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 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4659
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4454
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4465
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4419
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4409
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: 4.37.1

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_4.37.1.tar.gz

StartedAt: 2025-01-28 11:32:54 -0000 (Tue, 28 Jan 2025)

EndedAt: 2025-01-28 11:47:53 -0000 (Tue, 28 Jan 2025)

EllapsedTime: 898.9 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_4.37.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/HTSeqGenie.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.37.1’
* 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-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘HTSeqGenie’ ...
** 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) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 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/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:40:16.09948 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-28 11:40:16.108791 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-28 11:40:16.11455 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-28 11:40:16.117332 DEBUG::tools.R/processChunks: starting...
2025-01-28 11:40:19.423098 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-28 11:40:19.42531 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.2da48f1fef1ec8/chunks/chunk_000001/logs/progress.log
2025-01-28 11:40:22.320104 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-01-28 11:40:22.322089 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.2da48f1fef1ec8/chunks/chunk_000002/logs/progress.log
2025-01-28 11:40:25.197448 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.048 minutes
2025-01-28 11:40:25.199616 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.2da48f1fef1ec8/chunks/chunk_000003/logs/progress.log
2025-01-28 11:40:28.121867 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.049 minutes
2025-01-28 11:40:28.184851 DEBUG::tools.R/processChunks: done
2025-01-28 11:40:28.190531 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-28 11:40:28.194213 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.2da48f1fef1ec8/results/test_pe.adapter_contaminated_1.RData
2025-01-28 11:40:28.198422 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-28 11:40:28.201046 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.2da48f1fef1ec8/results/test_pe.adapter_contaminated_2.RData
2025-01-28 11:40:28.213762 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
2025-01-28 11:40:28.21696 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.2da48f1fef1ec8/results/test_pe.summary_preprocess.tab
2025-01-28 11:40:28.221566 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.2da48f1fef1ec8/bams/processed.aligner_input_1.fastq ...
2025-01-28 11:40:28.228358 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.2da48f1fef1ec8/bams/processed.aligner_input_2.fastq ...
2025-01-28 11:40:28.234143 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.2da48f1fef1ec8/reports/shortReadReport_1 ...
2025-01-28 11:40:30.217029 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.2da48f1fef1ec8/reports/shortReadReport_2 ...
2025-01-28 11:40:33.281314 INFO::preprocessReads.R/preprocessReads: done
2025-01-28 11:40:33.337327 INFO::alignReads.R/alignReads: starting alignment...
2025-01-28 11:40:33.343932 DEBUG::tools.R/processChunks: starting...
2025-01-28 11:40:36.668618 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-28 11:40:36.670789 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.2da48f1fef1ec8/chunks/chunk_000001/logs/progress.log
2025-01-28 11:40:39.794403 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.052 minutes
2025-01-28 11:40:39.796628 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.2da48f1fef1ec8/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.
2025-01-28 11:40:42.546804 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-01-28 11:40:42.548926 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.2da48f1fef1ec8/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.
2025-01-28 11:40:45.267837 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2025-01-28 11:40:45.271432 DEBUG::tools.R/processChunks: done
2025-01-28 11:40:45.273546 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.
2025-01-28 11:40:45.609544 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-28 11:40:45.621239 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.2da48f1fef1ec8/results/test_pe.summary_alignment.tab
2025-01-28 11:40:45.632411 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.2da48f1fef1ec8/results/test_pe.summary_analyzed_bamstats.tab
2025-01-28 11:40:45.63503 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-28 11:40:45.928669 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.2da48f1fef1ec8/results/test_pe.summary_target_lengths.tab
2025-01-28 11:40:45.99322 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-28 11:40:45.994588 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:40:46.301817 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-28 11:40:46.305382 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-28 11:40:46.387483 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2025-01-28 11:40:46.394249 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-28 11:40:46.398624 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-28 11:40:46.401379 DEBUG::tools.R/processChunks: starting...
