Package: QuasR

Version: 1.26.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:QuasR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings QuasR_1.26.0.tar.gz

StartedAt: 2020-04-15 05:49:54 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:00:52 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 658.0 seconds

RetCode: 0

Status:  OK

CheckDir: QuasR.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:QuasR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings QuasR_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'QuasR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      3.1Mb
* 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
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 ... OK
* 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 ... NOTE
GNU make is a SystemRequirements.
* 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
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/QuasR/libs/x64/QuasR.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)

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 ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
qCount         18.98   0.34   44.56
qMeth           0.50   0.18   20.27
qExportWig      0.13   0.06   14.53
qProject-class  0.10   0.06   15.75
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.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-3.10-bioc/meat/QuasR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch QuasR
###
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* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
* installing *source* package 'QuasR' ...
** using staged installation
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c R_init_QuasR.cpp -o R_init_QuasR.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bam.c -o bam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bam_cat.c -o bam_cat.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c cat_bam.c -o cat_bam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c count_alignments.c -o count_alignments.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c count_alignments_subregions.c -o count_alignments_subregions.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c count_junctions.cpp -o count_junctions.o
count_junctions.cpp: In function 'int _addJunction(const bam1_t*, void*)':
count_junctions.cpp:90:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = y = 0; i < hit->core.n_cigar; ++i) {
                       ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c export_wig.c -o export_wig.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c extract_unmapped_reads.c -o extract_unmapped_reads.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c filter_hisat2.c -o filter_hisat2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c idxstats_bam.c -o idxstats_bam.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c merge_reorder_sam.cpp -o merge_reorder_sam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c profile_alignments.c -o profile_alignments.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c quantify_methylation.cpp -o quantify_methylation.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sam.c -o sam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sam_utils.c -o sam_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c split_sam_chr.c -o split_sam_chr.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o QuasR.dll tmp.def R_init_QuasR.o bam.o bam_cat.o bam_plbuf.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 filter_hisat2.o idxstats_bam.o merge_reorder_sam.o nucleotide_alignment_frequencies.o profile_alignments.o quantify_methylation.o remove_unmapped_from_sam.o sam.o sam_utils.o split_sam_chr.o utilities.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/biocbuild/bbs-3.10-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/R/library/00LOCK-QuasR/00new/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  
    qProjectUpdate                          html  
    qQCReport                               html  
    finding level-2 HTML links ... done

** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (QuasR)
Making 'packages.html' ... done

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, 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
> 
> test_check("QuasR")
* installing *source* package 'BSgenome.HSapiens.QuasR.hg19sub' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BSgenome.HSapiens.QuasR.hg19sub'
    finding HTML links ... done
    package                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpctnEJ6/R.INSTALL35d011013c5d/BSgenome.HSapiens.QuasR.hg19sub/man/package.Rd:33: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpctnEJ6/R.INSTALL35d011013c5d/BSgenome.HSapiens.QuasR.hg19sub/man/package.Rd:36: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
** building package indices
* DONE (BSgenome.HSapiens.QuasR.hg19sub)
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK

Attaching package: 'Biostrings'

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

    strsplit

alignment files missing - need to:
    create alignment index for the genome
    create 2 genomic alignment(s)
Creating an Rbowtie index for C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpGsDwKm/RtmpGsDwKm\filec407d7e555c.fa
Finished creating index
* installing *source* package 'BSgenome.HSapiens.QuasR.hg19sub.Rbowtie' ...
** using staged installation
** inst
** help
*** installing help indices
  converting help for package 'BSgenome.HSapiens.QuasR.hg19sub.Rbowtie'
    finding HTML links ... done
    package                                 html  
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (BSgenome.HSapiens.QuasR.hg19sub.Rbowtie)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
TOKAY1: 2
Performing genomic alignments for 2 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_c40f511f54.txt
Genomic alignments have been created successfully

