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) (2024-10-21 r87258) -- "Unsuffered Consequences"	4754
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4472
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4426
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4381
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4373
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: 2024-12-24 07:41:23 -0000 (Tue, 24 Dec 2024)

EndedAt: 2024-12-24 07:56:27 -0000 (Tue, 24 Dec 2024)

EllapsedTime: 903.7 seconds

RetCode: 0

Status: OK

CheckDir: HTSeqGenie.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings HTSeqGenie_4.37.1.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/Rtmp44UO85/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 
2024-12-24 07:48:46.683962 INFO::preprocessReads.R/preprocessReads: starting...
2024-12-24 07:48:46.693233 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
2024-12-24 07:48:46.698846 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
2024-12-24 07:48:46.70156 DEBUG::tools.R/processChunks: starting...
2024-12-24 07:48:49.96567 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-12-24 07:48:49.967641 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.13c8b9237652ae/chunks/chunk_000001/logs/progress.log
2024-12-24 07:48:52.867592 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.048 minutes
2024-12-24 07:48:52.869648 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.13c8b9237652ae/chunks/chunk_000002/logs/progress.log
2024-12-24 07:48:55.773468 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.048 minutes
2024-12-24 07:48:55.775335 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.13c8b9237652ae/chunks/chunk_000003/logs/progress.log
2024-12-24 07:48:58.657022 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.048 minutes
2024-12-24 07:48:58.700581 DEBUG::tools.R/processChunks: done
2024-12-24 07:48:58.705918 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-12-24 07:48:58.709282 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.13c8b9237652ae/results/test_pe.adapter_contaminated_1.RData
2024-12-24 07:48:58.713567 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-12-24 07:48:58.721388 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.13c8b9237652ae/results/test_pe.adapter_contaminated_2.RData
2024-12-24 07:48:58.735101 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
2024-12-24 07:48:58.738468 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.13c8b9237652ae/results/test_pe.summary_preprocess.tab
2024-12-24 07:48:58.743322 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.13c8b9237652ae/bams/processed.aligner_input_1.fastq ...
2024-12-24 07:48:58.749926 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.13c8b9237652ae/bams/processed.aligner_input_2.fastq ...
2024-12-24 07:48:58.75547 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.13c8b9237652ae/reports/shortReadReport_1 ...
2024-12-24 07:49:00.710869 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.13c8b9237652ae/reports/shortReadReport_2 ...
2024-12-24 07:49:05.106192 INFO::preprocessReads.R/preprocessReads: done
2024-12-24 07:49:05.167084 INFO::alignReads.R/alignReads: starting alignment...
2024-12-24 07:49:05.173473 DEBUG::tools.R/processChunks: starting...
2024-12-24 07:49:08.449939 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-12-24 07:49:08.452075 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.13c8b9237652ae/chunks/chunk_000001/logs/progress.log
2024-12-24 07:49:11.572667 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.052 minutes
2024-12-24 07:49:11.574867 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.13c8b9237652ae/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.
2024-12-24 07:49:14.305124 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2024-12-24 07:49:14.307333 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.13c8b9237652ae/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.
2024-12-24 07:49:17.024447 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2024-12-24 07:49:17.027805 DEBUG::tools.R/processChunks: done
2024-12-24 07:49:17.029697 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.
2024-12-24 07:49:17.356244 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-12-24 07:49:17.36802 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.13c8b9237652ae/results/test_pe.summary_alignment.tab
2024-12-24 07:49:17.378716 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.13c8b9237652ae/results/test_pe.summary_analyzed_bamstats.tab
2024-12-24 07:49:17.381184 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-12-24 07:49:17.663037 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.13c8b9237652ae/results/test_pe.summary_target_lengths.tab
2024-12-24 07:49:17.724988 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-12-24 07:49:17.726339 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp44UO85/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 
2024-12-24 07:49:18.038817 INFO::preprocessReads.R/preprocessReads: starting...
2024-12-24 07:49:18.042356 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
2024-12-24 07:49:18.12696 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2024-12-24 07:49:18.133688 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
2024-12-24 07:49:18.138144 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
2024-12-24 07:49:18.140953 DEBUG::tools.R/processChunks: starting...
2024-12-24 07:49:21.766673 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-12-24 07:49:21.768648 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.sparsechunks.13c8b96ae51682/chunks/chunk_000001/logs/progress.log
2024-12-24 07:49:24.609958 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.047 minutes
2024-12-24 07:49:24.612021 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.sparsechunks.13c8b96ae51682/chunks/chunk_000002/logs/progress.log
2024-12-24 07:49:27.42 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.047 minutes
2024-12-24 07:49:27.422076 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.sparsechunks.13c8b96ae51682/chunks/chunk_000003/logs/progress.log
2024-12-24 07:49:30.33469 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.049 minutes
2024-12-24 07:49:30.336597 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.sparsechunks.13c8b96ae51682/chunks/chunk_000004/logs/progress.log
2024-12-24 07:49:33.172808 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.047 minutes
2024-12-24 07:49:33.21312 DEBUG::tools.R/processChunks: done
2024-12-24 07:49:33.217627 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-12-24 07:49:33.220932 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.sparsechunks.13c8b96ae51682/results/test_pe.adapter_contaminated_1.RData
2024-12-24 07:49:33.225384 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-12-24 07:49:33.228151 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.sparsechunks.13c8b96ae51682/results/test_pe.adapter_contaminated_2.RData
2024-12-24 07:49:33.243179 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
2024-12-24 07:49:33.246439 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.sparsechunks.13c8b96ae51682/results/test_pe.summary_preprocess.tab
2024-12-24 07:49:33.251436 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.sparsechunks.13c8b96ae51682/bams/processed.aligner_input_1.fastq ...
2024-12-24 07:49:33.258604 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.sparsechunks.13c8b96ae51682/bams/processed.aligner_input_2.fastq ...
2024-12-24 07:49:33.264234 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.sparsechunks.13c8b96ae51682/reports/shortReadReport_1 ...
2024-12-24 07:49:35.169314 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp44UO85/test.alignReads.sparsechunks.13c8b96ae51682/reports/shortReadReport_2 ...
2024-12-24 07:49:38.22795 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp44UO85/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 
2024-12-24 07:49:38.432761 INFO::alignReads.R/alignReadsChunk: running gsnap...
2024-12-24 07:49:38.447678 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/Rtmp44UO85/test.alignReadsOneSingleEnd.13c8b94081cb7/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
2024-12-24 07:49:38.597461 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2024-12-24 07:49:38.735327 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.alignReadsOneSingleEnd.13c8b94081cb7/results/test.alignReads.summary_alignment.tab
2024-12-24 07:49:38.78519 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.alignReadsOneSingleEnd.13c8b94081cb7/results/test.alignReads.summary_analyzed_bamstats.tab
2024-12-24 07:49:38.787209 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.002 0.002 0.003
Error in DEACTIVATED("Skipped annotateVariants() test") : 
  Skipped annotateVariants() test
In addition: There were 11 warnings (use warnings() to see them)
 done successfully.



