Multiple platform build/check report for BioC 3.21 - CHECK results for HTSeqGenie on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4833
merida1	macOS 12.7.6 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4614
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4555
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4586
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 HTSeqGenie on kunpeng2

To the developers/maintainers of the HTSeqGenie package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HTSeqGenie.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: HTSeqGenie

Version: 4.38.0

Command: /home/biocbuild/R/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HTSeqGenie_4.38.0.tar.gz

StartedAt: 2025-10-14 10:13:31 -0000 (Tue, 14 Oct 2025)

EndedAt: 2025-10-14 10:28:46 -0000 (Tue, 14 Oct 2025)

EllapsedTime: 914.7 seconds

RetCode: 0

Status: OK

CheckDir: HTSeqGenie.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HTSeqGenie_4.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/HTSeqGenie.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.38.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HTSeqGenie’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘ShortRead:::.set_omp_threads’ ‘gmapR:::..gsnap’ ‘gmapR:::GeneGenome’
  ‘gmapR:::checkPackageInstalled’ ‘gmapR:::getDefaultGmapGenomePath’
  ‘gmapR:::getGeneRoi’ ‘gmapR:::subsetRegion’ ‘parallel:::mckill’
  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 ... NOTE
.makePreprocessAlignPlots: no visible binding for global variable
  ‘data’
.plot.in.out.min.max.readlength: no visible global function definition
  for ‘median’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.lfqs’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.chunkid’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.subsampling_filter’
FastQStreamer.init: no visible binding for '<<-' assignment to
  ‘FastQStreamer.max_nbchunks’
addHandler: no visible binding for '<<-' assignment to
  ‘logging.handlers’
addHandler: no visible binding for global variable ‘logging.handlers’
addHandler: no visible binding for '<<-' assignment to ‘logging.file’
buildAnyFastaGenome: no visible global function definition for ‘getSeq’
buildGenomicFeaturesFromTxDb: no visible global function definition for
  ‘gaps’
buildGenomicFeaturesFromTxDb: no visible global function definition for
  ‘ranges’
buildTP53FastaGenome: no visible global function definition for
  ‘getSeq’
buildTallyParam: no visible global function definition for ‘seqinfo’
computeCoverage: no visible global function definition for ‘resize’
computeCoverage: no visible global function definition for ‘coverage’
estimateCutoffs : <anonymous>: no visible binding for global variable
  ‘quantile’
getGenomeSegments: no visible global function definition for ‘seqinfo’
hashVariants: no visible global function definition for ‘ranges’
isAboveQualityThresh: no visible global function definition for ‘Views’
isAboveQualityThresh: no visible global function definition for
  ‘viewMeans’
listIterator.init: no visible binding for '<<-' assignment to
  ‘listIterator.n’
listIterator.init: no visible binding for '<<-' assignment to
  ‘listIterator.x’
logReset: no visible binding for '<<-' assignment to ‘logging.handlers’
logReset: no visible binding for '<<-' assignment to ‘logging.loglevel’
logReset: no visible binding for '<<-' assignment to ‘logging.file’
loglevel: no visible binding for global variable ‘logging.loglevel’
loglevel: no visible binding for global variable ‘logging.handlers’
processChunks : tracefun: no visible binding for global variable
  ‘sjobs’
processChunks : tracefun: no visible binding for global variable
  ‘chunkid’
setLevel: no visible binding for '<<-' assignment to ‘logging.loglevel’
statCountFeatures: no visible global function definition for ‘quantile’
truncateReads: no visible global function definition for ‘subseq’
vcfStat: no visible global function definition for ‘quantile’
writeToFile: no visible binding for global variable ‘logging.file’
Undefined global functions or variables:
  Views chunkid coverage data gaps getSeq logging.file logging.handlers
  logging.loglevel median quantile ranges resize seqinfo sjobs subseq
  viewMeans
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) calculateTargetLengths.Rd:17: Lost braces; missing escapes or markup?
    17 | Target length table and writes two files in {save_dir}/reports/images/TargetLenghts.[pdf|png]"
       |                                             ^
checkRd: (-1) initLog.Rd:18: Lost braces; missing escapes or markup?
    18 | Setup logging file in {save_dir}/progress.log
       |                       ^
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'findVariantFile.Rd':
  ‘dir_path’

Documented arguments not in \usage in Rd file 'logdebug.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'logerror.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'loginfo.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'logwarn.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/HTSeqGenie.Rcheck/00check.log’
for details.

Installation output

HTSeqGenie.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL HTSeqGenie
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘HTSeqGenie’ ...
** this is package ‘HTSeqGenie’ version ‘4.38.0’
** using staged installation
** 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
Warning in fun(libname, pkgname) :
  Package 'HTSeqGenie' is deprecated and will be removed from
  Bioconductor version 3.22
** testing if installed package can be loaded from final location
Warning in fun(libname, pkgname) :
  Package 'HTSeqGenie' is deprecated and will be removed from
  Bioconductor version 3.22
** testing if installed package keeps a record of temporary installation path
* DONE (HTSeqGenie)

Tests output

HTSeqGenie.Rcheck/tests/doRUnit.Rout


R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> library("HTSeqGenie")
Loading required package: gmapR
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

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: GenomicRanges
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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")'.


Attaching package: 'Biobase'

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

    rowMedians

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

    anyMissing, rowMedians

Loading required package: VariantAnnotation

Attaching package: 'VariantAnnotation'

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

    tabulate

Warning message:
In fun(libname, pkgname) :
  Package 'HTSeqGenie' is deprecated and will be removed from
  Bioconductor version 3.22
> 
> source(getPackageFile("unitTests/runTests.R"))
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
did not source anything in dirname= ./R 