2025-01-28 11:40:49.674962 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-28 11:40:49.676917 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.sparsechunks.2da48f3da82332/chunks/chunk_000001/logs/progress.log
2025-01-28 11:40:52.539803 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2025-01-28 11:40:52.541991 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.sparsechunks.2da48f3da82332/chunks/chunk_000002/logs/progress.log
2025-01-28 11:40:55.368551 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2025-01-28 11:40:55.370486 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.sparsechunks.2da48f3da82332/chunks/chunk_000003/logs/progress.log
2025-01-28 11:40:58.292962 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.049 minutes
2025-01-28 11:40:58.294975 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.sparsechunks.2da48f3da82332/chunks/chunk_000004/logs/progress.log
2025-01-28 11:41:01.110428 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.047 minutes
2025-01-28 11:41:01.149612 DEBUG::tools.R/processChunks: done
2025-01-28 11:41:01.154285 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-28 11:41:01.157648 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.sparsechunks.2da48f3da82332/results/test_pe.adapter_contaminated_1.RData
2025-01-28 11:41:01.162075 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-28 11:41:01.164867 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.sparsechunks.2da48f3da82332/results/test_pe.adapter_contaminated_2.RData
2025-01-28 11:41:01.179483 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
2025-01-28 11:41:01.182611 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.sparsechunks.2da48f3da82332/results/test_pe.summary_preprocess.tab
2025-01-28 11:41:01.18784 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.sparsechunks.2da48f3da82332/bams/processed.aligner_input_1.fastq ...
2025-01-28 11:41:01.195442 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.sparsechunks.2da48f3da82332/bams/processed.aligner_input_2.fastq ...
2025-01-28 11:41:01.201317 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.sparsechunks.2da48f3da82332/reports/shortReadReport_1 ...
2025-01-28 11:41:03.116287 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReads.sparsechunks.2da48f3da82332/reports/shortReadReport_2 ...
2025-01-28 11:41:06.215494 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:41:06.413299 INFO::alignReads.R/alignReadsChunk: running gsnap...
2025-01-28 11:41:06.41922 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/Rtmp51XQQh/test.alignReadsOneSingleEnd.2da48f2669e5c4/bams/test.alignReads /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2025-01-28 11:41:06.572997 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2025-01-28 11:41:06.726009 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReadsOneSingleEnd.2da48f2669e5c4/results/test.alignReads.summary_alignment.tab
2025-01-28 11:41:06.776031 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.alignReadsOneSingleEnd.2da48f2669e5c4/results/test.alignReads.summary_analyzed_bamstats.tab
2025-01-28 11:41:06.778038 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.002 0.002 0.004
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/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:41:07.167491 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.genotype.2da48f7d398c37/results/test_pe.coverage.RData
2025-01-28 11:41:07.169863 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.genotype.2da48f7d398c37/results/test_pe.coverage.bw
2025-01-28 11:41:07.35159 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.genotype.2da48f7d398c37/results/test_pe.summary_coverage.tab
2025-01-28 11:41:07.353894 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-28 11:41:20.565015 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-28 11:41:20.700067 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-28 11:41:20.725849 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-28 11:41:20.727949 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.genotype.2da48f7d398c37/results/test_pe.raw_variants.RData
2025-01-28 11:41:20.731155 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.genotype.2da48f7d398c37/results/test_pe.filtered_variants.RData
2025-01-28 11:41:20.733096 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-28 11:41:20.734819 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-28 11:41:21.340747 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-28 11:41:21.3426 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2025-01-28 11:42:51.81612 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-28 11:42:52.425637 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-28 11:42:52.426921 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/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:42:53.047919 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-28 11:43:07.217149 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-28 11:43:07.345894 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-28 11:43:07.374713 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-28 11:43:07.377033 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.wrap.callVariants.2da48f2203ec1/results/test_pe.raw_variants.RData
2025-01-28 11:43:07.380624 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.wrap.callVariants.2da48f2203ec1/results/test_pe.filtered_variants.RData
2025-01-28 11:43:07.382909 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/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:43:07.593958 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-28 11:43:20.694342 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-28 11:43:20.785901 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-28 11:43:20.812099 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-28 11:43:20.814158 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.wrap.callVariants.filters.2da48f5b7a96cc/results/test_pe.raw_variants.RData
2025-01-28 11:43:20.817645 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.wrap.callVariants.filters.2da48f5b7a96cc/results/test_pe.filtered_variants.RData
2025-01-28 11:43:20.819813 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-28 11:43:20.822021 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-28 11:43:33.614562 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-28 11:43:33.672867 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-28 11:43:33.699037 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-28 11:43:33.700976 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.wrap.callVariants.filters.2da48f5b7a96cc/results/test_pe.raw_variants.RData
2025-01-28 11:43:33.704179 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.wrap.callVariants.filters.2da48f5b7a96cc/results/test_pe.filtered_variants.RData