Executing test function test.callVariantsVariantTools.genotype  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp44UO85/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 
2024-12-24 07:49:39.181344 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.genotype.13c8b9664eeb6/results/test_pe.coverage.RData
2024-12-24 07:49:39.183773 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.genotype.13c8b9664eeb6/results/test_pe.coverage.bw
2024-12-24 07:49:39.361433 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.genotype.13c8b9664eeb6/results/test_pe.summary_coverage.tab
2024-12-24 07:49:39.363734 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-12-24 07:49:52.562268 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-12-24 07:49:52.701448 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-12-24 07:49:52.727983 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-12-24 07:49:52.730159 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.genotype.13c8b9664eeb6/results/test_pe.raw_variants.RData
2024-12-24 07:49:52.733553 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.genotype.13c8b9664eeb6/results/test_pe.filtered_variants.RData
2024-12-24 07:49:52.735669 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-12-24 07:49:52.737548 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-12-24 07:49:53.349634 INFO::analyzeVariants.R/writeVCF: ...done
2024-12-24 07:49:53.351508 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2024-12-24 07:51:24.270564 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-12-24 07:51:24.953868 INFO::analyzeVariants.R/writeVCF: ...done
2024-12-24 07:51:24.955441 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/Rtmp44UO85/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 
2024-12-24 07:51:25.780232 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-12-24 07:51:39.008986 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-12-24 07:51:39.124804 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-12-24 07:51:39.150461 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-12-24 07:51:39.152516 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.wrap.callVariants.13c8b91c302c54/results/test_pe.raw_variants.RData
2024-12-24 07:51:39.15571 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.wrap.callVariants.13c8b91c302c54/results/test_pe.filtered_variants.RData
2024-12-24 07:51:39.157643 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/Rtmp44UO85/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 
2024-12-24 07:51:39.348378 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-12-24 07:51:52.516643 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-12-24 07:51:52.629432 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-12-24 07:51:52.660769 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-12-24 07:51:52.663245 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.wrap.callVariants.filters.13c8b97f8ee786/results/test_pe.raw_variants.RData
2024-12-24 07:51:52.667287 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.wrap.callVariants.filters.13c8b97f8ee786/results/test_pe.filtered_variants.RData
2024-12-24 07:51:52.67027 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-12-24 07:51:52.673313 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-12-24 07:52:06.051251 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-12-24 07:52:06.122546 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-12-24 07:52:06.154024 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-12-24 07:52:06.156624 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.wrap.callVariants.filters.13c8b97f8ee786/results/test_pe.raw_variants.RData
2024-12-24 07:52:06.160791 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.wrap.callVariants.filters.13c8b97f8ee786/results/test_pe.filtered_variants.RData
2024-12-24 07:52:06.164057 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/Rtmp44UO85/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 
2024-12-24 07:52:06.517372 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-12-24 07:52:06.519416 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2024-12-24 07:52:10.745727 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-12-24 07:52:10.868014 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-12-24 07:52:10.895083 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-12-24 07:52:10.89714 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.wrap.callVariants.which.13c8b949e8f7d1/results/test_pe.raw_variants.RData
2024-12-24 07:52:10.899641 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.wrap.callVariants.which.13c8b949e8f7d1/results/test_pe.filtered_variants.RData
2024-12-24 07:52:10.90164 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp44UO85/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 
2024-12-24 07:52:11.100941 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-12-24 07:52:11.102914 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp44UO85/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 
2024-12-24 07:52:11.353272 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-12-24 07:52:11.693815 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  ... 2024-12-24 07:53:26.658848 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/cdqhpeka/merged/results/bla.coverage.RData
2024-12-24 07:53:26.661995 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp44UO85/cdqhpeka/merged/results/bla.coverage.bw
2024-12-24 07:53:26.771431 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/cdqhpeka/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.mergeCoverage.sparse  ... 2024-12-24 07:53:28.13134 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/whxzgqip/merged/results/bla.coverage.RData
2024-12-24 07:53:28.133438 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp44UO85/whxzgqip/merged/results/bla.coverage.bw
2024-12-24 07:53:28.147901 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/whxzgqip/merged/results/bla.summary_coverage.tab
 done successfully.



