Package: QuasR

Version: 1.20.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:QuasR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings QuasR_1.20.0.tar.gz

StartedAt: 2018-10-17 04:11:29 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 04:26:02 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 873.4 seconds

RetCode: 0

Status:  OK

CheckDir: QuasR.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:QuasR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings QuasR_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.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 'QuasR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'QuasR' version '1.20.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'QuasR' 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 ... NOTE
'library' or 'require' call to 'RUnit' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  'ShortRead:::.ShortReadQQA' 'ShortRead:::.qa_adapterContamination'
  'ShortRead:::.set_omp_threads'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(ShortRead:::.set_omp_threads, ...)
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
test: no visible global function definition for 'defineTestSuite'
test: no visible global function definition for 'runTestSuite'
test: no visible global function definition for 'printTextProtocol'
Undefined global functions or variables:
  defineTestSuite printTextProtocol runTestSuite
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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 x64 is not available
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
qCount         13.43   0.95   44.13
qMeth           0.66   0.17   20.41
qProject-class  0.40   0.07   16.09
qExportWig      0.29   0.03   17.48
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'QuasR_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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/00check.log'
for details.

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch QuasR
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* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
* installing *source* package 'QuasR' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_init_QuasR.cpp -o R_init_QuasR.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c cat_bam.c -o cat_bam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c count_alignments.c -o count_alignments.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c count_alignments_subregions.c -o count_alignments_subregions.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c count_junctions.cpp -o count_junctions.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c export_wig.c -o export_wig.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c extract_unmapped_reads.c -o extract_unmapped_reads.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c idxstats_bam.c -o idxstats_bam.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c merge_reorder_sam.cpp -o merge_reorder_sam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c profile_alignments.c -o profile_alignments.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c quantify_methylation.cpp -o quantify_methylation.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c split_sam_chr.c -o split_sam_chr.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c utilities.c -o utilities.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o QuasR.dll tmp.def R_init_QuasR.o cat_bam.o convert_reads_id_bis_rc.o count_alignments.o count_alignments_subregions.o count_junctions.o export_wig.o extract_unmapped_reads.o idxstats_bam.o merge_reorder_sam.o nucleotide_alignment_frequencies.o profile_alignments.o quantify_methylation.o remove_unmapped_from_sam.o split_sam_chr.o utilities.o C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/biocbuild/bbs-3.7-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/R/library/QuasR/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'QuasR'
    finding HTML links ... done
    QuasR-package                           html  
    alignmentStats                          html  
    preprocessReads                         html  
    qAlign                                  html  
    qCount                                  html  
    qExportWig                              html  
    qMeth                                   html  
    qProfile                                html  
    qProject-class                          html  
    qQCReport                               html  
    finding level-2 HTML links ... done

** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (QuasR)
Making 'packages.html' ... done
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: 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.

> require("QuasR") || stop("unable to load QuasR package")
Loading required package: QuasR
Loading required package: parallel
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: Rbowtie
[1] TRUE
> QuasR:::test()


Executing test function test_input_fasta  ...   filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c4f191511.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c4f191511.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c4f191511.fa
 done successfully.



Executing test function test_input_fastq  ... Read 36 items
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtm.../file250c2a6d6cb.fq.gz
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\R.../file250c35dc66e9.fq.bz2
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c7896253a.fq.xz
 done successfully.



Executing test function test_paired_fasta  ... Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: Rsamtools
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

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 objects are masked from 'package:base':

    aperm, apply

  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\R.../file250c4f191511.fa and
    C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c205c77b9.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\R.../file250c4f191511.fa and
    C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c205c77b9.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\R.../file250c4f191511.fa and
    C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c205c77b9.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\R.../file250c4f191511.fa and
    C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c205c77b9.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\R.../file250c4f191511.fa and
    C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c205c77b9.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\R.../file250c4f191511.fa and
    C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c205c77b9.fa
 done successfully.



