Wolfgang Kaisers
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/seqTools |
| git_branch: RELEASE_3_13 |
| git_last_commit: f74d126 |
| git_last_commit_date: 2021-05-19 12:09:43 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:22 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the seqTools package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seqTools.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1743/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| seqTools 1.26.0 (landing page) Wolfgang Kaisers
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: seqTools |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seqTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings seqTools_1.26.0.tar.gz |
| StartedAt: 2021-10-15 05:32:55 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 05:33:39 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 44.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: seqTools.Rcheck |
| Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seqTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings seqTools_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/seqTools.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'seqTools/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'seqTools' version '1.26.0' * 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 whether package 'seqTools' can be installed ... OK * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... WARNING Undocumented code objects: 'kmerSvd' Undocumented S4 methods: generic 'kmerSvd' and siglist 'Fastqq' All user-level objects in a package (including S4 classes and methods) 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 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 use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/libs/i386/seqTools.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) File 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/libs/x64/seqTools.dll': Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... WARNING Found the following significant warnings: Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting ** running examples for arch 'x64' ... WARNING Found the following significant warnings: Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata', resetting * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'test-all.R' Running 'test_seqTools.r' OK ** running tests for arch 'x64' ... Running 'test-all.R' Running 'test_seqTools.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: 3 WARNINGs, 1 NOTE See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/seqTools.Rcheck/00check.log' for details.
seqTools.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/seqTools_1.26.0.tar.gz && rm -rf seqTools.buildbin-libdir && mkdir seqTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seqTools.buildbin-libdir seqTools_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL seqTools_1.26.0.zip && rm seqTools_1.26.0.tar.gz seqTools_1.26.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 109k 100 109k 0 0 575k 0 --:--:-- --:--:-- --:--:-- 580k
install for i386
* installing *source* package 'seqTools' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"c:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c seqTools.c -o seqTools.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o seqTools.dll tmp.def seqTools.o -lm -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/seqTools.buildbin-libdir/00LOCK-seqTools/00new/seqTools/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'seqTools'
finding HTML links ... done
Fastqq-class html
ascii2char html
cbDistMatrix html
collectDur html
countDnaKmers html
countFastaKmers html
countGenomeKmers html
countSpliceKmers html
fastqKmerLocs html
fastqKmerSubsetLocs html
fastqq html
gcContentMatrix html
kMerIndex html
meltDownK html
mergeFastqq html
mergedPhred html
phredDist html
phredTable html
plotGCcontent html
plotKmerCount html
plotNucCount html
plotNucFreq html
plotPhredQuant html
propPhred html
revCountDnaKmers html
seqTools-package html
simFastqqRunTimes html
sim_fq html
trimFastq html
writeFai html
writeSimContFastq html
writeSimFastq html
** 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
install for x64
* installing *source* package 'seqTools' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c seqTools.c -o seqTools.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o seqTools.dll tmp.def seqTools.o -lm -LC:/Users/biocbuild/bbs-3.13-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/seqTools.buildbin-libdir/seqTools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seqTools' as seqTools_1.26.0.zip
* DONE (seqTools)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'seqTools' successfully unpacked and MD5 sums checked
|
seqTools.Rcheck/tests_i386/test-all.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.
>
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Load prerequisites
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> library(seqTools)
Loading required package: zlibbioc
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Initialize example data
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> basedir<-system.file("extdata",package="seqTools")
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Run tests
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> filename <- "test_seqTools.R"
> basedir <- system.file("extdata", package = "seqTools")
> load(file.path(basedir,"test_res.RData"))
>
>
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## kmerCount.fastqq
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> fq <- fastqq(file.path(basedir, "test_l5_N.fq"), k = 2)
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata/test_l5_N.fq' done.
> if(!identical(kmerCount(fq), kmer_l5_N))
+ stop("[kmerCount.fastqq] Test 1 '", filename, "' FAILED!")
>
> fq<-fastqq(file.path(basedir, "test_l6.fq"), k = 2)
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata/test_l6.fq' done.
> if(!identical(kmerCount(fq), kmer_l6))
+ stop("[kmerCount.fastqq] Test 2 '", filename, "' FAILED!")
>
> fq<-fastqq(file.path(basedir, "test_l6_multi_line.fq"), k = 2)
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata/test_l6_multi_line.fq' done.
> if(!identical(kmerCount(fq), kmer_l6_ml))
+ stop("[kmerCount.fastqq] Test 3 '", filename, "' FAILED!")
