##############################################################################
##############################################################################
###
### 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_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Rbowtie.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rbowtie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rbowtie’ version ‘1.43.0’
* 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-3.19-bioc/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 code 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 ... NOTE
checkRd: (-1) SpliceMap.Rd:21: Lost braces
    21 |     (see sQuote{Details} or SpliceMap documentation).}
       |                ^
* 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 ... 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/Rbowtie.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rbowtie
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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="\"2024-03-27T15:11:24\"" -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/x86_64/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="\"2024-03-27T15:11:35\"" -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/x86_64/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)

R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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/4.4-x86_64/Resources/library/Rbowtie/bowtie version 1.3.0"  
[2] "64-bit"                                                                                              
[3] "Built on lconway"                                                                                    
[4] "2024-03-27T15:11:35"                                                                                 
[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 
  1.928   0.779   5.386