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This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
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

Package 1657/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QuasR 1.44.0  (landing page)
Michael Stadler
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/QuasR
git_branch: RELEASE_3_19
git_last_commit: 7508987
git_last_commit_date: 2024-04-30 10:30:09 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    NA  


CHECK results for QuasR on nebbiolo1

To the developers/maintainers of the QuasR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: QuasR
Version: 1.44.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:QuasR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings QuasR_1.44.0.tar.gz
StartedAt: 2024-06-20 02:46:10 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 02:59:03 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 773.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: QuasR.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:QuasR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings QuasR_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘QuasR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QuasR’ version ‘1.44.0’
* 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
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 code 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 loading without being on the library search path ... 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 ... NOTE
checkRd: (-1) qAlign.Rd:64-67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) qAlign.Rd:68-76: Lost braces in \itemize; meant \describe ?
checkRd: (-1) qQCReport.Rd:50: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qQCReport.Rd:51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qQCReport.Rd:52: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qQCReport.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qQCReport.Rd:54: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qQCReport.Rd:55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qQCReport.Rd:56: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) qQCReport.Rd:57: Lost braces in \itemize; \value handles \item{}{} directly
* 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 ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.19-bioc/R/site-library/QuasR/libs/QuasR.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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 nor [v]sprintf. 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         17.920  1.301  36.045
qMeth           0.609  0.289  17.385
qProject-class  0.153  0.141  16.605
qExportWig      0.135  0.004  15.447
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/00check.log’
for details.


Installation output

QuasR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL QuasR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘QuasR’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c R_init_QuasR.cpp -o R_init_QuasR.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c bam_cat.c -o bam_cat.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c cat_bam.c -o cat_bam.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c count_alignments.c -o count_alignments.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c count_alignments_subregions.c -o count_alignments_subregions.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c count_junctions.cpp -o count_junctions.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c export_wig.c -o export_wig.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c extract_unmapped_reads.c -o extract_unmapped_reads.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c filter_hisat2.c -o filter_hisat2.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c idxstats_bam.c -o idxstats_bam.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c merge_reorder_sam.cpp -o merge_reorder_sam.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c profile_alignments.c -o profile_alignments.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c quantify_methylation.cpp -o quantify_methylation.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c sam_opts.c -o sam_opts.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c sam_utils.c -o sam_utils.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c split_sam_chr.c -o split_sam_chr.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c utilities.c -o utilities.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.19-bioc/R/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 /home/biocbuild/bbs-3.19-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-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)

Tests output

QuasR.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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


Attaching package: 'rtracklayer'

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

    FileForFormat

alignment files missing - need to:
    create alignment index for the genome
    create 2 genomic alignment(s)
Creating an Rbowtie index for /tmp/RtmpKptIUV/RtmpKptIUV/file124292f3e0c7.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:
nebbiolo1: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1242924eafb57d.txt
Genomic alignments have been created successfully

alignment files missing - need to:
    create alignment index for the genome
    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:
nebbiolo1: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1242925ae4d50d.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/RtmpKptIUV/file1242926b05031c.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:
nebbiolo1: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12429277869ea1.txt
Genomic alignments have been created successfully

Creating .fai file for: /home/biocbuild/bbs-3.19-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 /home/biocbuild/bbs-3.19-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:
nebbiolo1: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1242924650f926.txt
Genomic alignments have been created successfully

Creating an Rbowtie index for /home/biocbuild/bbs-3.19-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
nebbiolo1 
        2 
Performing auxiliary alignments for 2 samples. See progress in the log file:
/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1242923e6aad32.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: /home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt
Creating the genome fasta file containing the SNPs: /home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Creating the genome fasta file containing the SNPs: /home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Creating a .fai file for the snp genome: /home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Creating a .fai file for the snp genome: /home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Creating an Rbowtie index for /home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Finished creating index
Creating an Rbowtie index for /home/biocbuild/bbs-3.19-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:
nebbiolo1: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1242925a029504.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:
nebbiolo1: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1242921be4f2bc.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:
nebbiolo1: 2
Performing genomic alignments for 4 samples. See progress in the log file:
/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1242923deb006f.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:
nebbiolo1: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_124292e94d56d.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 /home/biocbuild/bbs-3.19-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:
nebbiolo1: 2
Performing genomic alignments for 4 samples. See progress in the log file:
/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1242926bf49628.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:
nebbiolo1: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1242924da20ea5.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:
nebbiolo1: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_124292183e8919.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:
nebbiolo1: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12429251363b3c.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 /home/biocbuild/bbs-3.19-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:
nebbiolo1: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_124292f81c2e6.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:
nebbiolo1: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_12429257735417.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 /home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Finished creating index
Creating an RbowtieCtoT index for /home/biocbuild/bbs-3.19-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:
nebbiolo1: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/QuasR_log_124292462e98e4.txt
Genomic alignments have been created successfully

all necessary alignment files found
Creating .fai file for: /home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file1242926b8a6f9a.fa
all necessary alignment files found
Creating .fai file for: /home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file1242925a1e82eb.fa
all necessary alignment files found
Creating .fai file for: /home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file1242924ce784e0.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 '/home/biocbuild/bbs-3.19-bioc/meat/QuasR.Rcheck/tests/testthat/extdata/file12429248beb5f5.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 409 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (<-localhost:11771)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (<-localhost:11771)
> 
> proc.time()
   user  system elapsed 
 98.917  12.691 162.037 

Example timings

QuasR.Rcheck/QuasR-Ex.timings

nameusersystemelapsed
QuasR-package0.0000.0000.001
alignmentStats0.0000.0010.001
preprocessReads1.6080.0481.656
qAlign000
qCount17.920 1.30136.045
qExportWig 0.135 0.00415.447
qMeth 0.609 0.28917.385
qProfile0.3190.0680.388
qProject-class 0.153 0.14116.605
qQCReport3.4820.6644.144