Executing test function test.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:21:02.959707 INFO::preprocessReads.R/preprocessReads: starting...
2025-10-14 10:21:02.96942 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-10-14 10:21:02.974707 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-10-14 10:21:02.977663 DEBUG::tools.R/processChunks: starting...
2025-10-14 10:21:06.260365 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-10-14 10:21:06.262455 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.1132bd2de7c34b/chunks/chunk_000001/logs/progress.log
2025-10-14 10:21:09.143272 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-10-14 10:21:09.145295 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.1132bd2de7c34b/chunks/chunk_000002/logs/progress.log
2025-10-14 10:21:12.010186 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.048 minutes
2025-10-14 10:21:12.012137 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.1132bd2de7c34b/chunks/chunk_000003/logs/progress.log
2025-10-14 10:21:14.895734 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.048 minutes
2025-10-14 10:21:14.939058 DEBUG::tools.R/processChunks: done
2025-10-14 10:21:14.944446 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-10-14 10:21:14.947757 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.1132bd2de7c34b/results/test_pe.adapter_contaminated_1.RData
2025-10-14 10:21:14.951736 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-10-14 10:21:14.95438 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.1132bd2de7c34b/results/test_pe.adapter_contaminated_2.RData
2025-10-14 10:21:14.967834 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-10-14 10:21:14.971177 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.1132bd2de7c34b/results/test_pe.summary_preprocess.tab
2025-10-14 10:21:14.976079 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.1132bd2de7c34b/bams/processed.aligner_input_1.fastq ...
2025-10-14 10:21:14.983096 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.1132bd2de7c34b/bams/processed.aligner_input_2.fastq ...
2025-10-14 10:21:14.988933 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.1132bd2de7c34b/reports/shortReadReport_1 ...
2025-10-14 10:21:16.934651 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.1132bd2de7c34b/reports/shortReadReport_2 ...
2025-10-14 10:21:19.965437 INFO::preprocessReads.R/preprocessReads: done
2025-10-14 10:21:20.018589 INFO::alignReads.R/alignReads: starting alignment...
2025-10-14 10:21:20.024894 DEBUG::tools.R/processChunks: starting...
2025-10-14 10:21:23.505645 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-10-14 10:21:23.507767 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.1132bd2de7c34b/chunks/chunk_000001/logs/progress.log
2025-10-14 10:21:26.659226 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.052 minutes
2025-10-14 10:21:26.661545 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.1132bd2de7c34b/chunks/chunk_000002/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-10-14 10:21:29.432864 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-10-14 10:21:29.435106 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.1132bd2de7c34b/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-10-14 10:21:32.19343 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-10-14 10:21:32.196997 DEBUG::tools.R/processChunks: done
2025-10-14 10:21:32.19902 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-10-14 10:21:32.563124 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-10-14 10:21:32.582666 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.1132bd2de7c34b/results/test_pe.summary_alignment.tab
2025-10-14 10:21:32.594958 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.1132bd2de7c34b/results/test_pe.summary_analyzed_bamstats.tab
2025-10-14 10:21:32.597793 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-10-14 10:21:32.898648 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.1132bd2de7c34b/results/test_pe.summary_target_lengths.tab
2025-10-14 10:21:32.961792 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-10-14 10:21:32.963173 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:21:33.349069 INFO::preprocessReads.R/preprocessReads: starting...
2025-10-14 10:21:33.352597 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-10-14 10:21:33.432992 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-10-14 10:21:33.439472 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-10-14 10:21:33.443746 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-10-14 10:21:33.446353 DEBUG::tools.R/processChunks: starting...
2025-10-14 10:21:36.992255 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-10-14 10:21:36.994282 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.sparsechunks.1132bd5fcd8e23/chunks/chunk_000001/logs/progress.log
2025-10-14 10:21:39.853942 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-10-14 10:21:39.855893 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.sparsechunks.1132bd5fcd8e23/chunks/chunk_000002/logs/progress.log
2025-10-14 10:21:42.700996 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2025-10-14 10:21:42.702993 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.sparsechunks.1132bd5fcd8e23/chunks/chunk_000003/logs/progress.log
2025-10-14 10:21:45.634337 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.049 minutes
2025-10-14 10:21:45.636318 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.sparsechunks.1132bd5fcd8e23/chunks/chunk_000004/logs/progress.log
2025-10-14 10:21:48.467418 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.047 minutes
2025-10-14 10:21:48.510799 DEBUG::tools.R/processChunks: done
2025-10-14 10:21:48.515419 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-10-14 10:21:48.518821 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.sparsechunks.1132bd5fcd8e23/results/test_pe.adapter_contaminated_1.RData
2025-10-14 10:21:48.523174 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-10-14 10:21:48.525852 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.sparsechunks.1132bd5fcd8e23/results/test_pe.adapter_contaminated_2.RData
2025-10-14 10:21:48.54028 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=2 highqual_reads=1 adapter_contam=0 read_length=75 rRNA_contam_reads=0 processed_reads=1 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-10-14 10:21:48.543392 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.sparsechunks.1132bd5fcd8e23/results/test_pe.summary_preprocess.tab
2025-10-14 10:21:48.548282 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.sparsechunks.1132bd5fcd8e23/bams/processed.aligner_input_1.fastq ...
2025-10-14 10:21:48.555386 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.sparsechunks.1132bd5fcd8e23/bams/processed.aligner_input_2.fastq ...
2025-10-14 10:21:48.56123 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.sparsechunks.1132bd5fcd8e23/reports/shortReadReport_1 ...
2025-10-14 10:21:50.506572 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReads.sparsechunks.1132bd5fcd8e23/reports/shortReadReport_2 ...
2025-10-14 10:21:53.68375 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:21:53.904465 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-10-14 10:21:53.91059 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -D /home/biocbuild/.local/share/gmap -t 1 -d TP53_demo_3.2.2 --quality-protocol=illumina  -A sam --read-group-id=test_se -m 0 --split-output /home/biocbuild/tmp/RtmphG5Dl2/test.alignReadsOneSingleEnd.1132bd17a0b4e/bams/test.alignReads /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2025-10-14 10:21:54.060496 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-10-14 10:21:54.210098 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReadsOneSingleEnd.1132bd17a0b4e/results/test.alignReads.summary_alignment.tab
2025-10-14 10:21:54.27139 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.alignReadsOneSingleEnd.1132bd17a0b4e/results/test.alignReads.summary_analyzed_bamstats.tab
2025-10-14 10:21:54.273519 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0 0.003 0.003
Error in DEACTIVATED("Skipped annotateVariants() test") : 
  Skipped annotateVariants() test
In addition: There were 11 warnings (use warnings() to see them)
 done successfully.



Executing test function test.callVariantsVariantTools.genotype  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:21:54.701361 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.genotype.1132bd31022972/results/test_pe.coverage.RData
2025-10-14 10:21:54.703948 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.genotype.1132bd31022972/results/test_pe.coverage.bw
2025-10-14 10:21:54.89227 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.genotype.1132bd31022972/results/test_pe.summary_coverage.tab
2025-10-14 10:21:54.894752 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-10-14 10:22:07.089504 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-10-14 10:22:07.233345 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-10-14 10:22:07.262202 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-10-14 10:22:07.264518 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.genotype.1132bd31022972/results/test_pe.raw_variants.RData
2025-10-14 10:22:07.268094 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.genotype.1132bd31022972/results/test_pe.filtered_variants.RData
2025-10-14 10:22:07.270323 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-10-14 10:22:07.272219 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-10-14 10:22:07.921813 INFO::analyzeVariants.R/writeVCF: ...done
2025-10-14 10:22:07.923844 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-10-14 10:23:38.1501 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-10-14 10:23:38.807035 INFO::analyzeVariants.R/writeVCF: ...done
2025-10-14 10:23:38.808425 INFO::analyzeVariants.R/.callGenotypes: done
[W::bcf_hdr_check_sanity] PL should be declared as Number=G
 done successfully.