2025-01-28 11:43:33.706803 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/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:43:34.024193 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-28 11:43:34.026248 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2025-01-28 11:43:37.659256 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-28 11:43:37.775156 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-28 11:43:37.800216 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-28 11:43:37.802171 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.wrap.callVariants.which.2da48f390f10bf/results/test_pe.raw_variants.RData
2025-01-28 11:43:37.804546 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.wrap.callVariants.which.2da48f390f10bf/results/test_pe.filtered_variants.RData
2025-01-28 11:43:37.806402 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:43:38.006 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-28 11:43:38.007781 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:43:38.252735 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-28 11:43:38.587513 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  ... 2025-01-28 11:44:53.200715 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/yqixvmdp/merged/results/bla.coverage.RData
2025-01-28 11:44:53.204217 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp51XQQh/yqixvmdp/merged/results/bla.coverage.bw
2025-01-28 11:44:53.322749 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/yqixvmdp/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2025-01-28 11:44:54.717889 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/ryfktbpz/merged/results/bla.coverage.RData
2025-01-28 11:44:54.720153 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp51XQQh/ryfktbpz/merged/results/bla.coverage.bw
2025-01-28 11:44:54.735873 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/ryfktbpz/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.checkConfig.analyzeVariants  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:44:56.386475 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-01-28 11:44:56.388046 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp51XQQh/test.detectRRNA.2da48f2f06903c/bams/rRNA_contam/input1.fastq
2025-01-28 11:44:56.39265 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/Rtmp51XQQh/test.detectRRNA.2da48f2f06903c/bams/rRNA_contam/test_se /home/biocbuild/tmp/Rtmp51XQQh/test.detectRRNA.2da48f2f06903c/bams/rRNA_contam/input1.fastq 2>&1
2025-01-28 11:44:56.501513 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-01-28 11:44:56.502888 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.detectRRNA.paired_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:44:56.692653 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2025-01-28 11:44:56.694048 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp51XQQh/test.detectRRNA.paired_end.2da48f37bb92da/bams/rRNA_contam/input1.fastq
2025-01-28 11:44:56.696136 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp51XQQh/test.detectRRNA.paired_end.2da48f37bb92da/bams/rRNA_contam/input2.fastq
2025-01-28 11:44:56.699293 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/Rtmp51XQQh/test.detectRRNA.paired_end.2da48f37bb92da/bams/rRNA_contam/test_pe /home/biocbuild/tmp/Rtmp51XQQh/test.detectRRNA.paired_end.2da48f37bb92da/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/tmp/Rtmp51XQQh/test.detectRRNA.paired_end.2da48f37bb92da/bams/rRNA_contam/input2.fastq 2>&1
2025-01-28 11:44:56.954826 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2025-01-28 11:44:56.956215 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2025-01-28 11:44:56.984322 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/Rtmp51XQQh/test_get_rRNA_idsyjlnzxgk/test_pe /home/biocbuild/tmp/Rtmp51XQQh/test_get_rRNA_idsyjlnzxgk/1.fastq -a paired /home/biocbuild/tmp/Rtmp51XQQh/test_get_rRNA_idsyjlnzxgk/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2025-01-28 11:44:57.265893 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/Rtmp51XQQh/test_get_rRNAIds_randomekpgczxt/test_pe /home/biocbuild/tmp/Rtmp51XQQh/test_get_rRNAIds_randomekpgczxt/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2025-01-28 11:44:57.43521 INFO::filterQuality.R/filterQuality: filterByLength...
2025-01-28 11:44:57.43728 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2025-01-28 11:44:57.438592 INFO::filterQuality.R/filterByLength: done
2025-01-28 11:44:57.508859 INFO::filterQuality.R/filterQuality: filterByLength...
2025-01-28 11:44:57.510172 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2025-01-28 11:44:57.511438 INFO::filterQuality.R/filterByLength: done
 done successfully.



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



Executing test function test.trimTailsByQuality  ... 2025-01-28 11:44:57.588607 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-28 11:44:57.601839 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-28 11:44:57.603409 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-28 11:44:57.610207 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-28 11:44:57.611767 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-28 11:44:57.618515 INFO::preprocessReads.R/preprocessReadsChunk: done
2025-01-28 11:44:57.620077 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2025-01-28 11:44:57.62682 INFO::preprocessReads.R/preprocessReadsChunk: done
 done successfully.



Executing test function test.callVariantsGATK  ... Timing stopped at: 0 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 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
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/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:44:58.049125 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-28 11:44:58.052777 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:44:58.290544 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-28 11:44:58.420763 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-28 11:44:58.424891 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-28 11:44:58.42847 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:44:58.730055 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:44:58.92439 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:44:59.135581 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-28 11:44:59.224631 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-28 11:44:59.22823 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-28 11:44:59.231672 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:44:59.507415 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-28 11:44:59.568689 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2025-01-28 11:44:59.5727 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-28 11:44:59.576533 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
 done successfully.



