##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:HTSeqGenie.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings HTSeqGenie_4.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/HTSeqGenie.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSeqGenie/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSeqGenie’ version ‘4.32.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HTSeqGenie’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 1288430 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/doRUnit.R’ failed.
Last 13 lines of output:
  2023-11-02 11:32:20.2982 INFO::analyzeVariants.R/writeVCF: writing vcf file...
  2023-11-02 11:32:20.60838 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.
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/HTSeqGenie.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL HTSeqGenie
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HTSeqGenie)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

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

Attaching package: 'BiocGenerics'

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
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

> 
> 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/RtmpHdHHQe/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.3.1/site-library/HTSeqGenie/config/default-config.txt 
2023-11-02 11:29:15.495804 INFO::preprocessReads.R/preprocessReads: starting...
2023-11-02 11:29:15.505825 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.3.1/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2023-11-02 11:29:15.511708 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.3.1/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2023-11-02 11:29:15.514803 DEBUG::tools.R/processChunks: starting...
2023-11-02 11:29:20.576947 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2023-11-02 11:29:20.583598 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.13a8ee65bafa2b/chunks/chunk_000001/logs/progress.log
2023-11-02 11:29:23.557394 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.05 minutes
2023-11-02 11:29:23.559512 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.13a8ee65bafa2b/chunks/chunk_000002/logs/progress.log
2023-11-02 11:29:26.476696 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.049 minutes
2023-11-02 11:29:26.478732 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.13a8ee65bafa2b/chunks/chunk_000003/logs/progress.log
2023-11-02 11:29:29.416495 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.049 minutes
2023-11-02 11:29:29.45887 DEBUG::tools.R/processChunks: done
2023-11-02 11:29:29.463648 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2023-11-02 11:29:29.466578 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.13a8ee65bafa2b/results/test_pe.adapter_contaminated_1.RData
2023-11-02 11:29:29.470226 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2023-11-02 11:29:29.472579 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.13a8ee65bafa2b/results/test_pe.adapter_contaminated_2.RData
2023-11-02 11:29:29.485199 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
2023-11-02 11:29:29.488332 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.13a8ee65bafa2b/results/test_pe.summary_preprocess.tab
2023-11-02 11:29:29.492869 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.13a8ee65bafa2b/bams/processed.aligner_input_1.fastq ...
2023-11-02 11:29:29.501725 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.13a8ee65bafa2b/bams/processed.aligner_input_2.fastq ...
2023-11-02 11:29:29.507441 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.13a8ee65bafa2b/reports/shortReadReport_1 ...
2023-11-02 11:29:31.482425 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.13a8ee65bafa2b/reports/shortReadReport_2 ...
2023-11-02 11:29:35.097497 INFO::preprocessReads.R/preprocessReads: done
2023-11-02 11:29:35.156344 INFO::alignReads.R/alignReads: starting alignment...
2023-11-02 11:29:35.162901 DEBUG::tools.R/processChunks: starting...
2023-11-02 11:29:38.744437 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2023-11-02 11:29:38.75428 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.13a8ee65bafa2b/chunks/chunk_000001/logs/progress.log
2023-11-02 11:29:41.872086 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.052 minutes
2023-11-02 11:29:41.874233 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.13a8ee65bafa2b/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.
2023-11-02 11:29:44.66536 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.046 minutes
2023-11-02 11:29:44.667738 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.13a8ee65bafa2b/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.
2023-11-02 11:29:49.277126 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.077 minutes
2023-11-02 11:29:49.282966 DEBUG::tools.R/processChunks: done
2023-11-02 11:29:49.28506 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.
2023-11-02 11:29:49.675453 INFO::alignReads.R/mergeBAMsAcrossDirs: done
2023-11-02 11:29:49.693808 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.13a8ee65bafa2b/results/test_pe.summary_alignment.tab
2023-11-02 11:29:49.710408 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.13a8ee65bafa2b/results/test_pe.summary_analyzed_bamstats.tab
2023-11-02 11:29:49.713194 INFO::reportPipelineQA.R/writePreprocessAlignReport: creating joint preprocess-alignment report...
2023-11-02 11:29:50.195136 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.13a8ee65bafa2b/results/test_pe.summary_target_lengths.tab
2023-11-02 11:29:50.262281 INFO::reportPipelineQA.R/writePreprocessAlignReport: done
2023-11-02 11:29:50.263846 INFO::alignReads.R/alignReads: done
 done successfully.