Executing test function test.wrap.callVariants  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:23:39.408592 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-10-14 10:23:51.90266 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-10-14 10:23:52.033589 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-10-14 10:23:52.062491 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-10-14 10:23:52.064667 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.wrap.callVariants.1132bd274a6a94/results/test_pe.raw_variants.RData
2025-10-14 10:23:52.06813 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.wrap.callVariants.1132bd274a6a94/results/test_pe.filtered_variants.RData
2025-10-14 10:23:52.070361 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.filters  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:23:52.276239 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-10-14 10:24:04.231337 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-10-14 10:24:04.325716 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-10-14 10:24:04.352746 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-10-14 10:24:04.354793 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.wrap.callVariants.filters.1132bd7fcdd071/results/test_pe.raw_variants.RData
2025-10-14 10:24:04.35811 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.wrap.callVariants.filters.1132bd7fcdd071/results/test_pe.filtered_variants.RData
2025-10-14 10:24:04.360113 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-10-14 10:24:04.362268 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-10-14 10:24:16.498179 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-10-14 10:24:16.560128 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-10-14 10:24:16.587327 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-10-14 10:24:16.58951 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.wrap.callVariants.filters.1132bd7fcdd071/results/test_pe.raw_variants.RData
2025-10-14 10:24:16.592962 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.wrap.callVariants.filters.1132bd7fcdd071/results/test_pe.filtered_variants.RData
2025-10-14 10:24:16.59567 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.wrap.callVariants.which  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:24:16.919038 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-10-14 10:24:16.921139 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-10-14 10:24:20.838264 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-10-14 10:24:20.960689 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-10-14 10:24:20.988125 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-10-14 10:24:20.990306 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.wrap.callVariants.which.1132bd19ded582/results/test_pe.raw_variants.RData
2025-10-14 10:24:20.992971 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.wrap.callVariants.which.1132bd19ded582/results/test_pe.filtered_variants.RData
2025-10-14 10:24:20.995113 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:24:21.202331 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-10-14 10:24:21.204312 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:24:21.454648 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-10-14 10:24:21.794979 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.isFirstFragment  ...  done successfully.



Executing test function test.buildCountsGRangesList  ...   403 genes were dropped because they have exons located on both strands of the
  same reference sequence or on more than one reference sequence, so cannot be
  represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
  object, or use suppressMessages() to suppress this message.
 done successfully.



Executing test function test.generateSingleGeneDERs  ...  done successfully.



Executing test function test.computeCoverage  ...  done successfully.



Executing test function test.isSparse  ...  done successfully.



Executing test function test.mergeCoverage  ... 2025-10-14 10:25:41.078504 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/vrbfjpzs/merged/results/bla.coverage.RData
2025-10-14 10:25:41.082078 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmphG5Dl2/vrbfjpzs/merged/results/bla.coverage.bw
2025-10-14 10:25:41.202758 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/vrbfjpzs/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2025-10-14 10:25:42.590138 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/byesrckh/merged/results/bla.coverage.RData
2025-10-14 10:25:42.592239 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmphG5Dl2/byesrckh/merged/results/bla.coverage.bw
2025-10-14 10:25:42.607576 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/byesrckh/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.checkConfig.analyzeVariants  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.findTemplate  ...  done successfully.



Executing test function test.checkConfig  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.checkConfig.alignReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.getConfig  ...  done successfully.



Executing test function test.loadConfig  ...  done successfully.



Executing test function test.parseDCF  ...  done successfully.



Executing test function test.updateConfig  ...  done successfully.



Executing test function test.getAdapterSeqs  ...  done successfully.



Executing test function test.isAdapter  ...  done successfully.



Executing test function test.isAdapter3.primeEnd  ...  done successfully.



Executing test function test.detectRRNA  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:25:44.39742 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-10-14 10:25:44.398998 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmphG5Dl2/test.detectRRNA.1132bd514d1d4b/bams/rRNA_contam/input1.fastq
2025-10-14 10:25:44.403896 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /home/biocbuild/tmp/RtmphG5Dl2/test.detectRRNA.1132bd514d1d4b/bams/rRNA_contam/test_se /home/biocbuild/tmp/RtmphG5Dl2/test.detectRRNA.1132bd514d1d4b/bams/rRNA_contam/input1.fastq 2>&1
2025-10-14 10:25:44.526379 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-10-14 10:25:44.527847 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.detectRRNA.paired_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:25:44.738852 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-10-14 10:25:44.740288 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmphG5Dl2/test.detectRRNA.paired_end.1132bd1ca415bc/bams/rRNA_contam/input1.fastq
2025-10-14 10:25:44.742564 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/RtmphG5Dl2/test.detectRRNA.paired_end.1132bd1ca415bc/bams/rRNA_contam/input2.fastq
2025-10-14 10:25:44.745857 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /home/biocbuild/tmp/RtmphG5Dl2/test.detectRRNA.paired_end.1132bd1ca415bc/bams/rRNA_contam/test_pe /home/biocbuild/tmp/RtmphG5Dl2/test.detectRRNA.paired_end.1132bd1ca415bc/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/tmp/RtmphG5Dl2/test.detectRRNA.paired_end.1132bd1ca415bc/bams/rRNA_contam/input2.fastq 2>&1
2025-10-14 10:25:45.017885 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-10-14 10:25:45.019412 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2025-10-14 10:25:45.04934 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /home/biocbuild/tmp/RtmphG5Dl2/test_get_rRNA_idsirayhvbe/test_pe /home/biocbuild/tmp/RtmphG5Dl2/test_get_rRNA_idsirayhvbe/1.fastq -a paired /home/biocbuild/tmp/RtmphG5Dl2/test_get_rRNA_idsirayhvbe/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2025-10-14 10:25:45.34819 INFO::alignReads.R/alignReadsChunk: calling gsnap (from gmapR) with args= -t 0 -D /home/biocbuild/.local/share/gmap -n 1 -d TP53_demo_3.2.2 -A sam -B 2 --pairmax-rna=200000 --split-output /home/biocbuild/tmp/RtmphG5Dl2/test_get_rRNAIds_randomdsjxbrok/test_pe /home/biocbuild/tmp/RtmphG5Dl2/test_get_rRNAIds_randomdsjxbrok/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2025-10-14 10:25:45.525631 INFO::filterQuality.R/filterQuality: filterByLength...
2025-10-14 10:25:45.527647 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-10-14 10:25:45.528932 INFO::filterQuality.R/filterByLength: done
2025-10-14 10:25:45.599621 INFO::filterQuality.R/filterQuality: filterByLength...
2025-10-14 10:25:45.601007 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-10-14 10:25:45.602326 INFO::filterQuality.R/filterByLength: done
 done successfully.