Executing test function test.checkConfig.analyzeVariants  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp44UO85/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/Rtmp44UO85/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/Rtmp44UO85/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/Rtmp44UO85/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/Rtmp44UO85/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/Rtmp44UO85/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/Rtmp44UO85/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/Rtmp44UO85/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/Rtmp44UO85/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/Rtmp44UO85/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 
2024-12-24 07:53:29.950225 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2024-12-24 07:53:29.951831 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp44UO85/test.detectRRNA.13c8b91a5df7e5/bams/rRNA_contam/input1.fastq
2024-12-24 07:53:29.956583 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/Rtmp44UO85/test.detectRRNA.13c8b91a5df7e5/bams/rRNA_contam/test_se /home/biocbuild/tmp/Rtmp44UO85/test.detectRRNA.13c8b91a5df7e5/bams/rRNA_contam/input1.fastq 2>&1
2024-12-24 07:53:30.066101 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2024-12-24 07:53:30.067519 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.detectRRNA.paired_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp44UO85/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 
2024-12-24 07:53:30.275852 INFO::detectRRNA.R/detectRRNA: searching for rRNA contamination...
2024-12-24 07:53:30.277329 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp44UO85/test.detectRRNA.paired_end.13c8b92984e8e1/bams/rRNA_contam/input1.fastq
2024-12-24 07:53:30.279501 INFO::io.R/writeFastQFiles: writing filename= /home/biocbuild/tmp/Rtmp44UO85/test.detectRRNA.paired_end.13c8b92984e8e1/bams/rRNA_contam/input2.fastq
2024-12-24 07:53:30.282731 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/Rtmp44UO85/test.detectRRNA.paired_end.13c8b92984e8e1/bams/rRNA_contam/test_pe /home/biocbuild/tmp/Rtmp44UO85/test.detectRRNA.paired_end.13c8b92984e8e1/bams/rRNA_contam/input1.fastq -a paired /home/biocbuild/tmp/Rtmp44UO85/test.detectRRNA.paired_end.13c8b92984e8e1/bams/rRNA_contam/input2.fastq 2>&1
2024-12-24 07:53:30.539777 INFO::detectRRNA.R/detectRRNA: contaminated fraction= 1
2024-12-24 07:53:30.54117 INFO::detectRRNA.R/detectRRNA: done
 done successfully.



Executing test function test.getRRNAIds  ... 2024-12-24 07:53:30.570872 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/Rtmp44UO85/test_get_rRNA_idsqupliadz/test_pe /home/biocbuild/tmp/Rtmp44UO85/test_get_rRNA_idsqupliadz/1.fastq -a paired /home/biocbuild/tmp/Rtmp44UO85/test_get_rRNA_idsqupliadz/2.fastq 2>&1
 done successfully.



Executing test function test.getRRNAIds_random  ... 2024-12-24 07:53:30.861273 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/Rtmp44UO85/test_get_rRNAIds_randomhtgkeixa/test_pe /home/biocbuild/tmp/Rtmp44UO85/test_get_rRNAIds_randomhtgkeixa/1.fastq 2>&1
 done successfully.



Executing test function test.filterByLength  ... 2024-12-24 07:53:31.031112 INFO::filterQuality.R/filterQuality: filterByLength...
2024-12-24 07:53:31.033281 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 0.5
2024-12-24 07:53:31.03462 INFO::filterQuality.R/filterByLength: done
2024-12-24 07:53:31.105 INFO::filterQuality.R/filterQuality: filterByLength...
2024-12-24 07:53:31.106333 INFO::filterQuality.R/filterByLength: fraction of filtered short reads= 1
2024-12-24 07:53:31.107635 INFO::filterQuality.R/filterByLength: done
 done successfully.