Executing test function test_paired_fastq  ...   filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c7a4dadd.fq and
    C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c3bb64a92.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c7a4dadd.fq and
    C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c3bb64a92.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c7a4dadd.fq and
    C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c3bb64a92.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c7a4dadd.fq and
    C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c3bb64a92.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c7a4dadd.fq and
    C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c3bb64a92.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c7a4dadd.fq and
    C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rt.../file250c3bb64a92.fq
 done successfully.



Executing test function test_single_fasta  ...   filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c4f191511.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c205c77b9.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c4f191511.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c205c77b9.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c4f191511.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c205c77b9.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c4f191511.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c205c77b9.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c4f191511.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c205c77b9.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c4f191511.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c205c77b9.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c4f191511.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c205c77b9.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c4f191511.fa
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c205c77b9.fa
 done successfully.



Executing test function test_single_fastq  ...   filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp06.../file250c7a4dadd.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c3bb64a92.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp06.../file250c7a4dadd.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c3bb64a92.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp06.../file250c7a4dadd.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c3bb64a92.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp06.../file250c7a4dadd.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c3bb64a92.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp06.../file250c7a4dadd.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c3bb64a92.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp06.../file250c7a4dadd.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c3bb64a92.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp06.../file250c7a4dadd.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c3bb64a92.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp06.../file250c7a4dadd.fq
  filtering C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp0.../file250c3bb64a92.fq
 done successfully.



Executing test function test_allelic_paired  ... alignment files missing - need to:
    create alignment index for the genome
    create 1 genomic alignment(s)
Reading and processing the SNP file: C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests/extdata/hg19sub_snp.txt
Creating the genome fasta file containing the SNPs: C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Creating the genome fasta file containing the SNPs: C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Creating a .fai file for the snp genome: C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Creating a .fai file for the snp genome: C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Creating an Rbowtie index for C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Finished creating index
Creating an Rbowtie index for C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c2ee83bb7.txt
Genomic alignments have been created successfully

 done successfully.



Executing test function test_allelic_paired_fasta  ... [samopen] SAM header is present: 3 sequences.
Timing stopped at: 0 0 0
Error in DEACTIVATED("deactivated to prevent timeout on bioc build system") : 
  deactivated to prevent timeout on bioc build system
 done successfully.



Executing test function test_allelic_single  ... alignment files missing - need to:
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250cbb62263.txt
Genomic alignments have been created successfully

 done successfully.



Executing test function test_allelic_single_fasta  ... [samopen] SAM header is present: 3 sequences.
Timing stopped at: 0 0 0
Error in DEACTIVATED("deactivated to prevent timeout on bioc build system") : 
  deactivated to prevent timeout on bioc build system
 done successfully.



Executing test function test_aux_bisulfite_paired_undir  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("deactivated to prevent timeout on bioc build system") : 
  deactivated to prevent timeout on bioc build system
 done successfully.



Executing test function test_aux_bisulfite_single_undir  ... alignment files missing - need to:
    create alignment index for the genome
    create 1 genomic alignment(s)
    create 1 auxiliary alignment(s)
Creating an RbowtieCtoT index for C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests/extdata/hg19sub.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c2ee3eb0.txt
Genomic alignments have been created successfully

Creating an RbowtieCtoT index for C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests/extdata/NC_001422.1.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing auxiliary alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c553878c5.txt
Auxiliary alignments have been created successfully

 done successfully.



Executing test function test_aux_normal_paired  ... [samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 1 sequences.
Timing stopped at: 0 0 0
Error in DEACTIVATED("deactivated to prevent timeout on bioc build system") : 
  deactivated to prevent timeout on bioc build system
 done successfully.



Executing test function test_aux_normal_single  ... alignment files missing - need to:
    create alignment index for the genome
    create 1 genomic alignment(s)
    create 1 auxiliary alignment(s)
Creating an Rbowtie index for C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests/extdata/hg19sub.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c7957295e.txt
Genomic alignments have been created successfully

Creating an Rbowtie index for C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests/extdata/NC_001422.1.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing auxiliary alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250cafe6b6f.txt
Auxiliary alignments have been created successfully

 done successfully.



