Bioconductor Package Maintainer
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/ShortRead |
| Branch: RELEASE_3_6 |
| Last Commit: 176c34e |
| Last Changed Date: 2018-02-21 05:40:48 -0400 (Wed, 21 Feb 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:08:22 -0400 (Thu, 12 Apr 2018).
| Package 1287/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ShortRead 1.36.1 Bioconductor Package Maintainer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: ShortRead |
| Version: 1.36.1 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ShortRead_1.36.1.tar.gz |
| StartedAt: 2018-04-12 02:54:31 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:58:31 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 240.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ShortRead.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings ShortRead_1.36.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/ShortRead.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ShortRead/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ShortRead’ version ‘1.36.1’
* 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 ‘ShortRead’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.7Mb
sub-directories of 1Mb or more:
extdata 4.0Mb
* 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 ... NOTE
Unexported objects imported by ':::' calls:
‘Biostrings:::xscodes’ ‘S4Vectors:::V_recycle’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.plotCycleBaseCall: no visible binding for global variable ‘Base’
.readAligned_bam: no visible global function definition for
‘.readAligned_bamWhat’
flag,QAReadQuality: no visible binding for global variable ‘Score’
flag,QAReadQuality: no visible binding for global variable ‘Id’
flag,QAReadQuality: no visible binding for global variable ‘Density’
report,QAFrequentSequence: no visible binding for global variable
‘TopCount’
report,QAFrequentSequence: no visible binding for global variable ‘Id’
report,QANucleotideByCycle: no visible binding for global variable
‘Base’
report,QANucleotideUse: no visible binding for global variable
‘Nucleotide’
report,QAQualityUse: no visible binding for global variable ‘Count’
report,QAQualityUse: no visible binding for global variable ‘Id’
report,QAQualityUse: no visible binding for global variable ‘Quality’
report,QAReadQuality: no visible binding for global variable ‘Id’
report,QASequenceUse: no visible binding for global variable
‘Occurrences’
report,QASequenceUse: no visible binding for global variable ‘Id’
report,QASequenceUse: no visible binding for global variable ‘Reads’
Undefined global functions or variables:
.readAligned_bamWhat Base Count Density Id Nucleotide Occurrences
Quality Reads Score TopCount
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'AlignedRead-class.Rd':
‘[IRanges:IntervalTree-class]{overlap}’
Missing link or links in documentation object 'SRFilter-class.Rd':
‘[IRanges]{FilterRules}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘left’ ‘right’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Snapshot-class 6.5 0.088 6.677
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘ShortRead_unit_tests.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: 2 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.6-bioc/meat/ShortRead.Rcheck/00check.log’
for details.
ShortRead.Rcheck/00install.out
* installing *source* package ‘ShortRead’ ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of unsigned long... 8
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c alphabet.c -o alphabet.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c io.c -o io.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c io_bowtie.c -o io_bowtie.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c io_soap.c -o io_soap.o
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -Wall -c readBfaToc.cc -o readBfaToc.o
readBfaToc.cc: In function ‘SEXPREC* readBfaToc(SEXP)’:
readBfaToc.cc:19:40: warning: variable ‘status’ set but not used [-Wunused-but-set-variable]
int name_len, seq_ori_len, seq_len, status;
^
g++ -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic -g -O2 -Wall -c read_maq_map.cc -o read_maq_map.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c sampler.c -o sampler.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c trim.c -o trim.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c util.c -o util.o
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG -I"/home/biocbuild/bbs-3.6-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/Biostrings/include" -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c xsnap.c -o xsnap.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/ShortRead.Rcheck/ShortRead/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ShortRead)
ShortRead.Rcheck/tests/ShortRead_unit_tests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.