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



Executing test function test.trimTailsByQuality  ... 2024-12-24 07:53:31.185688 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-12-24 07:53:31.198937 INFO::preprocessReads.R/preprocessReadsChunk: done
2024-12-24 07:53:31.200568 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-12-24 07:53:31.207374 INFO::preprocessReads.R/preprocessReadsChunk: done
2024-12-24 07:53:31.208995 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-12-24 07:53:31.215789 INFO::preprocessReads.R/preprocessReadsChunk: done
2024-12-24 07:53:31.217398 INFO::preprocessReads.R/preprocessReadsChunk: Starting trimTailsByQuality ...
2024-12-24 07:53:31.224154 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: 0.001 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: 0.001 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/Rtmp44UO85/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 
2024-12-24 07:53:31.666895 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
2024-12-24 07:53:31.676357 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/Rtmp44UO85/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 
2024-12-24 07:53:31.93949 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
2024-12-24 07:53:32.101258 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2024-12-24 07:53:32.105244 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
2024-12-24 07:53:32.108746 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/Rtmp44UO85/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 
2024-12-24 07:53:33.753736 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/Rtmp44UO85/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 
2024-12-24 07:53:33.960946 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/Rtmp44UO85/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 
2024-12-24 07:53:34.200058 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
2024-12-24 07:53:34.319999 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2024-12-24 07:53:34.323647 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
2024-12-24 07:53:34.327122 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/Rtmp44UO85/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 
2024-12-24 07:53:34.638605 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
2024-12-24 07:53:34.710213 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 17 , totnbreads= 26 )
2024-12-24 07:53:34.713928 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
2024-12-24 07:53:34.717539 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/Rtmp44UO85/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/Rtmp44UO85/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 
2024-12-24 07:53:35.72962 INFO::preprocessReads.R/preprocessReads: starting...
2024-12-24 07:53:35.73706 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
2024-12-24 07:53:35.742134 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
2024-12-24 07:53:35.745678 DEBUG::tools.R/processChunks: starting...
2024-12-24 07:53:39.205421 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-12-24 07:53:39.207576 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/chunks/chunk_000001/logs/progress.log
2024-12-24 07:53:41.963874 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2024-12-24 07:53:41.96591 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/chunks/chunk_000002/logs/progress.log
2024-12-24 07:53:44.695223 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.045 minutes
2024-12-24 07:53:44.69752 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/chunks/chunk_000003/logs/progress.log
2024-12-24 07:53:47.401561 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.045 minutes
2024-12-24 07:53:47.464348 DEBUG::tools.R/processChunks: done
2024-12-24 07:53:47.468064 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-12-24 07:53:47.470583 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.adapter_contaminated_1.RData
2024-12-24 07:53:47.473752 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-12-24 07:53:47.47607 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.adapter_contaminated_2.RData
2024-12-24 07:53:47.487323 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
2024-12-24 07:53:47.489959 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.summary_preprocess.tab
2024-12-24 07:53:47.493426 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/bams/processed.aligner_input_1.fastq ...
2024-12-24 07:53:47.499981 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/bams/processed.aligner_input_2.fastq ...
2024-12-24 07:53:47.505555 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/reports/shortReadReport_1 ...
2024-12-24 07:53:49.295984 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/reports/shortReadReport_2 ...
2024-12-24 07:53:50.789935 INFO::preprocessReads.R/preprocessReads: done
2024-12-24 07:53:50.861698 INFO::alignReads.R/alignReads: starting alignment...
2024-12-24 07:53:50.866763 DEBUG::tools.R/processChunks: starting...
2024-12-24 07:53:54.456367 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-12-24 07:53:54.458727 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/chunks/chunk_000001/logs/progress.log
2024-12-24 07:53:57.084906 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2024-12-24 07:53:57.087227 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/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.
2024-12-24 07:53:59.719423 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.044 minutes
2024-12-24 07:53:59.721574 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/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.
2024-12-24 07:54:02.36151 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.044 minutes
2024-12-24 07:54:02.365005 DEBUG::tools.R/processChunks: done
2024-12-24 07:54:02.367061 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.
2024-12-24 07:54:02.674888 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-12-24 07:54:02.685579 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.summary_alignment.tab
2024-12-24 07:54:02.695635 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.summary_analyzed_bamstats.tab
2024-12-24 07:54:02.698243 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-12-24 07:54:02.989531 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.summary_target_lengths.tab
2024-12-24 07:54:03.057183 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-12-24 07:54:03.058571 INFO::alignReads.R/alignReads: done
2024-12-24 07:54:03.144051 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2024-12-24 07:54:03.166762 DEBUG::tools.R/processChunks: starting...
2024-12-24 07:54:06.643393 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-12-24 07:54:06.64557 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/chunks/chunk_000001/logs/progress.log
2024-12-24 07:54:09.206635 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.043 minutes
2024-12-24 07:54:09.208936 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/chunks/chunk_000002/logs/progress.log
2024-12-24 07:54:11.79607 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.043 minutes
2024-12-24 07:54:11.798239 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/chunks/chunk_000003/logs/progress.log
2024-12-24 07:54:14.370884 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.043 minutes