Executing test function test_aux_spliced_paired  ... [samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 1 sequences.
alignment files missing - need to:
    create 1 genomic alignment(s)
    create 1 auxiliary alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c68ee19bc.txt
Genomic alignments have been created successfully

Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing auxiliary alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c4aaa44cd.txt
[samopen] SAM header is present: 3 sequences.
Auxiliary alignments have been created successfully

 done successfully.



Executing test function test_aux_spliced_single  ... [samopen] SAM header is present: 1 sequences.
Timing stopped at: 0 0 0
Error in DEACTIVATED("deactivated to prevent timeout on bioc build system") : 
  deactivated to prevent timeout on bioc build system
 done successfully.



Executing test function test_bisulfite_paired_dir  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("deactivated to prevent timeout on bioc build system") : 
  deactivated to prevent timeout on bioc build system
 done successfully.



Executing test function test_bisulfite_paired_dir_allelic  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("deactivated to prevent timeout on bioc build system") : 
  deactivated to prevent timeout on bioc build system
 done successfully.



Executing test function test_bisulfite_paired_dir_fasta  ... alignment files missing - need to:
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     1 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250ce8c56d0.txt
Genomic alignments have been created successfully

[samopen] SAM header is present: 3 sequences.
 done successfully.



Executing test function test_bisulfite_paired_undir  ... alignment files missing - need to:
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     1 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c74c66996.txt
Genomic alignments have been created successfully

[samopen] SAM header is present: 3 sequences.
 done successfully.



Executing test function test_bisulfite_single_dir  ... alignment files missing - need to:
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     1 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250cc013706.txt
Genomic alignments have been created successfully

[samopen] SAM header is present: 3 sequences.
 done successfully.



Executing test function test_bisulfite_single_dir_allelic  ... alignment files missing - need to:
    create alignment index for the genome
    create 1 genomic alignment(s)
Creating an RbowtieCtoT index for C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Finished creating index
Creating an RbowtieCtoT index for C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     1 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c41274d23.txt
Genomic alignments have been created successfully

[samopen] SAM header is present: 3 sequences.
 done successfully.



Executing test function test_bisulfite_single_dir_fasta  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("deactivated to prevent timeout on bioc build system") : 
  deactivated to prevent timeout on bioc build system
 done successfully.



Executing test function test_bisulfite_single_undir  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("deactivated to prevent timeout on bioc build system") : 
  deactivated to prevent timeout on bioc build system
 done successfully.



Executing test function test_maxHits_allelic  ... alignment files missing - need to:
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c79ed70cd.txt
Genomic alignments have been created successfully

 done successfully.



Executing test function test_maxHits_bisulfite  ... [samopen] SAM header is present: 3 sequences.
alignment files missing - need to:
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c4bb4d0c.txt
Genomic alignments have been created successfully

 done successfully.



Executing test function test_maxHits_simple  ... [samopen] SAM header is present: 3 sequences.
alignment files missing - need to:
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c27d379d.txt
Genomic alignments have been created successfully

 done successfully.



Executing test function test_normal_paired  ... [samopen] SAM header is present: 3 sequences.
Timing stopped at: 0 0 0
Error in DEACTIVATED("deactivated to prevent timeout on bioc build system") : 
  deactivated to prevent timeout on bioc build system
 done successfully.



Executing test function test_normal_paired_fasta  ... alignment files missing - need to:
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c2a5e3384.txt
Genomic alignments have been created successfully

 done successfully.



Executing test function test_normal_single  ... [samopen] SAM header is present: 3 sequences.
alignment files missing - need to:
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250ccc34239.txt
Genomic alignments have been created successfully

 done successfully.



Executing test function test_normal_single_fasta  ... [samopen] SAM header is present: 3 sequences.
Timing stopped at: 0 0 0
Error in DEACTIVATED("deactivated to prevent timeout on bioc build system") : 
  deactivated to prevent timeout on bioc build system
 done successfully.



Executing test function test_spliced_paired  ... alignment files missing - need to:
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c60e078a0.txt
Genomic alignments have been created successfully

 done successfully.