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-3.10-bioc\tmpdir\RtmpGsDwKm\filec40468f6b62.fa
Finished creating index
* installing *source* package 'BSgenome.HSapiens.QuasR.hg19sub.RbowtieCtoT' ...
** using staged installation
** inst
** help
*** installing help indices
  converting help for package 'BSgenome.HSapiens.QuasR.hg19sub.RbowtieCtoT'
    finding HTML links ... done
    package                                 html  
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (BSgenome.HSapiens.QuasR.hg19sub.RbowtieCtoT)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
TOKAY1: 2
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_c4022ac6a2a.txt
Genomic alignments have been created successfully

Creating .fai file for: C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa
alignment files missing - need to:
    create alignment index for the genome
    create 2 genomic alignment(s)
    create 2 auxiliary alignment(s)
Creating an Rbowtie index for C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
TOKAY1: 2
Performing genomic alignments for 2 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_c40325e441c.txt
Genomic alignments have been created successfully

Creating an Rbowtie index for C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/NC_001422.1.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
nodeNames
TOKAY1 
     2 
Performing auxiliary alignments for 2 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_c40415f39bc.txt
Auxiliary alignments have been created successfully

alignment files missing - need to:
    create alignment index for the genome
    create 2 genomic alignment(s)
Reading and processing the SNP file: C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt
Creating the genome fasta file containing the SNPs: C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Creating the genome fasta file containing the SNPs: C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Creating a .fai file for the snp genome: C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Creating a .fai file for the snp genome: C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Creating an Rbowtie index for C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Finished creating index
Creating an Rbowtie index for C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat/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:
TOKAY1: 2
Performing genomic alignments for 2 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_c4091b10e2.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create 2 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
TOKAY1: 2
Performing genomic alignments for 2 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_c402eb221da.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create 4 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
TOKAY1: 2
Performing genomic alignments for 4 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_c406f2874a6.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create 2 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
TOKAY1: 2
Performing genomic alignments for 2 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_c404ae87eeb.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create alignment index for the genome
    create 4 genomic alignment(s)
Creating an Rhisat2 index for C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
TOKAY1: 2
Performing genomic alignments for 4 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_c401ead741b.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create 2 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
TOKAY1: 2
Performing genomic alignments for 2 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_c404f7724f3.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create splice site file for gene annotation
    create 2 genomic alignment(s)
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
TOKAY1: 2
Performing genomic alignments for 2 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_c4076be6922.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create splice site file for gene annotation
    create 2 genomic alignment(s)
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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")'.

Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
TOKAY1: 2
Performing genomic alignments for 2 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_c40345a5f94.txt
Genomic alignments have been created successfully

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-3.10-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
TOKAY1: 2
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_c403d972420.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create 1 genomic alignment(s)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...OK
Available cores:
TOKAY1: 2
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_c40314375c1.txt
Genomic alignments have been created successfully

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-3.10-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Finished creating index
Creating an RbowtieCtoT index for C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat/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:
TOKAY1: 2
Performing genomic alignments for 1 samples. See progress in the log file:
C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_c404b8a3985.txt
Genomic alignments have been created successfully

all necessary alignment files found
Creating .fai file for: C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/filec40756f2fd5.fa
all necessary alignment files found
Creating .fai file for: C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/filec407537a76.fa
all necessary alignment files found
Creating .fai file for: C:/Users/biocbuild/bbs-3.10-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/filec402ac743ac.fa
all necessary alignment files found
[E::hts_open_format] Failed to open file no-file
[samopen] no @SQ lines in the header.
samtools cat: fail to open output file 'not-there/bfile': No such file or directory
== testthat results  ===========================================================
[ OK: 388 | SKIPPED: 0 | WARNINGS: 15 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  60.35    3.25  247.95 
[E::hts_open_format] Failed to open file err
[E::hts_open_format] Failed to open file err
[E::hts_open_format] Failed to open file err
[E::hts_open_format] Failed to open file err/err
[E::hts_open_format] Failed to open file err

name	user	system	elapsed
QuasR-package	0	0	0
alignmentStats	0	0	0
preprocessReads	1.68	0.05	1.97
qAlign	0	0	0
qCount	18.98	0.34	44.56
qExportWig	0.13	0.06	14.53
qMeth	0.50	0.18	20.27
qProfile	0.32	0.06	0.87
qProject-class	0.10	0.06	15.75
qQCReport	4.25	0.02	4.31