2024-12-24 07:54:14.374707 DEBUG::tools.R/processChunks: done
2024-12-24 07:54:14.377316 INFO::countGenomicFeatures.R/mergeCounts: starting...
2024-12-24 07:54:14.394455 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.counts_exon.tab
2024-12-24 07:54:14.408158 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.counts_exon_disjoint.tab
2024-12-24 07:54:14.417197 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.counts_gene.tab
2024-12-24 07:54:14.424444 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.counts_gene_coding.tab
2024-12-24 07:54:14.431694 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.counts_gene_exonic.tab
2024-12-24 07:54:14.439254 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.counts_intergenic.tab
2024-12-24 07:54:14.451215 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.counts_intron.tab
2024-12-24 07:54:14.454806 INFO::countGenomicFeatures.R/mergeCounts: done
2024-12-24 07:54:14.462364 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.summary_counts.tab
2024-12-24 07:54:14.464626 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2024-12-24 07:54:14.828496 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2024-12-24 07:54:14.82972 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2024-12-24 07:54:14.902516 INFO::coverage.R/calculateCoverage: starting...
2024-12-24 07:54:14.907476 DEBUG::tools.R/processChunks: starting...
2024-12-24 07:54:18.404171 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-12-24 07:54:18.406376 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/chunks/chunk_000001/logs/progress.log
2024-12-24 07:54:20.608237 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.037 minutes
2024-12-24 07:54:20.610631 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/chunks/chunk_000002/logs/progress.log
2024-12-24 07:54:22.824515 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.037 minutes
2024-12-24 07:54:22.826796 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/chunks/chunk_000003/logs/progress.log
2024-12-24 07:54:25.032501 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.037 minutes
2024-12-24 07:54:25.040208 DEBUG::tools.R/processChunks: done
2024-12-24 07:54:26.803251 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.coverage.RData
2024-12-24 07:54:26.805134 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.coverage.bw
2024-12-24 07:54:26.820281 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.summary_coverage.tab
2024-12-24 07:54:26.822094 INFO::coverage.R/calculateCoverage: done
2024-12-24 07:54:26.828456 INFO::analyzeVariants/analyzeVariants: starting ...
2024-12-24 07:54:26.901539 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-12-24 07:54:30.634462 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-12-24 07:54:30.749917 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-12-24 07:54:30.775649 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-12-24 07:54:30.777643 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.raw_variants.RData
2024-12-24 07:54:30.78014 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.filtered_variants.RData
2024-12-24 07:54:30.782145 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-12-24 07:54:30.783747 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-12-24 07:54:31.128934 INFO::analyzeVariants.R/writeVCF: ...done
2024-12-24 07:54:31.283347 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/results/test_pe.summary_variants.tab
2024-12-24 07:54:31.286074 INFO::analyzeVariants/analyzeVariants: done
2024-12-24 07:54:31.294123 INFO::Pipeline run successful.
2024-12-24 07:54:31.48089 INFO::mergeLanes.R/doMergeLanes: starting...
2024-12-24 07:54:31.486192 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-12-24 07:54:31.489118 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.adapter_contaminated_1.RData
2024-12-24 07:54:31.493027 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-12-24 07:54:31.495831 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.adapter_contaminated_2.RData
2024-12-24 07:54:31.510087 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
2024-12-24 07:54:31.513189 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.summary_preprocess.tab
2024-12-24 07:54:31.516018 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.
2024-12-24 07:54:31.857507 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-12-24 07:54:31.866781 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.summary_alignment.tab
2024-12-24 07:54:31.885267 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.summary_analyzed_bamstats.tab
2024-12-24 07:54:31.888171 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-12-24 07:54:32.166454 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.summary_target_lengths.tab
2024-12-24 07:54:32.233585 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-12-24 07:54:32.274074 INFO::countGenomicFeatures.R/mergeCounts: starting...
2024-12-24 07:54:32.298567 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.counts_exon.tab
2024-12-24 07:54:32.313854 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.counts_exon_disjoint.tab
2024-12-24 07:54:32.323098 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.counts_gene.tab
2024-12-24 07:54:32.330973 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.counts_gene_coding.tab
2024-12-24 07:54:32.338731 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.counts_gene_exonic.tab
2024-12-24 07:54:32.346725 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.counts_intergenic.tab
2024-12-24 07:54:32.361502 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.counts_intron.tab
2024-12-24 07:54:32.365449 INFO::countGenomicFeatures.R/mergeCounts: done
2024-12-24 07:54:32.373634 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.summary_counts.tab
2024-12-24 07:54:32.376168 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2024-12-24 07:54:32.670182 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2024-12-24 07:54:34.933505 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.coverage.RData
2024-12-24 07:54:34.936539 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.coverage.bw
2024-12-24 07:54:34.951742 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.summary_coverage.tab
2024-12-24 07:54:34.98938 INFO::analyzeVariants/analyzeVariants: starting ...
2024-12-24 07:54:35.069403 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-12-24 07:54:38.83853 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-12-24 07:54:38.954512 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-12-24 07:54:38.980169 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-12-24 07:54:38.982136 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.raw_variants.RData
2024-12-24 07:54:38.984568 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.filtered_variants.RData
2024-12-24 07:54:38.986449 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-12-24 07:54:38.987968 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-12-24 07:54:39.322819 INFO::analyzeVariants.R/writeVCF: ...done
2024-12-24 07:54:39.46891 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.mergeLanes.13c8b956c85833/merged/results/merged.summary_variants.tab
2024-12-24 07:54:39.471854 INFO::analyzeVariants/analyzeVariants: done
2024-12-24 07:54:39.479825 INFO::mergeLanes.R/doMergeLanes: merge lanes successful.
 done successfully.