Executing test function test_spliced_paired_fasta  ... [samopen] SAM header is present: 3 sequences.
Timing stopped at: 0 0 0
Error in DEACTIVATED("deactivated to prevent timeout on bioc build system") : 
  deactivated to prevent timeout on bioc build system
 done successfully.



Executing test function test_spliced_single  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("deactivated to prevent timeout on bioc build system") : 
  deactivated to prevent timeout on bioc build system
 done successfully.



Executing test function test_spliced_single_fasta  ... alignment files missing - need to:
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c5fb54178.txt
Genomic alignments have been created successfully

 done successfully.

[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
Creating .fai file for: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp06538N/file250c39c64355.fa
all necessary alignment files found
[samopen] SAM header is present: 1 sequences.
Creating .fai file for: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp06538N/file250c4ff911be.fa
all necessary alignment files found
[samopen] SAM header is present: 1 sequences.
Creating .fai file for: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp06538N/file250c44536e.fa
all necessary alignment files found
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
Creating .fai file for: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp06538N/file250c31be7079.fa
all necessary alignment files found
Loading required package: rtracklayer


Executing test function test_auxiliaryName  ... alignment files missing - need to:
    create 2 genomic alignment(s)
    create 2 auxiliary alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 2 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c41f51d56.txt
Genomic alignments have been created successfully

Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing auxiliary alignments for 2 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c43d06989.txt
Auxiliary alignments have been created successfully

counting alignments...done
 done successfully.



Executing test function test_collapseBySample_GRanges  ... alignment files missing - need to:
    create 4 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 4 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c12de4afc.txt
Genomic alignments have been created successfully

counting alignments...done
collapsing counts by sample...done
collapsing counts by query name...done
counting alignments...done
collapsing counts by sample...done
collapsing counts by query name...done
counting alignments...done
collapsing counts by sample...done
collapsing counts by query name...done
alignment files missing - need to:
    create 4 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 4 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c61af1348.txt
Genomic alignments have been created successfully

counting alignments...done
collapsing counts by sample...done
collapsing counts by query name...done
counting alignments...done
collapsing counts by sample...done
collapsing counts by query name...done
counting alignments...done
collapsing counts by sample...done
collapsing counts by query name...done
 done successfully.



Executing test function test_includeSecondary  ... all necessary alignment files found
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
 done successfully.



Executing test function test_mapq  ... counting alignments...counting alignments...counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
 done successfully.



Executing test function test_maxInsertSize  ... counting alignments...done
counting alignments...done
 done successfully.



Executing test function test_orientation  ... counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
 done successfully.



Executing test function test_query_GRanges  ... counting alignments...done
collapsing counts by query name...done
counting alignments...done
collapsing counts by query name...done
counting alignments...done
collapsing counts by query name...done
counting alignments...done
counting alignments...done
counting alignments...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
removing 'mask' ranges from 'query'...done
counting alignments...done
removing 'mask' ranges from 'query'...done
counting alignments...done
removing 'mask' ranges from 'query'...done
counting alignments...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
 done successfully.



Executing test function test_query_GRangesList  ... hierarchically removing redundancy from 'query'...done
counting alignments...done
collapsing counts by query name...done
hierarchically removing redundancy from 'query'...done
counting alignments...done
collapsing counts by query name...done
hierarchically removing redundancy from 'query'...done
counting alignments...done
collapsing counts by query name...done
hierarchically removing redundancy from 'query'...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
hierarchically removing redundancy from 'query'...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
hierarchically removing redundancy from 'query'...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
hierarchically removing redundancy from 'query'...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
hierarchically removing redundancy from 'query'...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
 done successfully.



Executing test function test_query_GRangesList_allelic  ... hierarchically removing redundancy from 'query'...done
counting alignments...done
collapsing counts by query name...done
hierarchically removing redundancy from 'query'...done
counting alignments...done
collapsing counts by query name...done
hierarchically removing redundancy from 'query'...done
counting alignments...done
collapsing counts by query name...done
hierarchically removing redundancy from 'query'...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
hierarchically removing redundancy from 'query'...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
hierarchically removing redundancy from 'query'...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
 done successfully.