>
> fq<-fastqq(file.path(basedir, "test_l10_20_40.fq"),k = 2)
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata/test_l10_20_40.fq' done.
> if(!identical(kmerCount(fq), kmer_l10_20))
+ stop("[kmerCount.fastqq] Test 4 '", filename, "' FAILED!")
>
> fq<-fastqq(file.path(basedir, "test_l10_atcg.fq"), k = 2)
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata/test_l10_atcg.fq' done.
> if(!identical(kmerCount(fq), kmer_l10_atcg))
+ stop("[kmerCount.fastqq] Test 5 '", filename, "' FAILED!")
>
> fq<-fastqq(file.path(basedir, "test_l10_ATCGN.fq"), k = 2)
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata/test_l10_ATCGN.fq' done.
> if(!identical(kmerCount(fq), kmer_l10_ATCGN))
+ stop("[kmerCount.fastqq] Test 6 '", filename, "' FAILED!")
>
> # Counting k-mers on linux ('\n') and equal windows ('\r\n')
> # formatted FASTQ file should give equal results
> # fq<-fastqq(file.path(basedir, c("test_l4.fq", "test_win.fq")), k = 2)
> # kc <- kmerCount(fq)
> # if(!all(kc[,1]==kc[,2]))
> # stop("[kmerCount.fastqq] test_l4: kmerCount unequal to test_win.fq")
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## ascii2char, char2ascii
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> if(!identical(ascii2char(97:101, multiple = FALSE), "abcde"))
+ stop("[ascii2char] Test 1 '", filename, "' FAILED!")
>
> if(!identical(ascii2char(97:101, multiple = TRUE), letters[1:5]))
+ stop("[ascii2char] Test 2 '", filename, "' FAILED!")
>
> if(!identical(ascii2char(char2ascii("abcde")), "abcde"))
+ stop("[ascii2char] Test 3 '", filename, "' FAILED!")
>
> if(!identical(char2ascii("abcde"), 97:101))
+ stop("[char2ascii] Test 1 '", filename, "' FAILED!")
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## END OF FILE
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
>
> proc.time()
user system elapsed
0.43 0.00 0.42
|
seqTools.Rcheck/tests_x64/test-all.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
>
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Load prerequisites
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> library(seqTools)
Loading required package: zlibbioc
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Initialize example data
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> basedir<-system.file("extdata",package="seqTools")
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Run tests
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> filename <- "test_seqTools.R"
> basedir <- system.file("extdata", package = "seqTools")
> load(file.path(basedir,"test_res.RData"))
>
>
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## kmerCount.fastqq
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> fq <- fastqq(file.path(basedir, "test_l5_N.fq"), k = 2)
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata/test_l5_N.fq' done.
> if(!identical(kmerCount(fq), kmer_l5_N))
+ stop("[kmerCount.fastqq] Test 1 '", filename, "' FAILED!")
>
> fq<-fastqq(file.path(basedir, "test_l6.fq"), k = 2)
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata/test_l6.fq' done.
> if(!identical(kmerCount(fq), kmer_l6))
+ stop("[kmerCount.fastqq] Test 2 '", filename, "' FAILED!")
>
> fq<-fastqq(file.path(basedir, "test_l6_multi_line.fq"), k = 2)
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata/test_l6_multi_line.fq' done.
> if(!identical(kmerCount(fq), kmer_l6_ml))
+ stop("[kmerCount.fastqq] Test 3 '", filename, "' FAILED!")
>
> fq<-fastqq(file.path(basedir, "test_l10_20_40.fq"),k = 2)
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata/test_l10_20_40.fq' done.
> if(!identical(kmerCount(fq), kmer_l10_20))
+ stop("[kmerCount.fastqq] Test 4 '", filename, "' FAILED!")
>
> fq<-fastqq(file.path(basedir, "test_l10_atcg.fq"), k = 2)
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata/test_l10_atcg.fq' done.
> if(!identical(kmerCount(fq), kmer_l10_atcg))
+ stop("[kmerCount.fastqq] Test 5 '", filename, "' FAILED!")
>
> fq<-fastqq(file.path(basedir, "test_l10_ATCGN.fq"), k = 2)
[fastqq] File ( 1/1) 'C:/Users/biocbuild/bbs-3.13-bioc/R/library/seqTools/extdata/test_l10_ATCGN.fq' done.
