Wolfgang Kaisers
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/seqTools |
| Branch: RELEASE_3_8 |
| Last Commit: 420c3f6 |
| Last Changed Date: 2018-10-30 11:41:56 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:58:10 -0400 (Tue, 16 Apr 2019).
| Package 1427/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| seqTools 1.16.0 Wolfgang Kaisers
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: seqTools |
| Version: 1.16.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:seqTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings seqTools_1.16.0.tar.gz |
| StartedAt: 2019-04-16 02:44:35 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:45:05 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 30.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: seqTools.Rcheck |
| Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:seqTools.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings seqTools_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/seqTools.Rcheck’ * using R version 3.5.3 (2019-03-11) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘seqTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘seqTools’ version ‘1.16.0’ * 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 ‘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 * 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 is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... WARNING Found the following significant warnings: Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/extdata’, resetting * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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: 2 WARNINGs, 1 NOTE See ‘/Users/biocbuild/bbs-3.8-bioc/meat/seqTools.Rcheck/00check.log’ for details.
seqTools.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL seqTools ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘seqTools’ ... ** libs clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I/usr/local/include -fPIC -Wall -g -O2 -c seqTools.c -o seqTools.o clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o seqTools.so seqTools.o -lm -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/seqTools/libs ** 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 * DONE (seqTools)
seqTools.Rcheck/tests/test-all.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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) '/Library/Frameworks/R.framework/Versions/3.5/Resources/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) '/Library/Frameworks/R.framework/Versions/3.5/Resources/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) '/Library/Frameworks/R.framework/Versions/3.5/Resources/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) '/Library/Frameworks/R.framework/Versions/3.5/Resources/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) '/Library/Frameworks/R.framework/Versions/3.5/Resources/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) '/Library/Frameworks/R.framework/Versions/3.5/Resources/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
0.358 0.072 0.406
seqTools.Rcheck/tests/test_seqTools.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
0.359 0.074 0.410
seqTools.Rcheck/seqTools-Ex.timings
| name | user | system | elapsed | |
| ascii2char | 0.001 | 0.000 | 0.001 | |
| cbDistMatrix | 0.004 | 0.001 | 0.006 | |
| countDnaKmers | 0.000 | 0.000 | 0.001 | |
| countFastaKmers | 0.001 | 0.001 | 0.001 | |
| countGenomeKmers | 0.001 | 0.000 | 0.001 | |
| countSpliceKmers | 0.002 | 0.001 | 0.003 | |
| kMerIndex | 0.001 | 0.000 | 0.001 | |
| phredTable | 0.007 | 0.002 | 0.008 | |
| revCountDnaKmers | 0.001 | 0.000 | 0.001 | |
| simFastqqRunTimes | 0 | 0 | 0 | |
| sim_fq | 0 | 0 | 0 | |
| writeFai | 0.000 | 0.001 | 0.000 | |
| writeSimContFastq | 0 | 0 | 0 | |
| writeSimFastq | 0.001 | 0.000 | 0.002 | |