##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seqTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seqTools_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/seqTools.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.32.0’
* 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 use of PKG_*FLAGS in Makefiles ... 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/4.2/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/seqTools/extdata’, resetting
  Warning: working directory was changed to ‘/Library/Frameworks/R.framework/Versions/4.2/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-3.16-bioc/meat/seqTools.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘seqTools’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c seqTools.c -o seqTools.o
clang -mmacosx-version-min=10.13 -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/4.2/Resources/library/00LOCK-seqTools/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (seqTools)

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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/4.2/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/4.2/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/4.2/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/4.2/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/4.2/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/4.2/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 
  0.258   0.082   0.327 

R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  0.233   0.086   0.609