Executing test function test.alignReads.sparsechunks  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpHdHHQe/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.3.1/site-library/HTSeqGenie/config/default-config.txt 
2023-11-02 11:29:50.72665 INFO::preprocessReads.R/preprocessReads: starting...
2023-11-02 11:29:50.730984 INFO::io.R/FastQStreamer.init: counting number of reads in file= /home/biocbuild/R/R-4.3.1/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2023-11-02 11:29:50.841584 INFO::io.R/FastQStreamer.init: subsampling_filter set (subsampled reads= 2 , totnbreads= 26 )
2023-11-02 11:29:50.848239 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.3.1/site-library/HTSeqGenie/test-data/unit_tests_1.fastq
2023-11-02 11:29:50.853426 INFO::io.R/FastQStreamer.init: initialised FastQ streamer for filename= /home/biocbuild/R/R-4.3.1/site-library/HTSeqGenie/test-data/unit_tests_2.fastq
2023-11-02 11:29:50.856137 DEBUG::tools.R/processChunks: starting...
2023-11-02 11:29:55.089512 DEBUG::tools.R/processChunks: waiting for chunkid=[  ] ...
2023-11-02 11:29:55.091629 DEBUG::tools.R/processChunks: starting chunkid= 1 ; see logfile= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.sparsechunks.13a8ee4982c8be/chunks/chunk_000001/logs/progress.log
2023-11-02 11:29:58.038508 DEBUG::tools.R/processChunks: done with chunkid= 1 ; elapsed.time= 0.049 minutes
2023-11-02 11:29:58.043294 DEBUG::tools.R/processChunks: starting chunkid= 2 ; see logfile= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.sparsechunks.13a8ee4982c8be/chunks/chunk_000002/logs/progress.log
2023-11-02 11:30:00.922193 DEBUG::tools.R/processChunks: done with chunkid= 2 ; elapsed.time= 0.048 minutes
2023-11-02 11:30:00.92609 DEBUG::tools.R/processChunks: starting chunkid= 3 ; see logfile= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.sparsechunks.13a8ee4982c8be/chunks/chunk_000003/logs/progress.log
2023-11-02 11:30:03.879709 DEBUG::tools.R/processChunks: done with chunkid= 3 ; elapsed.time= 0.049 minutes
2023-11-02 11:30:03.881642 DEBUG::tools.R/processChunks: starting chunkid= 4 ; see logfile= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.sparsechunks.13a8ee4982c8be/chunks/chunk_000004/logs/progress.log
2023-11-02 11:30:06.723922 DEBUG::tools.R/processChunks: done with chunkid= 4 ; elapsed.time= 0.047 minutes
2023-11-02 11:30:06.767612 DEBUG::tools.R/processChunks: done
2023-11-02 11:30:06.772687 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_1 ...
2023-11-02 11:30:06.776592 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.sparsechunks.13a8ee4982c8be/results/test_pe.adapter_contaminated_1.RData
2023-11-02 11:30:06.78166 INFO::detectAdapterContam.R/mergeDetectAdapterContam: merging file= adapter_contaminated_2 ...
2023-11-02 11:30:06.785498 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.sparsechunks.13a8ee4982c8be/results/test_pe.adapter_contaminated_2.RData
2023-11-02 11:30:06.800987 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
2023-11-02 11:30:06.804315 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.sparsechunks.13a8ee4982c8be/results/test_pe.summary_preprocess.tab
2023-11-02 11:30:06.809671 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.sparsechunks.13a8ee4982c8be/bams/processed.aligner_input_1.fastq ...
2023-11-02 11:30:06.820496 INFO::preprocessReads.R/mergePreprocessedReads: merging file= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.sparsechunks.13a8ee4982c8be/bams/processed.aligner_input_2.fastq ...
2023-11-02 11:30:06.826498 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.sparsechunks.13a8ee4982c8be/reports/shortReadReport_1 ...
2023-11-02 11:30:08.760148 INFO::preprocessReads.R/buildShortReadReports: generating report_dir= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReads.sparsechunks.13a8ee4982c8be/reports/shortReadReport_2 ...
2023-11-02 11:30:11.770137 INFO::preprocessReads.R/preprocessReads: done
 done successfully.



Executing test function test.alignReadsOneSingleEnd  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpHdHHQe/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.3.1/site-library/HTSeqGenie/config/default-config.txt 
2023-11-02 11:30:12.019804 INFO::alignReads.R/alignReadsChunk: running gsnap...
2023-11-02 11:30:12.026246 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/RtmpHdHHQe/test.alignReadsOneSingleEnd.13a8ee200306ae/bams/test.alignReads /home/biocbuild/R/R-4.3.1/site-library/HTSeqGenie/test-data/unit_tests_1.fastq 2>&1
2023-11-02 11:30:12.690076 INFO::alignReads.R/createSummaryAlignment: counting unique bam reads...
2023-11-02 11:30:12.836812 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReadsOneSingleEnd.13a8ee200306ae/results/test.alignReads.summary_alignment.tab
2023-11-02 11:30:12.891809 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.alignReadsOneSingleEnd.13a8ee200306ae/results/test.alignReads.summary_analyzed_bamstats.tab
2023-11-02 11:30:12.893955 INFO::alignReads.R/alignReadsChunk: done
 done successfully.



Executing test function test.annotateVariants  ... Timing stopped at: 0.003 0.001 0.004
Error in DEACTIVATED("Skipped annotateVariants() test") : 
  Skipped annotateVariants() test
In addition: There were 11 warnings (use warnings() to see them)
 done successfully.