Executing test function test.markDuplicates  ... Timing stopped at: 0 0.001 0
Error in DEACTIVATED("Skipped markDuplicates() test") : 
  Skipped markDuplicates() test
In addition: There were 28 warnings (use warnings() to see them)
 done successfully.



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



Executing test function test.preprocessReads  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp44UO85/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 
2024-12-24 07:54:39.885377 INFO::preprocessReads.R/preprocessReads: starting...
2024-12-24 07:54:39.892683 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
2024-12-24 07:54:39.897864 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
2024-12-24 07:54:39.901073 DEBUG::tools.R/processChunks: starting...
2024-12-24 07:54:43.777386 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-12-24 07:54:43.779489 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.13c8b93044e682/chunks/chunk_000001/logs/progress.log
2024-12-24 07:54:46.526044 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2024-12-24 07:54:46.593894 DEBUG::tools.R/processChunks: done
2024-12-24 07:54:46.597001 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-12-24 07:54:46.599326 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.13c8b93044e682/results/test_pe.adapter_contaminated_1.RData
2024-12-24 07:54:46.601897 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-12-24 07:54:46.60415 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.13c8b93044e682/results/test_pe.adapter_contaminated_2.RData
2024-12-24 07:54:46.612717 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
2024-12-24 07:54:46.615431 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.13c8b93044e682/results/test_pe.summary_preprocess.tab
2024-12-24 07:54:46.618261 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.13c8b93044e682/bams/processed.aligner_input_1.fastq ...
2024-12-24 07:54:46.624313 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.13c8b93044e682/bams/processed.aligner_input_2.fastq ...
2024-12-24 07:54:46.629991 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.13c8b93044e682/reports/shortReadReport_1 ...
2024-12-24 07:54:48.568108 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.13c8b93044e682/reports/shortReadReport_2 ...
2024-12-24 07:54:50.06179 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads.minichunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp44UO85/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 
2024-12-24 07:54:50.403184 INFO::preprocessReads.R/preprocessReads: starting...
2024-12-24 07:54:50.411716 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
2024-12-24 07:54:50.416873 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
2024-12-24 07:54:50.419865 DEBUG::tools.R/processChunks: starting...
2024-12-24 07:54:54.012785 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-12-24 07:54:54.014873 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.minichunks.13c8b97d06fe1c/chunks/chunk_000001/logs/progress.log
2024-12-24 07:54:56.776014 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.046 minutes
2024-12-24 07:54:56.777897 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.minichunks.13c8b97d06fe1c/chunks/chunk_000002/logs/progress.log
2024-12-24 07:54:59.524347 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2024-12-24 07:54:59.526412 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.minichunks.13c8b97d06fe1c/chunks/chunk_000003/logs/progress.log
2024-12-24 07:55:02.260145 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.046 minutes
2024-12-24 07:55:02.328129 DEBUG::tools.R/processChunks: done
2024-12-24 07:55:02.332238 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-12-24 07:55:02.334929 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.minichunks.13c8b97d06fe1c/results/test_pe.adapter_contaminated_1.RData
2024-12-24 07:55:02.338473 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-12-24 07:55:02.34103 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.minichunks.13c8b97d06fe1c/results/test_pe.adapter_contaminated_2.RData
2024-12-24 07:55:02.352942 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
2024-12-24 07:55:02.355696 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.minichunks.13c8b97d06fe1c/results/test_pe.summary_preprocess.tab
2024-12-24 07:55:02.3594 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.minichunks.13c8b97d06fe1c/bams/processed.aligner_input_1.fastq ...
2024-12-24 07:55:02.366199 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.minichunks.13c8b97d06fe1c/bams/processed.aligner_input_2.fastq ...
2024-12-24 07:55:02.372052 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.minichunks.13c8b97d06fe1c/reports/shortReadReport_1 ...
2024-12-24 07:55:04.256035 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads.minichunks.13c8b97d06fe1c/reports/shortReadReport_2 ...
2024-12-24 07:55:05.806308 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.preprocessReads_single_end  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp44UO85/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 
2024-12-24 07:55:06.115737 INFO::preprocessReads.R/preprocessReads: starting...
2024-12-24 07:55:06.141399 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
2024-12-24 07:55:06.144623 DEBUG::tools.R/processChunks: starting...
2024-12-24 07:55:09.815579 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-12-24 07:55:09.817713 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads_single_end.13c8b97881e049/chunks/chunk_000001/logs/progress.log
2024-12-24 07:55:12.271848 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.041 minutes
2024-12-24 07:55:12.285244 DEBUG::tools.R/processChunks: done
2024-12-24 07:55:12.288355 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-12-24 07:55:12.29066 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads_single_end.13c8b97881e049/results/test_se.adapter_contaminated_1.RData
2024-12-24 07:55:12.299696 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
2024-12-24 07:55:12.302316 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads_single_end.13c8b97881e049/results/test_se.summary_preprocess.tab
2024-12-24 07:55:12.305191 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads_single_end.13c8b97881e049/bams/processed.aligner_input_1.fastq ...
2024-12-24 07:55:12.310924 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/Rtmp44UO85/test.preprocessReads_single_end.13c8b97881e049/reports/shortReadReport_1 ...