Executing test function test.isAboveQualityThresh  ...  done successfully.



Executing test function test.trimTailsByQuality  ... 2025-10-14 10:25:45.684176 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-10-14 10:25:45.697906 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-10-14 10:25:45.699575 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-10-14 10:25:45.706643 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-10-14 10:25:45.708238 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-10-14 10:25:45.715358 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-10-14 10:25:45.71701 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-10-14 10:25:45.724079 INFO::preprocessReads.R/preprocessReadsChunk: done
 done successfully.



Executing test function test.callVariantsGATK  ... Timing stopped at: 0.001 0 0
Error in DEACTIVATED("callVariantsGATK() tests need gatk.path option set") : 
  callVariantsGATK() tests need gatk.path option set
In addition: There were 50 or more warnings (use warnings() to see the first 50)
 done successfully.



Executing test function test.callVariantsGATK.withFiltering  ... Timing stopped at: 0.001 0 0
Error in DEACTIVATED("callVariantsGATK() tests need gatk.path option set") : 
  callVariantsGATK() tests need gatk.path option set
 done successfully.



Executing test function test.checkGATKJar  ... Timing stopped at: 0 0 0.001
Error in DEACTIVATED("checkGATKJar() test needs gatk.path option set") : 
  checkGATKJar() test needs gatk.path option set
 done successfully.



Executing test function test.excludeVariantsByRegion  ...  done successfully.



Executing test function test.gatk  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("gatk() tests need gatk.path option set") : 
  gatk() tests need gatk.path option set
 done successfully.



Executing test function test.realignIndels  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("test.realignIndels() tests need gatk.path option set") : 
  test.realignIndels() tests need gatk.path option set
 done successfully.



Executing test function test.realignIndelsGATK  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("realignIndelsGATK() tests need gatk.path option set") : 
  realignIndelsGATK() tests need gatk.path option set
 done successfully.



Executing test function test.realignIndelsGATK.parallel  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("realignIndelsGATK() tests need gatk.path option set") : 
  realignIndelsGATK() tests need gatk.path option set
 done successfully.



Executing test function test_zipUp  ...  done successfully.



Executing test function test.FastQStreamer.getReads.pefq  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:25:46.169369 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-10-14 10:25:46.172989 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.FastQStreamer.getReads.pefq.subsample  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:25:46.442242 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-10-14 10:25:46.606718 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-10-14 10:25:46.610788 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-10-14 10:25:46.614386 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.FastQStreamer.getReads.segz  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:25:46.971776 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/reads.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.getReads.truncated  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:25:47.188149 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/truncated.fastq.gz
 done successfully.



Executing test function test.FastQStreamer.subsampler.isdeterministic  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:25:47.443119 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-10-14 10:25:47.573505 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-10-14 10:25:47.57742 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-10-14 10:25:47.581078 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:25:47.910518 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-10-14 10:25:47.985865 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-10-14 10:25:47.989504 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-10-14 10:25:47.992993 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
 done successfully.



Executing test function test.createTmpDir  ...  done successfully.



Executing test function test.detectQualityInFASTQFile  ...  done successfully.



Executing test function test.getObjectFilename  ...  done successfully.



Executing test function test.safeUnlink  ...  done successfully.



