Multiple platform build/check report for BioC 3.7 - CHECK report for seqTools on tokay2

Package: seqTools

Version: 1.14.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seqTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings seqTools_1.14.0.tar.gz

StartedAt: 2018-10-17 04:47:51 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 04:48:38 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 46.6 seconds

RetCode: 0

Status: WARNINGS

CheckDir: seqTools.Rcheck

Warnings: 3

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##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seqTools.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings seqTools_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/seqTools.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '1.14.0'
* 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 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-3.7-bioc/R/library/seqTools/libs/i386/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-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqTools/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.7-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-3.7-bioc/meat/seqTools.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/seqTools_1.14.0.tar.gz && rm -rf seqTools.buildbin-libdir && mkdir seqTools.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seqTools.buildbin-libdir seqTools_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL seqTools_1.14.0.zip && rm seqTools_1.14.0.tar.gz seqTools_1.14.0.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  1898k      0 --:--:-- --:--:-- --:--:-- 2186k

install for i386

* installing *source* package 'seqTools' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c seqTools.c -o seqTools.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o seqTools.dll tmp.def seqTools.o -lm -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/seqTools.buildbin-libdir/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
In R CMD INSTALL

install for x64

* installing *source* package 'seqTools' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c seqTools.c -o seqTools.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o seqTools.dll tmp.def seqTools.o -lm -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/seqTools.buildbin-libdir/seqTools/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seqTools' as seqTools_1.14.0.zip
* DONE (seqTools)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'seqTools' successfully unpacked and MD5 sums checked
In R CMD INSTALL


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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-3.7-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-3.7-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-3.7-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-3.7-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-3.7-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-3.7-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 
   0.37    0.09    0.62


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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-3.7-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-3.7-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-3.7-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-3.7-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-3.7-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-3.7-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 
   0.28    0.04    0.31


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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 
   0.35    0.01    0.35


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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 
   0.34    0.06    0.39

name	user	system	elapsed
ascii2char	0	0	0
cbDistMatrix	0	0	0
countDnaKmers	0	0	0
countFastaKmers	0	0	0
countGenomeKmers	0	0	0
countSpliceKmers	0.02	0.00	0.02
kMerIndex	0	0	0
phredTable	0	0	0
revCountDnaKmers	0	0	0
simFastqqRunTimes	0	0	0
sim_fq	0	0	0
writeFai	0	0	0
writeSimContFastq	0	0	0
writeSimFastq	0.01	0.00	0.01

name	user	system	elapsed
ascii2char	0	0	0
cbDistMatrix	0	0	0
countDnaKmers	0	0	0
countFastaKmers	0	0	0
countGenomeKmers	0	0	0
countSpliceKmers	0.02	0.00	0.02
kMerIndex	0	0	0
phredTable	0.02	0.00	0.01
revCountDnaKmers	0	0	0
simFastqqRunTimes	0	0	0
sim_fq	0	0	0
writeFai	0	0	0
writeSimContFastq	0	0	0
writeSimFastq	0	0	0

CHECK report for seqTools on tokay2

Summary

Command output

Installation output

Tests output

Example timings