2024-12-24 07:55:14.22911 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 
2024-12-24 07:55:15.011785 INFO::preprocessReads.R/preprocessReads: starting...
2024-12-24 07:55:15.034842 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
2024-12-24 07:55:15.041416 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
2024-12-24 07:55:15.044732 DEBUG::tools.R/processChunks: starting...
2024-12-24 07:55:18.549102 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-12-24 07:55:18.551292 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2024-12-24 07:55:21.499102 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.049 minutes
2024-12-24 07:55:21.57022 DEBUG::tools.R/processChunks: done
2024-12-24 07:55:21.573311 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2024-12-24 07:55:21.5757 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_1.RData
2024-12-24 07:55:21.578316 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2024-12-24 07:55:21.580666 INFO::io.R/saveWithID: saving file= test/results/test.adapter_contaminated_2.RData
2024-12-24 07:55:21.589539 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
2024-12-24 07:55:21.592279 INFO::io.R/saveWithID: saving file= test/results/test.summary_preprocess.tab
2024-12-24 07:55:21.595031 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_1.fastq ...
2024-12-24 07:55:21.601293 INFO::preprocessReads.R/mergePreprocessedReads: merging file= test/bams/processed.aligner_input_2.fastq ...
2024-12-24 07:55:21.607323 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_1 ...
2024-12-24 07:55:23.779967 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= test/reports/shortReadReport_2 ...
2024-12-24 07:55:26.091198 INFO::preprocessReads.R/preprocessReads: done
2024-12-24 07:55:26.175363 INFO::alignReads.R/alignReads: starting alignment...
2024-12-24 07:55:26.180063 DEBUG::tools.R/processChunks: starting...
2024-12-24 07:55:29.666433 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-12-24 07:55:29.66864 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.
2024-12-24 07:55:35.478688 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.097 minutes
2024-12-24 07:55:35.481925 DEBUG::tools.R/processChunks: done
2024-12-24 07:55:35.483718 INFO::alignReads.R/mergeBAMsAcrossDirs: starting...
2024-12-24 07:55:35.521383 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2024-12-24 07:55:35.529267 INFO::io.R/saveWithID: saving file= test/results/test.summary_alignment.tab
2024-12-24 07:55:35.536469 INFO::io.R/saveWithID: saving file= test/results/test.summary_analyzed_bamstats.tab
2024-12-24 07:55:35.539063 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2024-12-24 07:55:35.734149 INFO::io.R/saveWithID: saving file= test/results/test.summary_target_lengths.tab
2024-12-24 07:55:35.796229 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2024-12-24 07:55:35.797528 INFO::alignReads.R/alignReads: done
2024-12-24 07:55:35.877333 INFO::countGenomicFeatures.R/countGenomicFeatures: starting...
2024-12-24 07:55:35.897461 DEBUG::tools.R/processChunks: starting...
2024-12-24 07:55:39.464397 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-12-24 07:55:39.466688 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2024-12-24 07:55:42.133357 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.044 minutes
2024-12-24 07:55:42.136815 DEBUG::tools.R/processChunks: done
2024-12-24 07:55:42.139032 INFO::countGenomicFeatures.R/mergeCounts: starting...
2024-12-24 07:55:42.151547 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon.tab
2024-12-24 07:55:42.161989 INFO::io.R/saveWithID: saving file= test/results/test.counts_exon_disjoint.tab
2024-12-24 07:55:42.169789 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene.tab
2024-12-24 07:55:42.175494 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_coding.tab
2024-12-24 07:55:42.181195 INFO::io.R/saveWithID: saving file= test/results/test.counts_gene_exonic.tab
2024-12-24 07:55:42.186787 INFO::io.R/saveWithID: saving file= test/results/test.counts_intergenic.tab
2024-12-24 07:55:42.195064 INFO::io.R/saveWithID: saving file= test/results/test.counts_intron.tab
2024-12-24 07:55:42.199129 INFO::countGenomicFeatures.R/mergeCounts: done
2024-12-24 07:55:42.204216 INFO::io.R/saveWithID: saving file= test/results/test.summary_counts.tab
2024-12-24 07:55:42.20664 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: creating report of genomic features counts...
2024-12-24 07:55:42.495814 INFO::reportPipelineQA.R/writeGenomicFeaturesReport: done
2024-12-24 07:55:42.497095 INFO::countGenomicFeatures.R/countGenomicFeatures: done...
2024-12-24 07:55:42.578547 INFO::coverage.R/calculateCoverage: starting...
2024-12-24 07:55:42.583061 DEBUG::tools.R/processChunks: starting...
2024-12-24 07:55:46.04464 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2024-12-24 07:55:46.046844 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= test/chunks/chunk_000001/logs/progress.log
2024-12-24 07:55:48.43079 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.04 minutes
2024-12-24 07:55:48.434321 DEBUG::tools.R/processChunks: done
2024-12-24 07:55:50.338974 INFO::io.R/saveWithID: saving file= test/results/test.coverage.RData
2024-12-24 07:55:50.340995 INFO::coverage.R/saveCoverage: saving file= test/results/test.coverage.bw
2024-12-24 07:55:50.445099 INFO::io.R/saveWithID: saving file= test/results/test.summary_coverage.tab
2024-12-24 07:55:50.44691 INFO::coverage.R/calculateCoverage: done
2024-12-24 07:55:50.448583 INFO::analyzeVariants/analyzeVariants: starting ...
2024-12-24 07:55:50.527786 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2024-12-24 07:56:04.825197 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2024-12-24 07:56:04.947048 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2024-12-24 07:56:04.97418 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2024-12-24 07:56:04.97631 INFO::io.R/saveWithID: saving file= test/results/test.raw_variants.RData
2024-12-24 07:56:04.979714 INFO::io.R/saveWithID: saving file= test/results/test.filtered_variants.RData
2024-12-24 07:56:04.981748 INFO::analyzeVariants.R/wrap.callVariants: ...done
2024-12-24 07:56:04.983254 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2024-12-24 07:56:05.354078 INFO::analyzeVariants.R/writeVCF: ...done
2024-12-24 07:56:05.529014 INFO::io.R/saveWithID: saving file= test/results/test.summary_variants.tab
2024-12-24 07:56:05.533149 INFO::analyzeVariants/analyzeVariants: done
2024-12-24 07:56:05.538992 INFO::Pipeline run successful.
 done successfully.