Executing test function test.writeAudit  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.mergeLanes  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:25:49.075486 INFO::preprocessReads.R/preprocessReads: starting...
2025-10-14 10:25:49.082821 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-10-14 10:25:49.087771 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-10-14 10:25:49.091091 DEBUG::tools.R/processChunks: starting...
2025-10-14 10:25:52.634124 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-10-14 10:25:52.636234 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/chunks/chunk_000001/logs/progress.log
2025-10-14 10:25:55.481106 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-10-14 10:25:55.483229 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/chunks/chunk_000002/logs/progress.log
2025-10-14 10:25:58.323778 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2025-10-14 10:25:58.325781 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/chunks/chunk_000003/logs/progress.log
2025-10-14 10:26:01.140584 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.047 minutes
2025-10-14 10:26:01.205394 DEBUG::tools.R/processChunks: done
2025-10-14 10:26:01.209245 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-10-14 10:26:01.211868 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.adapter_contaminated_1.RData
2025-10-14 10:26:01.215114 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-10-14 10:26:01.217665 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.adapter_contaminated_2.RData
2025-10-14 10:26:01.229522 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-10-14 10:26:01.232315 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.summary_preprocess.tab
2025-10-14 10:26:01.236152 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/bams/processed.aligner_input_1.fastq ...
2025-10-14 10:26:01.242933 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/bams/processed.aligner_input_2.fastq ...
2025-10-14 10:26:01.24871 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/reports/shortReadReport_1 ...
2025-10-14 10:26:03.227836 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/reports/shortReadReport_2 ...
2025-10-14 10:26:04.849461 INFO::preprocessReads.R/preprocessReads: done
2025-10-14 10:26:04.924092 INFO::alignReads.R/alignReads: starting alignment...
2025-10-14 10:26:04.929202 DEBUG::tools.R/processChunks: starting...
2025-10-14 10:26:08.460084 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-10-14 10:26:08.462423 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/chunks/chunk_000001/logs/progress.log
2025-10-14 10:26:11.125379 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-10-14 10:26:11.127666 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/chunks/chunk_000002/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-10-14 10:26:13.776813 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-10-14 10:26:13.779061 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/chunks/chunk_000003/logs/progress.log
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-10-14 10:26:16.454163 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2025-10-14 10:26:16.457745 DEBUG::tools.R/processChunks: done
2025-10-14 10:26:16.45994 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-10-14 10:26:16.767493 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-10-14 10:26:16.778358 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.summary_alignment.tab
2025-10-14 10:26:16.788788 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.summary_analyzed_bamstats.tab
2025-10-14 10:26:16.791461 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-10-14 10:26:17.051278 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.summary_target_lengths.tab
2025-10-14 10:26:17.114217 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-10-14 10:26:17.115648 INFO::alignReads.R/alignReads: done
2025-10-14 10:26:17.202762 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-10-14 10:26:17.226557 DEBUG::tools.R/processChunks: starting...
2025-10-14 10:26:21.057736 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-10-14 10:26:21.060133 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/chunks/chunk_000001/logs/progress.log
2025-10-14 10:26:23.681739 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-10-14 10:26:23.684013 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/chunks/chunk_000002/logs/progress.log
2025-10-14 10:26:26.254077 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2025-10-14 10:26:26.256392 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/chunks/chunk_000003/logs/progress.log
2025-10-14 10:26:28.851402 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-10-14 10:26:28.854823 DEBUG::tools.R/processChunks: done
2025-10-14 10:26:28.856998 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-10-14 10:26:28.874364 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.counts_exon.tab
2025-10-14 10:26:28.888919 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.counts_exon_disjoint.tab
2025-10-14 10:26:28.898077 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.counts_gene.tab
2025-10-14 10:26:28.905366 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.counts_gene_coding.tab
2025-10-14 10:26:28.912702 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.counts_gene_exonic.tab
2025-10-14 10:26:28.920287 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.counts_intergenic.tab
2025-10-14 10:26:28.932248 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.counts_intron.tab
2025-10-14 10:26:28.93595 INFO::countGenomicFeatures.R/mergeCounts: done
2025-10-14 10:26:28.943844 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.summary_counts.tab
2025-10-14 10:26:28.946187 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-10-14 10:26:29.30471 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-10-14 10:26:29.305959 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-10-14 10:26:29.387652 INFO::coverage.R/calculateCoverage: starting...
2025-10-14 10:26:29.392535 DEBUG::tools.R/processChunks: starting...
2025-10-14 10:26:33.097572 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-10-14 10:26:33.099934 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/chunks/chunk_000001/logs/progress.log
2025-10-14 10:26:35.30508 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.037 minutes
2025-10-14 10:26:35.307354 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/chunks/chunk_000002/logs/progress.log
2025-10-14 10:26:37.520129 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.037 minutes
2025-10-14 10:26:37.522453 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/chunks/chunk_000003/logs/progress.log
2025-10-14 10:26:39.724018 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.037 minutes
2025-10-14 10:26:39.727612 DEBUG::tools.R/processChunks: done
2025-10-14 10:26:41.557655 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.coverage.RData
2025-10-14 10:26:41.559522 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.coverage.bw
2025-10-14 10:26:41.575931 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.summary_coverage.tab
2025-10-14 10:26:41.577847 INFO::coverage.R/calculateCoverage: done
2025-10-14 10:26:41.58039 INFO::analyzeVariants/analyzeVariants: starting ...
2025-10-14 10:26:41.668733 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-10-14 10:26:45.548462 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-10-14 10:26:45.661989 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-10-14 10:26:45.68762 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-10-14 10:26:45.68956 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.raw_variants.RData
2025-10-14 10:26:45.691876 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.filtered_variants.RData
2025-10-14 10:26:45.693744 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-10-14 10:26:45.695194 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-10-14 10:26:46.023011 INFO::analyzeVariants.R/writeVCF: ...done
2025-10-14 10:26:46.167042 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/results/test_pe.summary_variants.tab
2025-10-14 10:26:46.169695 INFO::analyzeVariants/analyzeVariants: done
2025-10-14 10:26:46.174004 INFO::Pipeline run successful.
2025-10-14 10:26:46.355517 INFO::mergeLanes.R/doMergeLanes: starting...
2025-10-14 10:26:46.36102 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-10-14 10:26:46.364226 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.adapter_contaminated_1.RData
2025-10-14 10:26:46.368138 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-10-14 10:26:46.370982 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.adapter_contaminated_2.RData
2025-10-14 10:26:46.386128 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-10-14 10:26:46.389397 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.summary_preprocess.tab
2025-10-14 10:26:46.392324 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
[bam_translate] PG tag "A" on read "highqualAdapterContamIn3PrimeEnd:1:1:1:7#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInManyTxsOfMultiTxGene:1:1:1:16#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1MicrobialPE2MultimappingIntergenic:1:1:1:19#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1GeneFusionMidExonDiffChrPE2MultimappingIntergenic:1:1:1:25#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPE1UniqueUtrPE2MultimappingIntergenic:1:1:1:18#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "highqualPEsInOneTxOfMultiTxGene:1:1:1:15#0" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-10-14 10:26:46.726321 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-10-14 10:26:46.73597 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.summary_alignment.tab
2025-10-14 10:26:46.747521 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.summary_analyzed_bamstats.tab
2025-10-14 10:26:46.750448 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-10-14 10:26:47.02393 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.summary_target_lengths.tab
2025-10-14 10:26:47.089812 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-10-14 10:26:47.129195 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-10-14 10:26:47.154032 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.counts_exon.tab
2025-10-14 10:26:47.169449 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.counts_exon_disjoint.tab
2025-10-14 10:26:47.178843 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.counts_gene.tab
2025-10-14 10:26:47.18646 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.counts_gene_coding.tab
2025-10-14 10:26:47.194564 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.counts_gene_exonic.tab
2025-10-14 10:26:47.202533 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.counts_intergenic.tab
2025-10-14 10:26:47.217492 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.counts_intron.tab
2025-10-14 10:26:47.221346 INFO::countGenomicFeatures.R/mergeCounts: done
2025-10-14 10:26:47.229954 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.summary_counts.tab
2025-10-14 10:26:47.232536 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-10-14 10:26:47.526085 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-10-14 10:26:49.905901 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.coverage.RData
2025-10-14 10:26:49.908808 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.coverage.bw
2025-10-14 10:26:49.924498 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.summary_coverage.tab
2025-10-14 10:26:49.965088 INFO::analyzeVariants/analyzeVariants: starting ...
2025-10-14 10:26:50.045771 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-10-14 10:26:53.877846 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-10-14 10:26:53.994107 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-10-14 10:26:54.020427 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-10-14 10:26:54.022422 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.raw_variants.RData
2025-10-14 10:26:54.024846 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.filtered_variants.RData
2025-10-14 10:26:54.02673 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-10-14 10:26:54.028267 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-10-14 10:26:54.377992 INFO::analyzeVariants.R/writeVCF: ...done
2025-10-14 10:26:54.525436 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.mergeLanes.1132bd71cf015d/merged/results/merged.summary_variants.tab
2025-10-14 10:26:54.528061 INFO::analyzeVariants/analyzeVariants: done
2025-10-14 10:26:54.531168 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



Executing test function test.markDuplicates  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("Skipped markDuplicates() test") : 
  Skipped markDuplicates() test
In addition: There were 28 warnings (use warnings() to see them)
 done successfully.