Executing test function test.mergeLanes  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:45:00.509822 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-28 11:45:00.516939 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-28 11:45:00.521922 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-28 11:45:00.524916 DEBUG::tools.R/processChunks: starting...
2025-01-28 11:45:03.974167 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-28 11:45:03.976202 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/chunks/chunk_000001/logs/progress.log
2025-01-28 11:45:06.778997 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2025-01-28 11:45:06.78102 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/chunks/chunk_000002/logs/progress.log
2025-01-28 11:45:09.551847 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2025-01-28 11:45:09.553816 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/chunks/chunk_000003/logs/progress.log
2025-01-28 11:45:12.307012 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-01-28 11:45:12.35467 DEBUG::tools.R/processChunks: done
2025-01-28 11:45:12.358416 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-28 11:45:12.360934 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.adapter_contaminated_1.RData
2025-01-28 11:45:12.364042 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-28 11:45:12.366467 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.adapter_contaminated_2.RData
2025-01-28 11:45:12.377827 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
2025-01-28 11:45:12.380495 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.summary_preprocess.tab
2025-01-28 11:45:12.38402 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/bams/processed.aligner_input_1.fastq ...
2025-01-28 11:45:12.390583 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/bams/processed.aligner_input_2.fastq ...
2025-01-28 11:45:12.396356 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/reports/shortReadReport_1 ...
2025-01-28 11:45:14.341517 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/reports/shortReadReport_2 ...
2025-01-28 11:45:16.037379 INFO::preprocessReads.R/preprocessReads: done
2025-01-28 11:45:16.106067 INFO::alignReads.R/alignReads: starting alignment...
2025-01-28 11:45:16.110736 DEBUG::tools.R/processChunks: starting...
2025-01-28 11:45:19.710113 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-28 11:45:19.712363 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/chunks/chunk_000001/logs/progress.log
2025-01-28 11:45:22.360737 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-01-28 11:45:22.363171 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/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.
2025-01-28 11:45:24.98094 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2025-01-28 11:45:24.983183 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/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.
2025-01-28 11:45:27.645375 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2025-01-28 11:45:27.653266 DEBUG::tools.R/processChunks: done
2025-01-28 11:45:27.655478 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.
2025-01-28 11:45:27.970232 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-28 11:45:27.981324 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.summary_alignment.tab
2025-01-28 11:45:27.991812 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.summary_analyzed_bamstats.tab
2025-01-28 11:45:27.994502 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-28 11:45:28.256167 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.summary_target_lengths.tab
2025-01-28 11:45:28.320245 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-28 11:45:28.321611 INFO::alignReads.R/alignReads: done
2025-01-28 11:45:28.393174 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-01-28 11:45:28.413544 DEBUG::tools.R/processChunks: starting...
2025-01-28 11:45:31.899269 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-28 11:45:31.901419 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/chunks/chunk_000001/logs/progress.log
2025-01-28 11:45:34.463185 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2025-01-28 11:45:34.465465 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/chunks/chunk_000002/logs/progress.log
2025-01-28 11:45:37.014089 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.042 minutes
2025-01-28 11:45:37.016402 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/chunks/chunk_000003/logs/progress.log
2025-01-28 11:45:39.581589 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2025-01-28 11:45:39.58931 DEBUG::tools.R/processChunks: done
2025-01-28 11:45:39.591794 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-01-28 11:45:39.610682 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.counts_exon.tab
2025-01-28 11:45:39.626232 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.counts_exon_disjoint.tab
2025-01-28 11:45:39.635947 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.counts_gene.tab
2025-01-28 11:45:39.643741 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.counts_gene_coding.tab
2025-01-28 11:45:39.651449 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.counts_gene_exonic.tab
2025-01-28 11:45:39.659403 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.counts_intergenic.tab
2025-01-28 11:45:39.672005 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.counts_intron.tab
2025-01-28 11:45:39.675921 INFO::countGenomicFeatures.R/mergeCounts: done
2025-01-28 11:45:39.684559 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.summary_counts.tab
2025-01-28 11:45:39.687118 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-01-28 11:45:40.05351 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-01-28 11:45:40.054687 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-01-28 11:45:40.134355 INFO::coverage.R/calculateCoverage: starting...
2025-01-28 11:45:40.139358 DEBUG::tools.R/processChunks: starting...
