Back to Mac ARM64 build report for BioC 3.17
ABCDEFGHIJKLMNOP[Q]RSTUVWXYZ

This page was generated on 2023-10-20 09:38:09 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 1611/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
QuasR 1.40.1  (landing page)
Michael Stadler
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/QuasR
git_branch: RELEASE_3_17
git_last_commit: ededf94
git_last_commit_date: 2023-06-14 02:04:10 -0400 (Wed, 14 Jun 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for QuasR on kjohnson2


To the developers/maintainers of the QuasR package:
- 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: 1.40.1
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_1.40.1.tar.gz
StartedAt: 2023-10-18 17:03:11 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 17:19:04 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 953.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: QuasR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_1.40.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘QuasR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘QuasR’ version ‘1.40.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘QuasR’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/QuasR/libs/QuasR.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___sprintf_chk’, possibly from ‘sprintf’ (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)
  Found ‘_sprintf’, possibly from ‘sprintf’ (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         21.260  0.575  62.184
qQCReport       4.213  0.096   6.713
qMeth           0.730  0.169  32.376
qProject-class  0.185  0.084  26.194
qExportWig      0.161  0.033  26.848
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/00check.log’
for details.



Installation output

QuasR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘QuasR’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_QuasR.cpp -o R_init_QuasR.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bam_cat.c -o bam_cat.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c bam_plbuf.c -o bam_plbuf.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c cat_bam.c -o cat_bam.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c convert_reads_id_bis_rc.c -o convert_reads_id_bis_rc.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c count_alignments.c -o count_alignments.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c count_alignments_subregions.c -o count_alignments_subregions.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c count_junctions.cpp -o count_junctions.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c export_wig.c -o export_wig.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c extract_unmapped_reads.c -o extract_unmapped_reads.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c filter_hisat2.c -o filter_hisat2.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c idxstats_bam.c -o idxstats_bam.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c merge_reorder_sam.cpp -o merge_reorder_sam.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c nucleotide_alignment_frequencies.c -o nucleotide_alignment_frequencies.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c profile_alignments.c -o profile_alignments.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c quantify_methylation.cpp -o quantify_methylation.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c remove_unmapped_from_sam.c -o remove_unmapped_from_sam.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sam_opts.c -o sam_opts.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sam_utils.c -o sam_utils.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c split_sam_chr.c -o split_sam_chr.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhtslib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utilities.c -o utilities.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.3-arm64/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/4.3-arm64/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)

Tests output

QuasR.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 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

alignment files missing - need to:
    create alignment index for the genome
    create 2 genomic alignment(s)
Creating an Rbowtie index for /private/tmp/RtmpiKUvts/RtmpiKUvts/file1259c9094d29.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:
kjohnson2: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1259c41a8c361.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:
kjohnson2: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1259c47e9b6ca.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/RtmpiKUvts/file1259c1ca82391.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:
kjohnson2: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1259c24b9cbab.txt
Genomic alignments have been created successfully

Creating .fai file for: /Users/biocbuild/bbs-3.17-bioc-mac-arm64/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-3.17-bioc-mac-arm64/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:
kjohnson2: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1259cac6908f.txt
Genomic alignments have been created successfully

Creating an Rbowtie index for /Users/biocbuild/bbs-3.17-bioc-mac-arm64/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
kjohnson2 
        2 
Performing auxiliary alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1259c9ce0012.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-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt
Creating the genome fasta file containing the SNPs: /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Creating the genome fasta file containing the SNPs: /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Creating a .fai file for the snp genome: /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Creating a .fai file for the snp genome: /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.A.fa
Creating an Rbowtie index for /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Finished creating index
Creating an Rbowtie index for /Users/biocbuild/bbs-3.17-bioc-mac-arm64/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:
kjohnson2: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1259cd542618.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:
kjohnson2: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1259c3b39fa32.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:
kjohnson2: 2
Performing genomic alignments for 4 samples. See progress in the log file:
/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1259c33762046.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:
kjohnson2: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1259c713e6f42.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-3.17-bioc-mac-arm64/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:
kjohnson2: 2
Performing genomic alignments for 4 samples. See progress in the log file:
/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1259c6c0253b7.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:
kjohnson2: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1259c6c0e4670.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:
kjohnson2: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1259c1c62eaf2.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:
kjohnson2: 2
Performing genomic alignments for 2 samples. See progress in the log file:
/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1259c15d856be.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-3.17-bioc-mac-arm64/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:
kjohnson2: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1259c201e0ee4.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:
kjohnson2: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1259c28bc70c7.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-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/extdata/hg19sub_snp.txt.hg19sub.fa.R.fa
Finished creating index
Creating an RbowtieCtoT index for /Users/biocbuild/bbs-3.17-bioc-mac-arm64/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:
kjohnson2: 2
Performing genomic alignments for 1 samples. See progress in the log file:
/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/QuasR_log_1259c455b2403.txt
Genomic alignments have been created successfully

all necessary alignment files found
Creating .fai file for: /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/extdata/file1259c720570a.fa
all necessary alignment files found
Creating .fai file for: /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/extdata/file1259c3f2df88c.fa
all necessary alignment files found
Creating .fai file for: /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/extdata/file1259c32aed5e3.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-3.17-bioc-mac-arm64/meat/QuasR.Rcheck/tests/testthat/extdata/file1259c6c762ca4.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 ]
Warning messages:
1: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 8 (<-localhost:11885)
2: In .Internal(gc(verbose, reset, full)) :
  closing unused connection 7 (<-localhost:11885)
> 
> proc.time()
   user  system elapsed 
118.690   9.946 304.557 

Example timings

QuasR.Rcheck/QuasR-Ex.timings

nameusersystemelapsed
QuasR-package000
alignmentStats0.0000.0000.003
preprocessReads1.5640.0442.434
qAlign0.0000.0000.001
qCount21.260 0.57562.184
qExportWig 0.161 0.03326.848
qMeth 0.730 0.16932.376
qProfile0.4140.0600.700
qProject-class 0.185 0.08426.194
qQCReport4.2130.0966.713