (same as --solexa1.3-quals)" [31] " --solexa-quals input quals are from GA Pipeline ver. < 1.3" [32] " --solexa1.3-quals input quals are from GA Pipeline ver. >= 1.3" [33] " --integer-quals qualities are given as space-separated integers (not ASCII)" [34] "Alignment:" [35] " -v <int> report end-to-end hits w/ <=v mismatches; ignore qualities" [36] " or" [37] " -n/--seedmms <int> max mismatches in seed (can be 0-3, default: -n 2)" [38] " -e/--maqerr <int> max sum of mismatch quals across alignment for -n (def: 70)" [39] " -l/--seedlen <int> seed length for -n (default: 28)" [40] " --nomaqround disable Maq-like quality rounding for -n (nearest 10 <= 30)" [41] " -I/--minins <int> minimum insert size for paired-end alignment (default: 0)" [42] " -X/--maxins <int> maximum insert size for paired-end alignment (default: 250)" [43] " --fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (default: --fr)" [44] " --nofw/--norc do not align to forward/reverse-complement reference strand" [45] " --maxbts <int> max # backtracks for -n 2/3 (default: 125, 800 for --best)" [46] " --pairtries <int> max # attempts to find mate for anchor hit (default: 100)" [47] " -y/--tryhard try hard to find valid alignments, at the expense of speed" [48] " --chunkmbs <int> max megabytes of RAM for best-first search frames (def: 64)" [49] " --reads-per-batch # of reads to read from input file at once (default: 16)" [50] "Reporting:" [51] " -k <int> report up to <int> good alignments per read (default: 1)" [52] " -a/--all report all alignments per read (much slower than low -k)" [53] " -m <int> suppress all alignments if > <int> exist (def: no limit)" [54] " -M <int> like -m, but reports 1 random hit (MAPQ=0); requires --best" [55] " --best hits guaranteed best stratum; ties broken by quality" [56] " --strata hits in sub-optimal strata aren't reported (requires --best)" [57] "Output:" [58] " -t/--time print wall-clock time taken by search phases" [59] " -B/--offbase <int> leftmost ref offset = <int> in bowtie output (default: 0)" [60] " --quiet print nothing but the alignments" [61] " --refidx refer to ref. seqs by 0-based index rather than name" [62] " --al <fname> write aligned reads/pairs to file(s) <fname>" [63] " --un <fname> write unaligned reads/pairs to file(s) <fname>" [64] " --no-unal suppress SAM records for unaligned reads" [65] " --max <fname> write reads/pairs over -m limit to file(s) <fname>" [66] " --suppress <cols> suppresses given columns (comma-delim'ed) in default output" [67] " --fullref write entire ref name (default: only up to 1st space)" [68] "SAM:" [69] " -S/--sam write hits in SAM format" [70] " --mapq <int> default mapping quality (MAPQ) to print for SAM alignments" [71] " --sam-nohead supppress header lines (starting with @) for SAM output" [72] " --sam-nosq supppress @SQ header lines for SAM output" [73] " --sam-RG <text> add <text> (usually \"lab=value\") to @RG line of SAM header" [74] "Performance:" [75] " -o/--offrate <int> override offrate of index; must be >= index's offrate" [76] " -p/--threads <int> number of alignment threads to launch (default: 1)" [77] " --mm use memory-mapped I/O for index; many 'bowtie's can share" [78] " --shmem use shared mem for index; many 'bowtie's can share" [79] "Other:" [80] " --seed <int> seed for random number generator" [81] " --verbose verbose output (for debugging)" [82] " --version print version information and quit" [83] " -h/--help print this usage message" [1] "/home/biocbuild/bbs-3.17-bioc/R/library/Rbowtie/bowtie version 1.3.0" [2] "64-bit" [3] "Built on kunpeng1" [4] "2023-02-27T09:37:38" [5] "Compiler: gcc version 11.3.0 (Ubuntu 11.3.0-1ubuntu1~22.04) " [6] "Options: -O3 -Wl,--hash-style=both -g -O2 -Wall -g -O2 -Wall " [7] "Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}" # reads processed: 3 # reads with at least one alignment: 2 (66.67%) # reads that failed to align: 1 (33.33%) Reported 2 alignments # reads processed: 3 # reads with at least one alignment: 2 (66.67%) # reads that failed to align: 1 (33.33%) Reported 2 alignments # reads processed: 3 # reads with at least one alignment: 0 (0.00%) # reads that failed to align: 3 (100.00%) No alignments # reads processed: 3 # reads with at least one alignment: 2 (66.67%) # reads that failed to align: 1 (33.33%) Reported 2 alignments # reads processed: 3 # reads with at least one alignment: 0 (0.00%) # reads that failed to align: 3 (100.00%) No alignments [ FAIL 0 | WARN 0 | SKIP 0 | PASS 68 ] > > proc.time() user system elapsed 1.719 0.441 3.452
Rbowtie.Rcheck/Rbowtie-Ex.timings
name | user | system | elapsed | |
Rbowtie | 0.346 | 0.128 | 0.483 | |
SpliceMap | 0.383 | 0.125 | 1.005 | |