##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:QuasR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings QuasR_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.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 ‘QuasR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QuasR’ version ‘1.38.0’
* package encoding: UTF-8
* 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 ‘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
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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/QuasR/libs/QuasR.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (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 (user + system) or elapsed time > 5s
                 user system elapsed
qCount         17.770  0.426  35.209
qMeth           0.601  0.185  18.543
qProject-class  0.590  0.090  14.249
qExportWig      0.139  0.036  14.875
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘QuasR’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_QuasR.cpp -o R_init_QuasR.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam_cat.c -o bam_cat.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c bam_plbuf.c -o bam_plbuf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cat_bam.c -o cat_bam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_alignments.c -o count_alignments.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_alignments_subregions.c -o count_alignments_subregions.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c count_junctions.cpp -o count_junctions.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c export_wig.c -o export_wig.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c extract_unmapped_reads.c -o extract_unmapped_reads.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c filter_hisat2.c -o filter_hisat2.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c idxstats_bam.c -o idxstats_bam.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c merge_reorder_sam.cpp -o merge_reorder_sam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c profile_alignments.c -o profile_alignments.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c quantify_methylation.cpp -o quantify_methylation.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sam_opts.c -o sam_opts.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sam_utils.c -o sam_utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c split_sam_chr.c -o split_sam_chr.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c utilities.c -o utilities.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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 QuasR.so R_init_QuasR.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_opts.o sam_utils.o split_sam_chr.o utilities.o /Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-QuasR/00new/QuasR/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 (QuasR)

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.

> # 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:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, 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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
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
** 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 /private/tmp/Rtmpo5Hbhb/Rtmpo5Hbhb/file1043a1b1d2d26.fa
Finished creating index
* installing *source* package ‘BSgenome.HSapiens.QuasR.hg19sub.Rbowtie’ ...
** using staged installation
** inst
** help
*** installing help indices
** building package indices
** 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 (BSgenome.HSapiens.QuasR.hg19sub.Rbowtie)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
lconway: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1043a187f27b2.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 /tmp/Rtmpo5Hbhb/file1043a6acf1f52.fa
Finished creating index
* installing *source* package ‘BSgenome.HSapiens.QuasR.hg19sub.RbowtieCtoT’ ...
** using staged installation
** inst
** help
*** installing help indices
** building package indices
** 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 (BSgenome.HSapiens.QuasR.hg19sub.RbowtieCtoT)
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
lconway: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1043a26ef405a.txt
Genomic alignments have been created successfully

Creating .fai file for: /Users/biocbuild/bbs-3.16-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 /Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
lconway: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1043afc241f1.txt
Genomic alignments have been created successfully

Creating an Rbowtie index for /Users/biocbuild/bbs-3.16-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...preparing to run on 2 nodes...done
Available cores:
nodeNames
lconway 
      2 
Performing auxiliary alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1043a6f271fbf.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: /Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt
Creating the genome fasta file containing the SNPs: /Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Creating the genome fasta file containing the SNPs: /Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Creating a .fai file for the snp genome: /Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Creating a .fai file for the snp genome: /Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Creating an Rbowtie index for /Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Finished creating index
Creating an Rbowtie index for /Users/biocbuild/bbs-3.16-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...preparing to run on 2 nodes...done
Available cores:
lconway: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1043a74569d30.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...preparing to run on 2 nodes...done
Available cores:
lconway: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1043a6bae5d14.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...preparing to run on 2 nodes...done
Available cores:
lconway: 2
Performing genomic alignments for 4 samples. See progress in the log file:
/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1043a61347a37.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...preparing to run on 2 nodes...done
Available cores:
lconway: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1043a51690506.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 /Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
lconway: 2
Performing genomic alignments for 4 samples. See progress in the log file:
/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1043a32580640.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...preparing to run on 2 nodes...done
Available cores:
lconway: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1043a67222ca5.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...preparing to run on 2 nodes...done
Available cores:
lconway: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1043a3bac45bd.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...preparing to run on 2 nodes...done
Available cores:
lconway: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1043a3589580f.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 /Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub.fa
Finished creating index
Testing the compute nodes...OK
Loading QuasR on the compute nodes...preparing to run on 2 nodes...done
Available cores:
lconway: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1043a85c7aed.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...preparing to run on 2 nodes...done
Available cores:
lconway: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1043a7eb7ca98.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 /Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Finished creating index
Creating an RbowtieCtoT index for /Users/biocbuild/bbs-3.16-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...preparing to run on 2 nodes...done
Available cores:
lconway: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1043a68615e56.txt
Genomic alignments have been created successfully

all necessary alignment files found
Creating .fai file for: /Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file1043a2b45d2cc.fa
all necessary alignment files found
Creating .fai file for: /Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file1043ae4ffeb9.fa
all necessary alignment files found
Creating .fai file for: /Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file1043a4e0ce77.fa
all necessary alignment files found
[E::hts_open_format] Failed to open file "no-file" : No such file or directory
[samopen] no @SQ lines in the header.
samtools cat: fail to open output file 'not-there/bfile': No such file or directory
[E::hts_open_format] Failed to open file "err" : No such file or directory
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file1043aab6d10f.sam'
[E::hts_open_format] Failed to open file "err" : No such file or directory
[E::hts_open_format] Failed to open file "err" : No such file or directory
[E::hts_open_format] Failed to open file "err/err" : No such file or directory
[E::hts_open_format] Failed to open file "err" : No such file or directory
Error in checkForRemoteErrors(lapply(cl, recvResult)) : 
  2 nodes produced errors; first error: there is no package called ‘does_not_exist’
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 404 ]
> 
> proc.time()
   user  system elapsed 
 87.297   9.157 150.870