Michael Stadler
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/Rbowtie |
| git_branch: RELEASE_3_17 |
| git_last_commit: 91e3f09 |
| git_last_commit_date: 2023-04-25 10:25:11 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1640/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rbowtie 1.40.0 (landing page) Michael Stadler
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the Rbowtie package: - 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: Rbowtie |
| Version: 1.40.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rbowtie.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rbowtie_1.40.0.tar.gz |
| StartedAt: 2023-10-18 17:27:35 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 17:28:24 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 49.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Rbowtie.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rbowtie.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rbowtie_1.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Rbowtie.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rbowtie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rbowtie’ version ‘1.40.0’
* 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 ... WARNING
Found the following significant warnings:
./ebwt_search_util.h:37:14: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
./util.h:50:18: warning: overlapping comparisons always evaluate to false [-Wtautological-overlap-compare]
See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Rbowtie.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/Rbowtie.Rcheck/00check.log’
for details.
Rbowtie.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rbowtie
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘Rbowtie’ ...
** using staged installation
** libs
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="\"2023-10-15T15:18:21\"" -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:1524:
In file included from ./ebwt_search_backtrack.h:8:
./ebwt_search_util.h:70:12: warning: variable 'qual' set but not used [-Wunused-but-set-variable]
uint32_t qual = 0;
^
./ebwt_search_util.h:37:14: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef union {
^
PartialAlignment
./ebwt_search_util.h:69:2: note: type is not C-compatible due to this member declaration
bool repOk(uint32_t qualMax, uint32_t slen, const BTString& quals, bool maqPenalty) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./ebwt_search_util.h:88:3: note: type is given name 'PartialAlignment' for linkage purposes by this typedef declaration
} PartialAlignment;
^
In file included from ebwt_build.cpp:10:
In file included from ./ebwt.h:1524:
./ebwt_search_backtrack.h:1674:12: warning: variable 'cumSz' set but not used [-Wunused-but-set-variable]
uint32_t cumSz = 0;
^
In file included from ebwt_build.cpp:10:
./ebwt.h:3889:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
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);
^
5 warnings 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="\"2023-10-15T15:18:45\"" -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:18:
In file included from ./ebwt.h:1524:
In file included from ./ebwt_search_backtrack.h:8:
./ebwt_search_util.h:70:12: warning: variable 'qual' set but not used [-Wunused-but-set-variable]
uint32_t qual = 0;
^
./ebwt_search_util.h:37:14: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef union {
^
PartialAlignment
./ebwt_search_util.h:69:2: note: type is not C-compatible due to this member declaration
bool repOk(uint32_t qualMax, uint32_t slen, const BTString& quals, bool maqPenalty) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./ebwt_search_util.h:88:3: note: type is given name 'PartialAlignment' for linkage purposes by this typedef declaration
} PartialAlignment;
^
In file included from ebwt_search.cpp:17:
In file included from ./aligner.h:18:
In file included from ./ebwt.h:1524:
./ebwt_search_backtrack.h:1674:12: warning: variable 'cumSz' set but not used [-Wunused-but-set-variable]
uint32_t cumSz = 0;
^
In file included from ebwt_search.cpp:17:
In file included from ./aligner.h:18:
./ebwt.h:3889:14: warning: variable 'patoff' set but not used [-Wunused-but-set-variable]
TIndexOffU patoff = 0;
^
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);
^
5 warnings 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:
./ebwt_search_util.h:70:12: warning: variable 'qual' set but not used [-Wunused-but-set-variable]
uint32_t qual = 0;
^
./ebwt_search_util.h:37:14: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef union {
^
PartialAlignment
./ebwt_search_util.h:69:2: note: type is not C-compatible due to this member declaration
bool repOk(uint32_t qualMax, uint32_t slen, const BTString& quals, bool maqPenalty) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./ebwt_search_util.h:88:3: note: type is given name 'PartialAlignment' for linkage purposes by this typedef declaration
} PartialAlignment;
^
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);
^
3 warnings 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();
^
runSpliceMap_QuasR.cpp:1327:9: warning: variable 'min_mismatch' set but not used [-Wunused-but-set-variable]
int min_mismatch;
^
2 warnings 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
amalgamateSAM.cpp:695:17: warning: variable 'front_clip' set but not used [-Wunused-but-set-variable]
uint_fast32_t front_clip = 0;
^
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 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)
Rbowtie.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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] "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rbowtie/bowtie version 1.3.0"
[2] "64-bit"
[3] "Built on kjohnson2"
[4] "2023-10-15T15:18:45"
[5] "Compiler: InstalledDir: /Library/Developer/CommandLineTools/usr/bin"
[6] "Options: -O3 -stdlib=libc++ -falign-functions=64 -Wall -g -O2 -falign-functions=64 -Wall -g -O2 "
[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
1.708 0.517 6.706
Rbowtie.Rcheck/Rbowtie-Ex.timings
| name | user | system | elapsed | |
| Rbowtie | 0.336 | 0.098 | 0.602 | |
| SpliceMap | 0.380 | 0.146 | 1.477 | |