Executing test function test_query_GRanges_allelic  ... counting alignments...done
collapsing counts by query name...done
counting alignments...done
collapsing counts by query name...done
counting alignments...done
collapsing counts by query name...done
counting alignments...done
counting alignments...done
counting alignments...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
removing 'mask' ranges from 'query'...done
counting alignments...done
removing 'mask' ranges from 'query'...done
counting alignments...done
removing 'mask' ranges from 'query'...done
counting alignments...done
 done successfully.



Executing test function test_query_TxDb  ... alignment files missing - need to:
    create 4 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 4 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c43fa2e31.txt
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
Genomic alignments have been created successfully

Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
extracting gene regions from TxDb...done
counting alignments...done
collapsing counts by query name...done
extracting gene regions from TxDb...done
counting alignments...done
collapsing counts by query name...done
counting alignments...done
collapsing counts by query name...done
extracting exon regions from TxDb...done
counting alignments...done
counting alignments...done
extracting promoter regions from TxDb...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting junctions...done
extracting gene regions from TxDb...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by query name...done
extracting gene regions from TxDb...done
removing 'mask' ranges from 'query'...done
counting alignments...done
collapsing counts by sample...done
collapsing counts by query name...done
 done successfully.



Executing test function test_shift  ... counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
 done successfully.



Executing test function test_shift_allelic  ... counting alignments...done
counting alignments...done
counting alignments...done
 done successfully.



Executing test function test_useRead  ... counting alignments...done
counting alignments...done
counting alignments...done
counting alignments...done
 done successfully.



Executing test function test_exportWig  ... all necessary alignment files found
start creating wig files...
  C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp06538N\file250c17a04ad7.wig (Sample1)
  C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp06538N\file250c457d6a79.wig (Sample2)
done
counting alignments...done
alignment files missing - need to:
    create 2 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 2 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c352e4f.txt
Genomic alignments have been created successfully

start creating wig files...
  C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp06538N\file250c476e7a9e.wig (Sample1)
  C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp06538N\file250c185e4284.wig (Sample2)
done
counting alignments...done
all necessary alignment files found
start creating wig file...
  C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp06538N\file250c73ae50f8.wig.gz (test)
done
start creating wig file...
  C:\Users\biocbuild\bbs-3.7-bioc\tmpdir\Rtmp06538N\file250c73ae50f8.wig.gz (test)
done
counting alignments...done
counting alignments...done
 done successfully.

[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.


Executing test function test_full_meth_paired_dir  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("deactivated to prevent timeout on bioc build system") : 
  deactivated to prevent timeout on bioc build system
In addition: Warning message:
In .get_cds_IDX(type, phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
 done successfully.



Executing test function test_full_meth_paired_undir  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("deactivated to prevent timeout on bioc build system") : 
  deactivated to prevent timeout on bioc build system
 done successfully.



Executing test function test_full_meth_single_undir  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("deactivated to prevent timeout on bioc build system") : 
  deactivated to prevent timeout on bioc build system
 done successfully.



Executing test function test_partial_meth_paired_dir  ... alignment files missing - need to:
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c508b119d.txt
Genomic alignments have been created successfully

 done successfully.



Executing test function test_un_meth_paired_dir  ... alignment files missing - need to:
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c561e12c0.txt
Genomic alignments have been created successfully

 done successfully.



Executing test function test_un_meth_paired_undir  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("deactivated to prevent timeout on bioc build system") : 
  deactivated to prevent timeout on bioc build system
 done successfully.



Executing test function test_un_meth_single_undir  ... alignment files missing - need to:
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c18ba468a.txt
Genomic alignments have been created successfully

 done successfully.



Executing test function test_qProfile  ... all necessary alignment files found
profiling alignments...done
counting alignments...done
profiling alignments...done
counting alignments...done
profiling alignments...done
counting alignments...done
all necessary alignment files found
profiling alignments...done
counting alignments...done
all necessary alignment files found
counting alignments...done
counting alignments...done
profiling alignments...done
profiling alignments...done
 done successfully.

all necessary alignment files found
alignment files missing - need to:
    create 4 auxiliary alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY2 
     2 
Performing auxiliary alignments for 4 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rcheck/tests\QuasR_log_250c5e0c3c32.txt
Auxiliary alignments have been created successfully



Executing test function test_alignment  ...  done successfully.