2025-01-28 11:45:43.627833 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-28 11:45:43.630122 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/chunks/chunk_000001/logs/progress.log
2025-01-28 11:45:45.827375 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.037 minutes
2025-01-28 11:45:45.829713 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/chunks/chunk_000002/logs/progress.log
2025-01-28 11:45:48.025668 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.037 minutes
2025-01-28 11:45:48.027833 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/chunks/chunk_000003/logs/progress.log
2025-01-28 11:45:50.221987 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.037 minutes
2025-01-28 11:45:50.225384 DEBUG::tools.R/processChunks: done
2025-01-28 11:45:52.382755 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.coverage.RData
2025-01-28 11:45:52.384881 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.coverage.bw
2025-01-28 11:45:52.401577 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.summary_coverage.tab
2025-01-28 11:45:52.403514 INFO::coverage.R/calculateCoverage: done
2025-01-28 11:45:52.405827 INFO::analyzeVariants/analyzeVariants: starting ...
2025-01-28 11:45:52.48322 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-28 11:45:56.196452 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-28 11:45:56.307693 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-28 11:45:56.33271 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-28 11:45:56.334631 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.raw_variants.RData
2025-01-28 11:45:56.336925 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.filtered_variants.RData
2025-01-28 11:45:56.338837 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-28 11:45:56.340259 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-28 11:45:56.665306 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-28 11:45:56.806892 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/results/test_pe.summary_variants.tab
2025-01-28 11:45:56.809492 INFO::analyzeVariants/analyzeVariants: done
2025-01-28 11:45:56.813626 INFO::Pipeline run successful.
2025-01-28 11:45:56.987204 INFO::mergeLanes.R/doMergeLanes: starting...
2025-01-28 11:45:56.992369 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-28 11:45:56.995257 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.adapter_contaminated_1.RData
2025-01-28 11:45:56.99904 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-28 11:45:57.001869 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.adapter_contaminated_2.RData
2025-01-28 11:45:57.016824 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
2025-01-28 11:45:57.020084 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.summary_preprocess.tab
2025-01-28 11:45:57.02304 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.
2025-01-28 11:45:57.352833 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-28 11:45:57.362325 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.summary_alignment.tab
2025-01-28 11:45:57.373353 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.summary_analyzed_bamstats.tab
2025-01-28 11:45:57.376144 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-28 11:45:57.651242 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.summary_target_lengths.tab
2025-01-28 11:45:57.719251 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-28 11:45:57.755444 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-01-28 11:45:57.779229 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.counts_exon.tab
2025-01-28 11:45:57.794225 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.counts_exon_disjoint.tab
2025-01-28 11:45:57.80367 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.counts_gene.tab
2025-01-28 11:45:57.811724 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.counts_gene_coding.tab
2025-01-28 11:45:57.819702 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.counts_gene_exonic.tab
2025-01-28 11:45:57.827693 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.counts_intergenic.tab
2025-01-28 11:45:57.842159 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.counts_intron.tab
2025-01-28 11:45:57.846038 INFO::countGenomicFeatures.R/mergeCounts: done
2025-01-28 11:45:57.854753 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.summary_counts.tab
2025-01-28 11:45:57.857318 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-01-28 11:45:58.159815 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-01-28 11:46:00.49605 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.coverage.RData
2025-01-28 11:46:00.499197 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.coverage.bw
2025-01-28 11:46:00.515729 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.summary_coverage.tab
2025-01-28 11:46:00.555119 INFO::analyzeVariants/analyzeVariants: starting ...
2025-01-28 11:46:00.626436 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-28 11:46:04.487734 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-28 11:46:04.606504 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-28 11:46:04.633249 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-28 11:46:04.635291 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.raw_variants.RData
2025-01-28 11:46:04.637752 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.filtered_variants.RData
2025-01-28 11:46:04.639683 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-28 11:46:04.64125 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-28 11:46:04.996418 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-28 11:46:05.15055 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.mergeLanes.2da48f67a3ddb5/merged/results/merged.summary_variants.tab
2025-01-28 11:46:05.153383 INFO::analyzeVariants/analyzeVariants: done
2025-01-28 11:46:05.156888 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



Executing test function test.markDuplicates  ... Timing stopped at: 0 0 0.001
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 0.001 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/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:46:05.488408 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-28 11:46:05.511012 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-28 11:46:05.523842 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-28 11:46:05.526927 DEBUG::tools.R/processChunks: starting...
2025-01-28 11:46:09.091722 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-28 11:46:09.093843 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.2da48f1814d764/chunks/chunk_000001/logs/progress.log
2025-01-28 11:46:11.862442 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-01-28 11:46:11.915022 DEBUG::tools.R/processChunks: done
2025-01-28 11:46:11.918184 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-28 11:46:11.920534 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.2da48f1814d764/results/test_pe.adapter_contaminated_1.RData
2025-01-28 11:46:11.923166 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-28 11:46:11.925513 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.2da48f1814d764/results/test_pe.adapter_contaminated_2.RData
2025-01-28 11:46:11.934798 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
2025-01-28 11:46:11.937681 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.2da48f1814d764/results/test_pe.summary_preprocess.tab
2025-01-28 11:46:11.940725 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.2da48f1814d764/bams/processed.aligner_input_1.fastq ...