> BiocGenerics:::testPackage("ShortRead")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following object is masked from 'package:Biostrings':
type
The following object is masked from 'package:base':
apply
RUNIT TEST PROTOCOL -- Thu Apr 12 02:58:26 2018
***********************************************
Number of test functions: 103
Number of errors: 0
Number of failures: 0
1 Test Suite :
ShortRead RUnit Tests - 103 test functions, 0 errors, 0 failures
Number of test functions: 103
Number of errors: 0
Number of failures: 0
Warning messages:
1: In .Internal(gc(verbose, reset)) :
closing unused connection 6 (/home/biocbuild/bbs-3.6-bioc/meat/ShortRead.Rcheck/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
2: In .Internal(gc(verbose, reset)) :
closing unused connection 5 (/home/biocbuild/bbs-3.6-bioc/meat/ShortRead.Rcheck/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt)
3: In .Internal(gc(verbose, reset)) :
closing unused connection 3 (/tmp/Rtmpy81Cdk/file2c3238dd493a)
>
> proc.time()
user system elapsed
54.824 0.860 64.118
ShortRead.Rcheck/ShortRead-Ex.timings
| name | user | system | elapsed | |
| AlignedRead-class | 0.820 | 0.024 | 0.846 | |
| BowtieQA-class | 0.000 | 0.000 | 0.001 | |
| ExperimentPath-class | 0.000 | 0.000 | 0.001 | |
| FastqQA-class | 0.000 | 0.000 | 0.001 | |
| Intensity-class | 0.160 | 0.000 | 0.157 | |
| MAQMapQA-class | 0.000 | 0.000 | 0.001 | |
| QA-class | 0.000 | 0.004 | 0.001 | |
| QualityScore-class | 0.016 | 0.000 | 0.016 | |
| QualityScore | 0.004 | 0.000 | 0.005 | |
| RochePath-class | 0.000 | 0.000 | 0.001 | |
| RocheSet-class | 0.000 | 0.000 | 0.001 | |
| RtaIntensity-class | 0.044 | 0.000 | 0.044 | |
| RtaIntensity | 0.024 | 0.000 | 0.025 | |
| SRFilter-class | 0.000 | 0.000 | 0.001 | |
| SRFilterResult-class | 0.064 | 0.000 | 0.064 | |
| SRSet-class | 0 | 0 | 0 | |
| SRUtil-class | 0.004 | 0.000 | 0.004 | |
| Sampler-class | 0.956 | 0.008 | 0.964 | |
| ShortRead-class | 0.052 | 0.000 | 0.050 | |
| ShortReadQ-class | 0.276 | 0.008 | 0.284 | |
| Snapshot-class | 6.500 | 0.088 | 6.677 | |
| SnapshotFunction-class | 0.000 | 0.000 | 0.001 | |
| SolexaExportQA-class | 0.000 | 0.000 | 0.001 | |
| SolexaIntensity-class | 0.164 | 0.012 | 0.174 | |
| SolexaPath-class | 0.068 | 0.000 | 0.068 | |
| SolexaSet-class | 0.056 | 0.004 | 0.062 | |
| SpTrellis-class | 0.444 | 0.000 | 0.445 | |
| accessors | 0.000 | 0.000 | 0.002 | |
| alphabetByCycle | 0.012 | 0.008 | 0.018 | |
| clean | 0.000 | 0.000 | 0.001 | |
| countLines | 0.108 | 0.008 | 0.119 | |
| dotQA-class | 0.000 | 0.000 | 0.001 | |
| dustyScore | 0.048 | 0.000 | 0.047 | |
| filterFastq | 0.600 | 0.000 | 0.603 | |
| polyn | 0.000 | 0.000 | 0.001 | |
| qa | 0.416 | 0.016 | 0.433 | |
| qa2 | 3.548 | 0.048 | 3.596 | |
| readAligned | 0.236 | 0.000 | 0.236 | |
| readBaseQuality | 0.080 | 0.100 | 0.196 | |
| readFasta | 0.144 | 0.012 | 0.201 | |
| readFastq | 0.080 | 0.000 | 0.079 | |
| readIntensities | 0.068 | 0.004 | 0.073 | |
| readPrb | 0.052 | 0.008 | 0.059 | |
| readQseq | 0.008 | 0.004 | 0.010 | |
| readXStringColumns | 0.032 | 0.016 | 0.046 | |
| renew | 0.032 | 0.004 | 0.038 | |
| report | 0.004 | 0.000 | 0.005 | |
| spViewPerFeature | 3.036 | 0.076 | 3.112 | |
| srFilter | 0.308 | 0.004 | 0.311 | |
| srdistance | 0.188 | 0.048 | 0.348 | |
| srduplicated | 0.036 | 0.004 | 0.041 | |
| tables | 0.160 | 0.012 | 0.172 | |
| trimTails | 0.044 | 0.000 | 0.042 | |