Executing test function test.callVariantsVariantTools.genotype  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpHdHHQe/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.3.1/site-library/HTSeqGenie/config/default-config.txt 
2023-11-02 11:30:13.341969 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.genotype.13a8ee5c535bf/results/test_pe.coverage.RData
2023-11-02 11:30:13.34441 INFO::coverage.R/saveCoverage: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.genotype.13a8ee5c535bf/results/test_pe.coverage.bw
2023-11-02 11:30:13.540378 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.genotype.13a8ee5c535bf/results/test_pe.summary_coverage.tab
2023-11-02 11:30:13.5428 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2023-11-02 11:30:26.477543 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2023-11-02 11:30:26.605666 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2023-11-02 11:30:26.630024 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2023-11-02 11:30:26.63206 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.genotype.13a8ee5c535bf/results/test_pe.raw_variants.RData
2023-11-02 11:30:26.635225 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.genotype.13a8ee5c535bf/results/test_pe.filtered_variants.RData
2023-11-02 11:30:26.637118 INFO::analyzeVariants.R/wrap.callVariants: ...done
2023-11-02 11:30:26.63879 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2023-11-02 11:30:27.219205 INFO::analyzeVariants.R/writeVCF: ...done
2023-11-02 11:30:27.220648 INFO::analyzeVariants.R/.callGenotypes: calling genotypes...
2023-11-02 11:31:39.169504 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2023-11-02 11:31:39.831016 INFO::analyzeVariants.R/writeVCF: ...done
2023-11-02 11:31:39.832289 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/RtmpHdHHQe/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.3.1/site-library/HTSeqGenie/config/default-config.txt 
2023-11-02 11:31:40.457804 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2023-11-02 11:31:52.777728 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2023-11-02 11:31:52.884617 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2023-11-02 11:31:52.908415 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2023-11-02 11:31:52.910236 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.wrap.callVariants.13a8ee45eaa1dd/results/test_pe.raw_variants.RData
2023-11-02 11:31:52.913359 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.wrap.callVariants.13a8ee45eaa1dd/results/test_pe.filtered_variants.RData
2023-11-02 11:31:52.915134 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/RtmpHdHHQe/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.3.1/site-library/HTSeqGenie/config/default-config.txt 
2023-11-02 11:31:53.099295 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2023-11-02 11:32:05.019416 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2023-11-02 11:32:05.098238 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2023-11-02 11:32:05.121875 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2023-11-02 11:32:05.123745 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.wrap.callVariants.filters.13a8ee4cceddfe/results/test_pe.raw_variants.RData
2023-11-02 11:32:05.126679 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.wrap.callVariants.filters.13a8ee4cceddfe/results/test_pe.filtered_variants.RData
2023-11-02 11:32:05.128292 INFO::analyzeVariants.R/wrap.callVariants: ...done
2023-11-02 11:32:05.129957 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2023-11-02 11:32:16.855946 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2023-11-02 11:32:16.90826 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2023-11-02 11:32:16.931531 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2023-11-02 11:32:16.933228 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.wrap.callVariants.filters.13a8ee4cceddfe/results/test_pe.raw_variants.RData
2023-11-02 11:32:16.936167 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.wrap.callVariants.filters.13a8ee4cceddfe/results/test_pe.filtered_variants.RData
2023-11-02 11:32:16.93857 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/RtmpHdHHQe/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.3.1/site-library/HTSeqGenie/config/default-config.txt 
2023-11-02 11:32:17.131548 INFO::analyzeVariants.R/wrap.callVariants: Tallying variants...
2023-11-02 11:32:17.133315 INFO::analyzeVariants.R/buildTallyParam: restricting variant calls using 'which'
2023-11-02 11:32:19.745299 INFO::analyzeVariants.R/wrap.callVariants: calling variants...
2023-11-02 11:32:19.854049 INFO::analyzeVariants.R/wrap.postFilerVariants: post filtering variants...
2023-11-02 11:32:19.875804 INFO::analyzeVariants.R/wrap.callVariants: Saving GRanges of raw and filtered variants...
2023-11-02 11:32:19.877512 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.wrap.callVariants.which.13a8ee6175813a/results/test_pe.raw_variants.RData
2023-11-02 11:32:19.879565 INFO::io.R/saveWithID: saving file= /home/biocbuild/tmp/RtmpHdHHQe/test.wrap.callVariants.which.13a8ee6175813a/results/test_pe.filtered_variants.RData
2023-11-02 11:32:19.881145 INFO::analyzeVariants.R/wrap.callVariants: ...done
 done successfully.



Executing test function test.writeVCF.NULL  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpHdHHQe/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.3.1/site-library/HTSeqGenie/config/default-config.txt 
2023-11-02 11:32:20.05895 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2023-11-02 11:32:20.060547 INFO::analyzeVariants.R/writeVCF: ...done
 done successfully.



Executing test function test.writeVCF.vcfStat  ... checkConfig.R/checkConfig.template: loading template config= //home/biocbuild/tmp/RtmpHdHHQe/tp53-config.txt 
checkConfig.R/checkConfig.template: loading template config= /home/biocbuild/R/R-4.3.1/site-library/HTSeqGenie/config/default-config.txt 
2023-11-02 11:32:20.2982 INFO::analyzeVariants.R/writeVCF: writing vcf file...
2023-11-02 11:32:20.60838 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.