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This page was generated on 2022-06-24 11:07:01 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for QuasR on palomino4


To the developers/maintainers of the QuasR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/QuasR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1532/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QuasR 1.37.1  (landing page)
Michael Stadler
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/QuasR
git_branch: master
git_last_commit: ff049af
git_last_commit_date: 2022-05-03 14:20:29 -0400 (Tue, 03 May 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    ERROR    OK  

Summary

Package: QuasR
Version: 1.37.1
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QuasR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings QuasR_1.37.1.tar.gz
StartedAt: 2022-06-24 04:46:32 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 04:56:50 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 617.7 seconds
RetCode: 0
Status:   OK  
CheckDir: QuasR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:QuasR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings QuasR_1.37.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (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 '1.37.1'
* 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 whether package 'QuasR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      8.1Mb
* 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/QuasR/libs/x64/QuasR.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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         18.44   0.48   40.78
qMeth           0.43   0.12   19.53
qProject-class  0.09   0.11   15.53
qExportWig      0.14   0.05   15.50
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/00check.log'
for details.



Installation output

QuasR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/QuasR_1.37.1.tar.gz && rm -rf QuasR.buildbin-libdir && mkdir QuasR.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=QuasR.buildbin-libdir QuasR_1.37.1.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL QuasR_1.37.1.zip && rm QuasR_1.37.1.tar.gz QuasR_1.37.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1078k  100 1078k    0     0  7506k      0 --:--:-- --:--:-- --:--:-- 7595k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'QuasR' ...
** using staged installation
** libs
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c R_init_QuasR.cpp -o R_init_QuasR.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bam_cat.c -o bam_cat.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c bam_plbuf.c -o bam_plbuf.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c cat_bam.c -o cat_bam.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c count_alignments.c -o count_alignments.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c count_alignments_subregions.c -o count_alignments_subregions.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c count_junctions.cpp -o count_junctions.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c export_wig.c -o export_wig.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c extract_unmapped_reads.c -o extract_unmapped_reads.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c filter_hisat2.c -o filter_hisat2.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c idxstats_bam.c -o idxstats_bam.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c merge_reorder_sam.cpp -o merge_reorder_sam.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c profile_alignments.c -o profile_alignments.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c quantify_methylation.cpp -o quantify_methylation.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sam_opts.c -o sam_opts.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sam_utils.c -o sam_utils.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c split_sam_chr.c -o split_sam_chr.o
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c utilities.c -o utilities.o
g++ -std=gnu++11 -shared -s -static-libgcc -o QuasR.dll tmp.def 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 F:/biocbuild/bbs-3.16-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -lz -lm -lbz2 -llzma -lcurl -lidn2 -lunistring -liconv -lssl -lcrypto -lcrypt32 -lwsock32 -lwldap32 -lssh2 -lgcrypt -lgpg-error -lws2_32 -lzstd -lregex -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/meat/QuasR.buildbin-libdir/00LOCK-QuasR/00new/QuasR/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'QuasR' as QuasR_1.37.1.zip
* DONE (QuasR)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'QuasR' successfully unpacked and MD5 sums checked

Tests output

QuasR.Rcheck/tests/testthat.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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: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.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

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
** 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 F:/biocbuild/bbs-3.16-bioc/tmpdir/RtmpmOh78y/RtmpmOh78y\file2060065be11cf.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:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_2060038ac7ade.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 F:\biocbuild\bbs-3.16-bioc\tmpdir\RtmpmOh78y\file20600454e2ed4.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:
PALOMINO4: 2
Performing genomic alignments for 1 samples. See progress in the log file:
F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_206006d7157e5.txt
Genomic alignments have been created successfully

Creating .fai file for: F:/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 F:/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:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_2060079204b85.txt
Genomic alignments have been created successfully

Creating an Rbowtie index for F:/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
PALOMINO4 
        2 
Performing auxiliary alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_206007e567273.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: F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt
Creating the genome fasta file containing the SNPs: F:/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: F:/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: F:/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: F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Creating an Rbowtie index for F:/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 F:/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:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_20600731a4c75.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:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_206001b244d0a.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:
PALOMINO4: 2
Performing genomic alignments for 4 samples. See progress in the log file:
F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_2060072f077e8.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:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_20600ea064d2.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 F:/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:
PALOMINO4: 2
Performing genomic alignments for 4 samples. See progress in the log file:
F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_206004e943306.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:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_2060070873935.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:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_206006f9d4d18.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:
PALOMINO4: 2
Performing genomic alignments for 2 samples. See progress in the log file:
F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_206004b09826.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 F:/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:
PALOMINO4: 2
Performing genomic alignments for 1 samples. See progress in the log file:
F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_2060019022d92.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:
PALOMINO4: 2
Performing genomic alignments for 1 samples. See progress in the log file:
F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_206003a144c5.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 F:/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 F:/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:
PALOMINO4: 2
Performing genomic alignments for 1 samples. See progress in the log file:
F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat\QuasR_log_206001256287b.txt
Genomic alignments have been created successfully

all necessary alignment files found
Creating .fai file for: F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file2060072ab1ae5.fa
all necessary alignment files found
Creating .fai file for: F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file20600724b6c34.fa
all necessary alignment files found
Creating .fai file for: F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file2060057952919.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 'F:/biocbuild/bbs-3.16-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file206002efdb02.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 
  47.01    4.21  182.79 

Example timings

QuasR.Rcheck/QuasR-Ex.timings

nameusersystemelapsed
QuasR-package000
alignmentStats000
preprocessReads1.690.041.72
qAlign000
qCount18.44 0.4840.78
qExportWig 0.14 0.0515.50
qMeth 0.43 0.1219.53
qProfile2.500.082.64
qProject-class 0.09 0.1115.53
qQCReport1.220.061.42