Executing test function test.markDuplicates_w_outfile  ... Timing stopped at: 0 0 0
Error in DEACTIVATED("Skipped markDuplicates() test") : 
  Skipped markDuplicates() test
 done successfully.



Executing test function test.preprocessReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:26:54.88848 INFO::preprocessReads.R/preprocessReads: starting...
2025-10-14 10:26:54.912053 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-10-14 10:26:54.933388 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-10-14 10:26:54.936527 DEBUG::tools.R/processChunks: starting...
2025-10-14 10:26:58.709141 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-10-14 10:26:58.711262 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.1132bd7866a65c/chunks/chunk_000001/logs/progress.log
2025-10-14 10:27:01.61135 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-10-14 10:27:01.677913 DEBUG::tools.R/processChunks: done
2025-10-14 10:27:01.681135 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-10-14 10:27:01.683496 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.1132bd7866a65c/results/test_pe.adapter_contaminated_1.RData
2025-10-14 10:27:01.686116 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-10-14 10:27:01.688434 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.1132bd7866a65c/results/test_pe.adapter_contaminated_2.RData
2025-10-14 10:27:01.69756 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-10-14 10:27:01.700343 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.1132bd7866a65c/results/test_pe.summary_preprocess.tab
2025-10-14 10:27:01.703281 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.1132bd7866a65c/bams/processed.aligner_input_1.fastq ...
2025-10-14 10:27:01.709106 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.1132bd7866a65c/bams/processed.aligner_input_2.fastq ...
2025-10-14 10:27:01.714538 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.1132bd7866a65c/reports/shortReadReport_1 ...
2025-10-14 10:27:03.613546 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.1132bd7866a65c/reports/shortReadReport_2 ...
2025-10-14 10:27:05.145073 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads.minichunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:27:05.459296 INFO::preprocessReads.R/preprocessReads: starting...
2025-10-14 10:27:05.466148 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-10-14 10:27:05.470942 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-10-14 10:27:05.473977 DEBUG::tools.R/processChunks: starting...
2025-10-14 10:27:09.039782 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-10-14 10:27:09.041754 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.minichunks.1132bd5c558842/chunks/chunk_000001/logs/progress.log
2025-10-14 10:27:11.859162 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-10-14 10:27:11.861177 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.minichunks.1132bd5c558842/chunks/chunk_000002/logs/progress.log
2025-10-14 10:27:14.669152 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2025-10-14 10:27:14.671307 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.minichunks.1132bd5c558842/chunks/chunk_000003/logs/progress.log
2025-10-14 10:27:17.505525 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.047 minutes
2025-10-14 10:27:17.582586 DEBUG::tools.R/processChunks: done
2025-10-14 10:27:17.58669 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-10-14 10:27:17.589423 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.minichunks.1132bd5c558842/results/test_pe.adapter_contaminated_1.RData
2025-10-14 10:27:17.592802 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-10-14 10:27:17.595332 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.minichunks.1132bd5c558842/results/test_pe.adapter_contaminated_2.RData
2025-10-14 10:27:17.607565 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-10-14 10:27:17.610433 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.minichunks.1132bd5c558842/results/test_pe.summary_preprocess.tab
2025-10-14 10:27:17.614188 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.minichunks.1132bd5c558842/bams/processed.aligner_input_1.fastq ...
2025-10-14 10:27:17.621135 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.minichunks.1132bd5c558842/bams/processed.aligner_input_2.fastq ...
2025-10-14 10:27:17.626987 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.minichunks.1132bd5c558842/reports/shortReadReport_1 ...
2025-10-14 10:27:19.565028 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads.minichunks.1132bd5c558842/reports/shortReadReport_2 ...
2025-10-14 10:27:21.145694 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads_single_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:27:21.484086 INFO::preprocessReads.R/preprocessReads: starting...
2025-10-14 10:27:21.508691 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-10-14 10:27:21.51183 DEBUG::tools.R/processChunks: starting...
2025-10-14 10:27:25.449738 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-10-14 10:27:25.451746 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads_single_end.1132bdd471726/chunks/chunk_000001/logs/progress.log
2025-10-14 10:27:27.970581 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.042 minutes
2025-10-14 10:27:27.985699 DEBUG::tools.R/processChunks: done
2025-10-14 10:27:27.989312 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-10-14 10:27:27.991932 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads_single_end.1132bdd471726/results/test_se.adapter_contaminated_1.RData
2025-10-14 10:27:28.002525 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=26 highqual_reads=25 adapter_contam=1 read_length=75 rRNA_contam_reads=0 processed_reads=25 input_min_read_length=75 input_max_read_length=75 processed_min_read_length=75 processed_max_read_length=75
2025-10-14 10:27:28.005669 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads_single_end.1132bdd471726/results/test_se.summary_preprocess.tab
2025-10-14 10:27:28.009002 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads_single_end.1132bdd471726/bams/processed.aligner_input_1.fastq ...
2025-10-14 10:27:28.01491 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmphG5Dl2/test.preprocessReads_single_end.1132bdd471726/reports/shortReadReport_1 ...
2025-10-14 10:27:29.967986 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.readRNASeqEnds  ...  done successfully.



Executing test function test.readRNASeqEnds.dupmark  ...  done successfully.



Executing test function test.how_many  ...  done successfully.



Executing test function test.plotDF  ...  done successfully.



Executing test function test.relativeBarPlot  ...  done successfully.