Executing test function test_auxiliary  ... [samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
[samopen] SAM header is present: 1 sequences.
 done successfully.



Executing test function test_genome  ...  done successfully.



Executing test function test_length  ...  done successfully.



Executing test function test_show  ... Project: qProject
 Options   : maxHits         : 1
             paired          : no
             splicedAlignment: FALSE
             bisulfite       : no
             snpFile         : none
 Aligner   : Rbowtie v1.20.0 (parameters: -m 1 --best --strata)
 Genome    : C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rch.../hg19sub.fa (file)

 Reads     : 4 files, 2 samples (fastq format):
   1. rna_1_1.fq.bz2  Sample1 (phred33)
   2. rna_1_2.fq.bz2  Sample1 (phred33)
   3. rna_2_1.fq.bz2  Sample2 (phred33)
   4. rna_2_2.fq.bz2  Sample2 (phred33)

 Genome alignments: directory: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp06538N
   1. rna_1_1_250c5d61bd3.bam 
   2. rna_1_2_250c2bac516.bam 
   3. rna_2_1_250c189c765e.bam
   4. rna_2_2_250c118d31d2.bam

 Aux. alignments: none

Project: qProject
 Options   : maxHits         : 1
             paired          : no
             splicedAlignment: FALSE
             bisulfite       : no
             snpFile         : none
 Aligner   : Rbowtie v1.20.0 (parameters: -m 1 --best --strata)
 Genome    : C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rch.../hg19sub.fa (file)

 Reads     : 4 files, 2 samples (fastq format):
   1. rna_1_1.fq.bz2  Sample1 (phred33)
   2. rna_1_2.fq.bz2  Sample1 (phred33)
   3. rna_2_1.fq.bz2  Sample2 (phred33)
   4. rna_2_2.fq.bz2  Sample2 (phred33)

 Genome alignments: directory: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp06538N
   1. rna_1_1_250c5d61bd3.bam 
   2. rna_1_2_250c2bac516.bam 
   3. rna_2_1_250c189c765e.bam
   4. rna_2_2_250c118d31d2.bam

 Aux. alignments: 1 file, directory: C:/Users/biocbuild/bbs-3.7-b.../Rtmp06538N
   a. C:/Users/biocbuild/bbs-3.7-bioc/meat/QuasR.Rche.../NC_001422.1.fa  phiX174
     1. rna_1_1_250c57734f5f.bam
     2. rna_1_2_250c3d4248fd.bam
     3. rna_2_1_250c10c91334.bam
     4. rna_2_2_250c71f612bd.bam

 done successfully.



Executing test function test_subset_project  ...  done successfully.



Executing test function test_alignmentStats  ... all necessary alignment files found
all necessary alignment files found
all necessary alignment files found
all necessary alignment files found
 done successfully.



Executing test function test_md5subsum  ...  done successfully.



RUNIT TEST PROTOCOL -- Wed Oct 17 04:25:56 2018 
*********************************************** 
Number of test functions: 49 
Number of deactivated test functions: 17 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
QuasR RUnit Tests - 49 test functions, 0 errors, 0 failures
Number of test functions: 49 
Number of deactivated test functions: 17 
Number of errors: 0 
Number of failures: 0 
> 
> 
> proc.time()
   user  system elapsed 
  83.25   10.31  500.21 
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.
[samopen] SAM header is present: 3 sequences.

name	user	system	elapsed
QuasR-package	0	0	0
alignmentStats	0	0	0
preprocessReads	1.51	0.08	1.67
qAlign	0	0	0
qCount	13.43	0.95	44.13
qExportWig	0.29	0.03	17.48
qMeth	0.66	0.17	20.41
qProfile	1.05	0.03	1.08
qProject-class	0.40	0.07	16.09
qQCReport	3.10	0.09	3.35