2025-01-28 11:46:11.947065 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.2da48f1814d764/bams/processed.aligner_input_2.fastq ...
2025-01-28 11:46:11.953506 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.2da48f1814d764/reports/shortReadReport_1 ...
2025-01-28 11:46:13.815497 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.2da48f1814d764/reports/shortReadReport_2 ...
2025-01-28 11:46:15.466959 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads.minichunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:46:15.751302 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-28 11:46:15.758292 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-28 11:46:15.763047 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2025-01-28 11:46:15.765983 DEBUG::tools.R/processChunks: starting...
2025-01-28 11:46:19.250193 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-28 11:46:19.252222 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.minichunks.2da48f621ce938/chunks/chunk_000001/logs/progress.log
2025-01-28 11:46:22.023253 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2025-01-28 11:46:22.025293 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.minichunks.2da48f621ce938/chunks/chunk_000002/logs/progress.log
2025-01-28 11:46:24.826754 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2025-01-28 11:46:24.828769 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.minichunks.2da48f621ce938/chunks/chunk_000003/logs/progress.log
2025-01-28 11:46:27.60213 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2025-01-28 11:46:27.664475 DEBUG::tools.R/processChunks: done
2025-01-28 11:46:27.668459 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-28 11:46:27.671283 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.minichunks.2da48f621ce938/results/test_pe.adapter_contaminated_1.RData
2025-01-28 11:46:27.67497 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-28 11:46:27.677692 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.minichunks.2da48f621ce938/results/test_pe.adapter_contaminated_2.RData
2025-01-28 11:46:27.69109 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
2025-01-28 11:46:27.694091 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.minichunks.2da48f621ce938/results/test_pe.summary_preprocess.tab
2025-01-28 11:46:27.698102 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.minichunks.2da48f621ce938/bams/processed.aligner_input_1.fastq ...
2025-01-28 11:46:27.705407 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.minichunks.2da48f621ce938/bams/processed.aligner_input_2.fastq ...
2025-01-28 11:46:27.711348 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.minichunks.2da48f621ce938/reports/shortReadReport_1 ...
2025-01-28 11:46:29.615192 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads.minichunks.2da48f621ce938/reports/shortReadReport_2 ...
2025-01-28 11:46:31.307425 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads_single_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:46:31.61003 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-28 11:46:31.632925 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2025-01-28 11:46:31.636075 DEBUG::tools.R/processChunks: starting...
2025-01-28 11:46:35.499708 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-28 11:46:35.501804 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads_single_end.2da48f477c4ab4/chunks/chunk_000001/logs/progress.log
2025-01-28 11:46:38.003312 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.042 minutes
2025-01-28 11:46:38.016994 DEBUG::tools.R/processChunks: done
2025-01-28 11:46:38.020285 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-28 11:46:38.022669 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads_single_end.2da48f477c4ab4/results/test_se.adapter_contaminated_1.RData
2025-01-28 11:46:38.032519 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
2025-01-28 11:46:38.035276 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads_single_end.2da48f477c4ab4/results/test_se.summary_preprocess.tab
2025-01-28 11:46:38.038188 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads_single_end.2da48f477c4ab4/bams/processed.aligner_input_1.fastq ...
2025-01-28 11:46:38.044058 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp51XQQh/test.preprocessReads_single_end.2da48f477c4ab4/reports/shortReadReport_1 ...
2025-01-28 11:46:39.853357 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-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:46:40.629767 INFO::preprocessReads.R/preprocessReads: starting...
2025-01-28 11:46:40.652196 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_1.fastq.gz
2025-01-28 11:46:40.658185 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/extdata/H1993_TP53_subset2500_2.fastq.gz
2025-01-28 11:46:40.661245 DEBUG::tools.R/processChunks: starting...
2025-01-28 11:46:44.254613 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-28 11:46:44.256679 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-01-28 11:46:47.232727 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.05 minutes
2025-01-28 11:46:47.299044 DEBUG::tools.R/processChunks: done
2025-01-28 11:46:47.302127 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2025-01-28 11:46:47.30449 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2025-01-28 11:46:47.307109 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2025-01-28 11:46:47.309373 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2025-01-28 11:46:47.318242 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
2025-01-28 11:46:47.321048 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2025-01-28 11:46:47.323917 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2025-01-28 11:46:47.330072 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2025-01-28 11:46:47.33581 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2025-01-28 11:46:49.385133 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_2 ...