> if(!identical(kmerCount(fq), kmer_l10_ATCGN))
+ stop("[kmerCount.fastqq] Test 6 '", filename, "' FAILED!")
>
> # Counting k-mers on linux ('\n') and equal windows ('\r\n')
> # formatted FASTQ file should give equal results
> # fq<-fastqq(file.path(basedir, c("test_l4.fq", "test_win.fq")), k = 2)
> # kc <- kmerCount(fq)
> # if(!all(kc[,1]==kc[,2]))
> # stop("[kmerCount.fastqq] test_l4: kmerCount unequal to test_win.fq")
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## ascii2char, char2ascii
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> if(!identical(ascii2char(97:101, multiple = FALSE), "abcde"))
+ stop("[ascii2char] Test 1 '", filename, "' FAILED!")
>
> if(!identical(ascii2char(97:101, multiple = TRUE), letters[1:5]))
+ stop("[ascii2char] Test 2 '", filename, "' FAILED!")
>
> if(!identical(ascii2char(char2ascii("abcde")), "abcde"))
+ stop("[ascii2char] Test 3 '", filename, "' FAILED!")
>
> if(!identical(char2ascii("abcde"), 97:101))
+ stop("[char2ascii] Test 1 '", filename, "' FAILED!")
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## END OF FILE
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
>
> proc.time()
user system elapsed
0.40 0.03 0.42
|
|
seqTools.Rcheck/tests_i386/test_seqTools.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Load prerequisites
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> library(seqTools)
Loading required package: zlibbioc
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Initialize example data
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> basedir<-system.file("extdata",package="seqTools")
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Run tests
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> filename <- "test_seqTools.R"
> basedir <- system.file("extdata", package = "seqTools")
> load(file.path(basedir,"test_res.RData"))
>
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## countDnaKmers
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> if(!identical(countDnaKmers("ACGT", k = 1, start = 3:1, width = 1), cdk_ACGT))
+ stop("[countDnaKmers] Test 1 '", filename, "' FAILED!")
>
> if(!identical(countDnaKmers("ACGT", k = 1, start = 3, width = 1), cdk_ACGT_one))
+ stop("[countDnaKmers] Test 2 '", filename, "' FAILED!")
>
> if(!identical(
+ countDnaKmers("ATTNAC", k = 2, start = 1:3, width = 1), cdk_ATTNAC))
+ stop("[countDnaKmers] Test 3 '", filename, "' FAILED!")
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## revCountDnaKmers
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> if(!identical(
+ revCountDnaKmers("ACGTACGT", k = 2, start = 6:4, width = 2), rck_ACGT))
+ stop("[revCountDnaKmers] Test 1 '", filename, "' FAILED!")
>
>
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## END OF FILE
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> proc.time()
user system elapsed
0.37 0.09 0.43
|
seqTools.Rcheck/tests_x64/test_seqTools.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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.
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Load prerequisites
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> library(seqTools)
Loading required package: zlibbioc
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Initialize example data
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> basedir<-system.file("extdata",package="seqTools")
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## Run tests
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> filename <- "test_seqTools.R"
> basedir <- system.file("extdata", package = "seqTools")
> load(file.path(basedir,"test_res.RData"))
>
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## countDnaKmers
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> if(!identical(countDnaKmers("ACGT", k = 1, start = 3:1, width = 1), cdk_ACGT))
+ stop("[countDnaKmers] Test 1 '", filename, "' FAILED!")
>
> if(!identical(countDnaKmers("ACGT", k = 1, start = 3, width = 1), cdk_ACGT_one))
+ stop("[countDnaKmers] Test 2 '", filename, "' FAILED!")
>
> if(!identical(
+ countDnaKmers("ATTNAC", k = 2, start = 1:3, width = 1), cdk_ATTNAC))
+ stop("[countDnaKmers] Test 3 '", filename, "' FAILED!")
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## revCountDnaKmers
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> if(!identical(
+ revCountDnaKmers("ACGTACGT", k = 2, start = 6:4, width = 2), rck_ACGT))
+ stop("[revCountDnaKmers] Test 1 '", filename, "' FAILED!")
>
>
>
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
> ## END OF FILE
> ## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
>
> proc.time()
user system elapsed
0.35 0.04 0.39
|
|
seqTools.Rcheck/examples_i386/seqTools-Ex.timings
|
seqTools.Rcheck/examples_x64/seqTools-Ex.timings
|