Executing test function test.runPipeline  ... checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:27:30.790277 INFO::preprocessReads.R/preprocessReads: starting...
2025-10-14 10:27:30.81356 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_1.fastq.gz
2025-10-14 10:27:30.835636 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_2.fastq.gz
2025-10-14 10:27:30.838702 DEBUG::tools.R/processChunks: starting...
2025-10-14 10:27:35.024654 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-10-14 10:27:35.026662 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-10-14 10:27:38.097396 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.051 minutes
2025-10-14 10:27:38.176828 DEBUG::tools.R/processChunks: done
2025-10-14 10:27:38.180068 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-10-14 10:27:38.182467 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2025-10-14 10:27:38.185138 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-10-14 10:27:38.187723 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2025-10-14 10:27:38.197358 INFO::preprocessReads.R/mergeSummaryPreprocess: total_reads=2500 highqual_reads=2500 adapter_contam=0 read_length=100 rRNA_contam_reads=0 processed_reads=2500 input_min_read_length=100 input_max_read_length=100 processed_min_read_length=71 processed_max_read_length=100
2025-10-14 10:27:38.200433 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2025-10-14 10:27:38.203601 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2025-10-14 10:27:38.209781 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2025-10-14 10:27:38.215945 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2025-10-14 10:27:40.446116 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_2 ...
2025-10-14 10:27:42.412296 INFO::preprocessReads.R/preprocessReads: done
2025-10-14 10:27:42.496117 INFO::alignReads.R/alignReads: starting alignment...
2025-10-14 10:27:42.501072 DEBUG::tools.R/processChunks: starting...
2025-10-14 10:27:46.101073 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-10-14 10:27:46.103279 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
[bam_translate] PG tag "A" on read "HISEQ1:109:D093LACXX:4:2205:16499:6611" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "HISEQ1:109:D093LACXX:4:1206:17367:135118" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "HISEQ1:109:D093LACXX:4:1304:1838:53573" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "A" on read "HISEQ1:109:D093LACXX:4:2303:2956:116587" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "M" on read "HISEQ1:109:D093LACXX:4:2205:16499:6611" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "T" on read "HISEQ1:109:D093LACXX:4:1206:20028:108227" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "T" on read "HISEQ1:109:D093LACXX:4:1207:19518:143960" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
[bam_translate] PG tag "T" on read "HISEQ1:109:D093LACXX:4:2207:4065:173048" encountered with no corresponding entry in header, tag lost. Unknown tags are only reported once per input file for each tag ID.
2025-10-14 10:27:52.103831 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.1 minutes
2025-10-14 10:27:52.107398 DEBUG::tools.R/processChunks: done
2025-10-14 10:27:52.10949 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
2025-10-14 10:27:52.146148 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-10-14 10:27:52.154866 INFO::io.R/saveWithID: saving file= test/results/test.summary_alignment.tab
2025-10-14 10:27:52.162952 INFO::io.R/saveWithID: saving file= test/results/test.summary_analyzed_bamstats.tab
2025-10-14 10:27:52.165882 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-10-14 10:27:52.364818 INFO::io.R/saveWithID: saving file= test/results/test.summary_target_lengths.tab
2025-10-14 10:27:52.426422 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-10-14 10:27:52.427848 INFO::alignReads.R/alignReads: done
2025-10-14 10:27:52.51103 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-10-14 10:27:52.530693 DEBUG::tools.R/processChunks: starting...
2025-10-14 10:27:56.106285 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-10-14 10:27:56.108506 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-10-14 10:27:58.736294 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-10-14 10:27:58.739672 DEBUG::tools.R/processChunks: done
2025-10-14 10:27:58.741911 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-10-14 10:27:58.754447 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon.tab
2025-10-14 10:27:58.764854 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon_disjoint.tab
2025-10-14 10:27:58.772796 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene.tab
2025-10-14 10:27:58.778894 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_coding.tab
2025-10-14 10:27:58.785077 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_exonic.tab
2025-10-14 10:27:58.791026 INFO::io.R/saveWithID: saving file= test/results/test.counts_intergenic.tab
2025-10-14 10:27:58.799634 INFO::io.R/saveWithID: saving file= test/results/test.counts_intron.tab
2025-10-14 10:27:58.803765 INFO::countGenomicFeatures.R/mergeCounts: done
2025-10-14 10:27:58.808797 INFO::io.R/saveWithID: saving file= test/results/test.summary_counts.tab
2025-10-14 10:27:58.811307 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-10-14 10:27:59.08735 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-10-14 10:27:59.088622 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-10-14 10:27:59.171172 INFO::coverage.R/calculateCoverage: starting...
2025-10-14 10:27:59.175777 DEBUG::tools.R/processChunks: starting...
2025-10-14 10:28:03.97104 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-10-14 10:28:03.973294 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-10-14 10:28:06.3572 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.04 minutes
2025-10-14 10:28:06.360674 DEBUG::tools.R/processChunks: done
2025-10-14 10:28:08.536637 INFO::io.R/saveWithID: saving file= test/results/test.coverage.RData
2025-10-14 10:28:08.538755 INFO::coverage.R/saveCoverage: saving file= test/results/test.coverage.bw
2025-10-14 10:28:08.662273 INFO::io.R/saveWithID: saving file= test/results/test.summary_coverage.tab
2025-10-14 10:28:08.665266 INFO::coverage.R/calculateCoverage: done
2025-10-14 10:28:08.667369 INFO::analyzeVariants/analyzeVariants: starting ...
2025-10-14 10:28:08.750535 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-10-14 10:28:21.473078 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-10-14 10:28:21.595209 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-10-14 10:28:21.621333 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-10-14 10:28:21.623325 INFO::io.R/saveWithID: saving file= test/results/test.raw_variants.RData
2025-10-14 10:28:21.626556 INFO::io.R/saveWithID: saving file= test/results/test.filtered_variants.RData
2025-10-14 10:28:21.628572 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-10-14 10:28:21.630079 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-10-14 10:28:21.978883 INFO::analyzeVariants.R/writeVCF: ...done
2025-10-14 10:28:22.134509 INFO::io.R/saveWithID: saving file= test/results/test.summary_variants.tab
2025-10-14 10:28:22.1377 INFO::analyzeVariants/analyzeVariants: done
2025-10-14 10:28:22.144003 INFO::Pipeline run successful.
 done successfully.



Executing test function test.calculateTargetLength  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmphG5Dl2/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/config/default-config.txt 
2025-10-14 10:28:22.464125 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmphG5Dl2/test.calcTargetLengths.1132bd3a8ac56a/results/test_pe.summary_target_lengths.tab
 done successfully.



Executing test function test.sclapply  ...  done successfully.



Executing test function test.tryKeepTraceback  ...  done successfully.



Executing test function test.truncateReads  ...  done successfully.



Executing test function test.truncateReads.trim5  ...  done successfully.