Executing test function test.calculateTargetLength  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/Rtmp44UO85/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 
2024-12-24 07:56:05.840721 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/Rtmp44UO85/test.calcTargetLengths.13c8b9143b5171/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 Dec 24 07:56:20 2024 
*********************************************** 
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 (32.77 seconds)
test.alignReads.sparsechunks: (2 checks) ... OK (20.49 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 (106.74 seconds)
test.wrap.callVariants: (4 checks) ... OK (13.62 seconds)
test.wrap.callVariants.filters: (2 checks) ... OK (27.01 seconds)
test.wrap.callVariants.which: (1 checks) ... OK (4.74 seconds)
test.writeVCF.NULL: (1 checks) ... OK (0.2 seconds)
test.writeVCF.vcfStat: (4 checks) ... OK (0.76 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 (39.8 seconds)
test.generateSingleGeneDERs: (4 checks) ... OK (32.37 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 (0.96 seconds)
test.isSparse: (5 checks) ... OK (0.13 seconds)
test.mergeCoverage: (1 checks) ... OK (1.64 seconds)
test.mergeCoverage.sparse: (2 checks) ... OK (1.41 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 (0.19 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 (0.46 seconds)
test.checkConfig.alignReads: (5 checks) ... OK (0.54 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 (0.17 seconds)
test.isAdapter3.primeEnd: (1 checks) ... OK (0.12 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 (0.33 seconds)
test.detectRRNA.paired_end: (1 checks) ... OK (0.47 seconds)
test.getRRNAIds: (1 checks) ... OK (0.29 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 (0.28 seconds)
test.FastQStreamer.getReads.pefq.subsample: (1 checks) ... OK (1.8 seconds)
test.FastQStreamer.getReads.segz: (1 checks) ... OK (0.22 seconds)
test.FastQStreamer.getReads.truncated: (1 checks) ... OK (0.25 seconds)
test.FastQStreamer.subsampler.isdeterministic: (3 checks) ... OK (0.84 seconds)
test.createTmpDir: (4 checks) ... OK (0 seconds)
test.detectQualityInFASTQFile: (3 checks) ... OK (0.21 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 (64.22 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 (10.52 seconds)
test.preprocessReads.minichunks: (5 checks) ... OK (15.74 seconds)
test.preprocessReads_single_end: (5 checks) ... OK (8.42 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 (0.12 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 (50.84 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 (0.3 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 (14.56 seconds)
test.tryKeepTraceback: (3 checks) ... OK (0.02 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 (0.25 seconds) 

runTests.R: OK !
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
326.075 103.261 476.916

Example timings

HTSeqGenie.Rcheck/HTSeqGenie-Ex.timings

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