2025-01-28 11:46:51.203514 INFO::preprocessReads.R/preprocessReads: done
2025-01-28 11:46:51.276366 INFO::alignReads.R/alignReads: starting alignment...
2025-01-28 11:46:51.28103 DEBUG::tools.R/processChunks: starting...
2025-01-28 11:46:54.758132 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-28 11:46:54.760252 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.
2025-01-28 11:47:00.675831 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.099 minutes
2025-01-28 11:47:00.679153 DEBUG::tools.R/processChunks: done
2025-01-28 11:47:00.681064 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
2025-01-28 11:47:00.715157 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2025-01-28 11:47:00.723257 INFO::io.R/saveWithID: saving file= test/results/test.summary_alignment.tab
2025-01-28 11:47:00.730764 INFO::io.R/saveWithID: saving file= test/results/test.summary_analyzed_bamstats.tab
2025-01-28 11:47:00.733425 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2025-01-28 11:47:00.930836 INFO::io.R/saveWithID: saving file= test/results/test.summary_target_lengths.tab
2025-01-28 11:47:00.991779 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2025-01-28 11:47:00.99311 INFO::alignReads.R/alignReads: done
2025-01-28 11:47:01.072271 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2025-01-28 11:47:01.090379 DEBUG::tools.R/processChunks: starting...
2025-01-28 11:47:04.668069 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-28 11:47:04.670193 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-01-28 11:47:07.292896 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2025-01-28 11:47:07.296226 DEBUG::tools.R/processChunks: done
2025-01-28 11:47:07.298406 INFO::countGenomicFeatures.R/mergeCounts: starting...
2025-01-28 11:47:07.310113 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon.tab
2025-01-28 11:47:07.320204 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon_disjoint.tab
2025-01-28 11:47:07.327767 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene.tab
2025-01-28 11:47:07.333263 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_coding.tab
2025-01-28 11:47:07.338625 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_exonic.tab
2025-01-28 11:47:07.34407 INFO::io.R/saveWithID: saving file= test/results/test.counts_intergenic.tab
2025-01-28 11:47:07.352139 INFO::io.R/saveWithID: saving file= test/results/test.counts_intron.tab
2025-01-28 11:47:07.356176 INFO::countGenomicFeatures.R/mergeCounts: done
2025-01-28 11:47:07.361269 INFO::io.R/saveWithID: saving file= test/results/test.summary_counts.tab
2025-01-28 11:47:07.363646 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2025-01-28 11:47:07.651954 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2025-01-28 11:47:07.653293 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2025-01-28 11:47:07.726424 INFO::coverage.R/calculateCoverage: starting...
2025-01-28 11:47:07.730814 DEBUG::tools.R/processChunks: starting...
2025-01-28 11:47:11.212442 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2025-01-28 11:47:11.214816 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2025-01-28 11:47:13.595583 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.04 minutes
2025-01-28 11:47:13.599015 DEBUG::tools.R/processChunks: done
2025-01-28 11:47:15.381252 INFO::io.R/saveWithID: saving file= test/results/test.coverage.RData
2025-01-28 11:47:15.383412 INFO::coverage.R/saveCoverage: saving file= test/results/test.coverage.bw
2025-01-28 11:47:15.493163 INFO::io.R/saveWithID: saving file= test/results/test.summary_coverage.tab
2025-01-28 11:47:15.494945 INFO::coverage.R/calculateCoverage: done
2025-01-28 11:47:15.496635 INFO::analyzeVariants/analyzeVariants: starting ...
2025-01-28 11:47:15.573695 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2025-01-28 11:47:29.553623 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2025-01-28 11:47:29.699256 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2025-01-28 11:47:29.730797 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2025-01-28 11:47:29.733182 INFO::io.R/saveWithID: saving file= test/results/test.raw_variants.RData
2025-01-28 11:47:29.73685 INFO::io.R/saveWithID: saving file= test/results/test.filtered_variants.RData
2025-01-28 11:47:29.739063 INFO::analyzeVariants.R/wrap.callVariants: ...done
2025-01-28 11:47:29.740867 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2025-01-28 11:47:30.167459 INFO::analyzeVariants.R/writeVCF: ...done
2025-01-28 11:47:30.358676 INFO::io.R/saveWithID: saving file= test/results/test.summary_variants.tab
2025-01-28 11:47:30.362409 INFO::analyzeVariants/analyzeVariants: done
2025-01-28 11:47:30.379553 INFO::Pipeline run successful.
 done successfully.