RUNIT TEST PROTOCOL -- Tue Oct 14 10:28:39 2025 
*********************************************** 
Number of test functions: 61 
Number of deactivated test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
HTSeqGenie unit testing - 61 test functions, 0 errors, 0 failures



Details 
*************************** 
Test Suite: HTSeqGenie unit testing 
Test function regexp: ^test.+ 
Test file regexp: ^runit.+\.[rR]$ 
Involved directory: 
/home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests 
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.alignReads.R 
test.alignReads: (2 checks) ... OK (31.63 seconds)
test.alignReads.sparsechunks: (2 checks) ... OK (20.71 seconds)
test.alignReadsOneSingleEnd: (2 checks) ... OK (0.58 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.analyzeVariants.R 
test.annotateVariants : DEACTIVATED, Skipped annotateVariants() test
test.callVariantsVariantTools.genotype: (2 checks) ... OK (104.95 seconds)
test.wrap.callVariants: (4 checks) ... OK (12.84 seconds)
test.wrap.callVariants.filters: (2 checks) ... OK (24.52 seconds)
test.wrap.callVariants.which: (1 checks) ... OK (4.4 seconds)
test.writeVCF.NULL: (1 checks) ... OK (0.21 seconds)
test.writeVCF.vcfStat: (4 checks) ... OK (0.75 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.bamUtils.R 
test.isFirstFragment: (5 checks) ... OK (0 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.buildGenomicFeatures.R 
test.buildCountsGRangesList: (3 checks) ... OK (41.48 seconds)
test.generateSingleGeneDERs: (4 checks) ... OK (34.87 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.calculateCoverage.R 
test.computeCoverage: (9 checks) ... OK (1 seconds)
test.isSparse: (5 checks) ... OK (0.14 seconds)
test.mergeCoverage: (1 checks) ... OK (1.75 seconds)
test.mergeCoverage.sparse: (2 checks) ... OK (1.43 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.checkConfig.R 
test.checkConfig.analyzeVariants: (5 checks) ... OK (0.2 seconds)
test.findTemplate: (5 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.config.R 
test.checkConfig: (5 checks) ... OK (0.47 seconds)
test.checkConfig.alignReads: (5 checks) ... OK (0.52 seconds)
test.getConfig: (14 checks) ... OK (0 seconds)
test.loadConfig: (2 checks) ... OK (0 seconds)
test.parseDCF: (7 checks) ... OK (0 seconds)
test.updateConfig: (1 checks) ... OK (0 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.detectAdapterContam.R 
test.getAdapterSeqs: (5 checks) ... OK (0.05 seconds)
test.isAdapter: (5 checks) ... OK (0.16 seconds)
test.isAdapter3.primeEnd: (1 checks) ... OK (0.12 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.detectRRNA.R 
test.detectRRNA: (1 checks) ... OK (0.33 seconds)
test.detectRRNA.paired_end: (1 checks) ... OK (0.49 seconds)
test.getRRNAIds: (1 checks) ... OK (0.3 seconds)
test.getRRNAIds_random: (1 checks) ... OK (0.2 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.filterQuality.R 
test.filterByLength: (2 checks) ... OK (0.08 seconds)
test.isAboveQualityThresh: (3 checks) ... OK (0.07 seconds)
test.trimTailsByQuality: (4 checks) ... OK (0.05 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.gatk.R 
test.callVariantsGATK : DEACTIVATED, callVariantsGATK() tests need gatk.path option set
test.callVariantsGATK.withFiltering : DEACTIVATED, callVariantsGATK() tests need gatk.path option set
test.checkGATKJar : DEACTIVATED, checkGATKJar() test needs gatk.path option set
test.excludeVariantsByRegion: (3 checks) ... OK (0.23 seconds)
test.gatk : DEACTIVATED, gatk() tests need gatk.path option set
test.realignIndels : DEACTIVATED, test.realignIndels() tests need gatk.path option set
test.realignIndelsGATK : DEACTIVATED, realignIndelsGATK() tests need gatk.path option set
test.realignIndelsGATK.parallel : DEACTIVATED, realignIndelsGATK() tests need gatk.path option set
test_zipUp: (3 checks) ... OK (0 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.io.R 
test.FastQStreamer.getReads.pefq: (1 checks) ... OK (0.27 seconds)
test.FastQStreamer.getReads.pefq.subsample: (1 checks) ... OK (0.52 seconds)
test.FastQStreamer.getReads.segz: (1 checks) ... OK (0.22 seconds)
test.FastQStreamer.getReads.truncated: (1 checks) ... OK (0.26 seconds)
test.FastQStreamer.subsampler.isdeterministic: (3 checks) ... OK (0.88 seconds)
test.createTmpDir: (4 checks) ... OK (0 seconds)
test.detectQualityInFASTQFile: (3 checks) ... OK (0.23 seconds)
test.getObjectFilename: (4 checks) ... OK (0.01 seconds)
test.safeUnlink: (2 checks) ... OK (0.01 seconds)
test.writeAudit: (0 checks) ... OK (0.24 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.mergeLanes.R 
test.mergeLanes: (6 checks) ... OK (65.93 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.picard.R 
test.markDuplicates : DEACTIVATED, Skipped markDuplicates() test
test.markDuplicates_w_outfile : DEACTIVATED, Skipped markDuplicates() test
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.preprocessReads.R 
test.preprocessReads: (5 checks) ... OK (10.58 seconds)
test.preprocessReads.minichunks: (5 checks) ... OK (16 seconds)
test.preprocessReads_single_end: (5 checks) ... OK (8.82 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.readRNASeqEnds.R 
test.readRNASeqEnds: (6 checks) ... OK (0.13 seconds)
test.readRNASeqEnds.dupmark: (2 checks) ... OK (0.13 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.reportPipelineQA.R 
test.how_many: (3 checks) ... OK (0 seconds)
test.plotDF: (3 checks) ... OK (0.15 seconds)
test.relativeBarPlot: (2 checks) ... OK (0.05 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.runPipeline.R 
test.runPipeline: (1 checks) ... OK (51.7 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.targetLengths.R 
test.calculateTargetLength: (4 checks) ... OK (0.32 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.tools.R 
test.sclapply: (10 checks) ... OK (16.41 seconds)
test.tryKeepTraceback: (3 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-devel_2025-02-19/site-library/HTSeqGenie/unitTests/runit.trimReads.R 
test.truncateReads: (7 checks) ... OK (0.08 seconds)
test.truncateReads.trim5: (15 checks) ... OK (0.26 seconds) 

runTests.R: OK !
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
330.335 100.472 479.746

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

name	user	system	elapsed
HTSeqGenie	0	0	0
buildGenomicFeaturesFromTxDb	0	0	0
runPipeline	0	0	0