Executing test function test.calculateTargetLength  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp51XQQh/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/config/default-config.txt 
2025-01-28 11:47:30.670725 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp51XQQh/test.calcTargetLengths.2da48f30a96054/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 Jan 28 11:47:46 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-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests 
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.alignReads.R 
test.alignReads: (2 checks) ... OK (31.61 seconds)
test.alignReads.sparsechunks: (2 checks) ... OK (20.21 seconds)
test.alignReadsOneSingleEnd: (2 checks) ... OK (0.56 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.analyzeVariants.R 
test.annotateVariants : DEACTIVATED, Skipped annotateVariants() test
test.callVariantsVariantTools.genotype: (2 checks) ... OK (106.06 seconds)
test.wrap.callVariants: (4 checks) ... OK (14.54 seconds)
test.wrap.callVariants.filters: (2 checks) ... OK (26.32 seconds)
test.wrap.callVariants.which: (1 checks) ... OK (4.1 seconds)
test.writeVCF.NULL: (1 checks) ... OK (0.2 seconds)
test.writeVCF.vcfStat: (4 checks) ... OK (0.73 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.bamUtils.R 
test.isFirstFragment: (5 checks) ... OK (0 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.buildGenomicFeatures.R 
test.buildCountsGRangesList: (3 checks) ... OK (38.19 seconds)
test.generateSingleGeneDERs: (4 checks) ... OK (33.66 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.calculateCoverage.R 
test.computeCoverage: (9 checks) ... OK (0.95 seconds)
test.isSparse: (5 checks) ... OK (0.13 seconds)
test.mergeCoverage: (1 checks) ... OK (1.65 seconds)
test.mergeCoverage.sparse: (2 checks) ... OK (1.44 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.checkConfig.R 
test.checkConfig.analyzeVariants: (5 checks) ... OK (0.21 seconds)
test.findTemplate: (5 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.config.R 
test.checkConfig: (5 checks) ... OK (0.41 seconds)
test.checkConfig.alignReads: (5 checks) ... OK (0.46 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-4.5.0-devel_2024-11-24/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 (0.11 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.detectRRNA.R 
test.detectRRNA: (1 checks) ... OK (0.3 seconds)
test.detectRRNA.paired_end: (1 checks) ... OK (0.45 seconds)
test.getRRNAIds: (1 checks) ... OK (0.28 seconds)
test.getRRNAIds_random: (1 checks) ... OK (0.19 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.filterQuality.R 
test.filterByLength: (2 checks) ... OK (0.08 seconds)
test.isAboveQualityThresh: (3 checks) ... OK (0.06 seconds)
test.trimTailsByQuality: (4 checks) ... OK (0.05 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.io.R 
test.FastQStreamer.getReads.pefq: (1 checks) ... OK (0.24 seconds)
test.FastQStreamer.getReads.pefq.subsample: (1 checks) ... OK (0.43 seconds)
test.FastQStreamer.getReads.segz: (1 checks) ... OK (0.2 seconds)
test.FastQStreamer.getReads.truncated: (1 checks) ... OK (0.22 seconds)
test.FastQStreamer.subsampler.isdeterministic: (3 checks) ... OK (0.71 seconds)
test.createTmpDir: (4 checks) ... OK (0 seconds)
test.detectQualityInFASTQFile: (3 checks) ... OK (0.18 seconds)
test.getObjectFilename: (4 checks) ... OK (0.01 seconds)
test.safeUnlink: (2 checks) ... OK (0.01 seconds)
test.writeAudit: (0 checks) ... OK (0.22 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.mergeLanes.R 
test.mergeLanes: (6 checks) ... OK (65.08 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.preprocessReads.R 
test.preprocessReads: (5 checks) ... OK (10.28 seconds)
test.preprocessReads.minichunks: (5 checks) ... OK (15.84 seconds)
test.preprocessReads_single_end: (5 checks) ... OK (8.55 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.runPipeline.R 
test.runPipeline: (1 checks) ... OK (50.05 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.targetLengths.R 
test.calculateTargetLength: (4 checks) ... OK (0.29 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/HTSeqGenie/unitTests/runit.tools.R 
test.sclapply: (10 checks) ... OK (15.46 seconds)
test.tryKeepTraceback: (3 checks) ... OK (0.01 seconds)
--------------------------- 
Test file: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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 
325.725  97.569 473.246

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

name	user	system	elapsed
HTSeqGenie	0	0	0
buildGenomicFeaturesFromTxDb	0	0	0
runPipeline	0.000	0.000	0.001