Multiple platform build/check report for BioC 3.14 - CHECK results for ORFik on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

Package: ORFik

Version: 1.14.7

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ORFik.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ORFik_1.14.7.tar.gz

StartedAt: 2022-04-13 00:04:39 -0400 (Wed, 13 Apr 2022)

EndedAt: 2022-04-13 00:25:34 -0400 (Wed, 13 Apr 2022)

EllapsedTime: 1255.1 seconds

RetCode: 0

Status: OK

CheckDir: ORFik.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ORFik.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ORFik_1.14.7.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ORFik.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ORFik/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ORFik' version '1.14.7'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'ORFik' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    html   1.7Mb
    libs   2.2Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'GenomicFeatures:::.merge_seqinfo_and_infer_missing_seqlengths'
  'IRanges:::regroupBySupergroup' 'S4Vectors:::normarg_mcols'
  'biomartr:::getENSEMBL.Seq' 'biomartr:::getENSEMBL.gtf'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'find_url_ebi' 'trimming.table'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DEG.plot.static: no visible binding for global variable 'Regulation'
DEG.plot.static: no visible binding for global variable 'meanCounts'
DEG.plot.static: no visible binding for global variable 'LFC'
DTEG.plot: no visible binding for global variable 'Regulation'
DTEG.plot: no visible binding for global variable 'rna'
DTEG.plot: no visible binding for global variable 'rfp'
QCplots: no visible binding for global variable 'leaders'
QCplots: no visible binding for global variable 'trailers'
QCstats.plot: no visible binding for global variable 'variable'
QCstats.plot: no visible binding for global variable 'sample_total'
QCstats.plot: no visible binding for global variable 'value'
QCstats.plot: no visible global function definition for '.'
QCstats.plot: no visible binding for global variable 'sample_id'
QCstats.plot: no visible binding for global variable 'percentage'
QCstats.plot: no visible binding for global variable
  'perc_of_counts_per_sample'
QCstats.plot: no visible binding for global variable 'read length'
RiboQC.plot: no visible binding for global variable 'variable'
RiboQC.plot: no visible binding for global variable 'sample_total'
RiboQC.plot: no visible binding for global variable 'value'
RiboQC.plot: no visible global function definition for '.'
RiboQC.plot: no visible binding for global variable 'sample_id'
RiboQC.plot: no visible binding for global variable 'percentage'
RiboQC.plot: no visible binding for global variable 'percent'
RiboQC.plot: no visible binding for global variable 'frame'
STAR.multiQC: no visible binding for global variable 'sample_id'
STAR.multiQC: no visible binding for global variable 'value'
TOP.Motif.ecdf: no visible binding for global variable 'seq1'
TOP.Motif.ecdf: no visible binding for global variable 'TOP'
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable 'percentage_mrna_aligned'
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable 'mRNA'
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable 'percentage_tx_aligned'
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable 'Transcript'
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable 'ratio_cds_mrna'
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable 'CDS'
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable 'ratio_cds_leader'
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable 'LEADERS'
allFeaturesHelper: no visible binding for global variable 'te'
allFeaturesHelper: no visible binding for global variable 'fpkmRFP'
allFeaturesHelper: no visible binding for global variable 'fpkmRNA'
allFeaturesHelper: no visible binding for global variable 'countRFP'
allFeaturesHelper: no visible binding for global variable 'entropyRFP'
allFeaturesHelper: no visible binding for global variable
  'disengagementScores'
allFeaturesHelper: no visible binding for global variable 'RRS'
allFeaturesHelper: no visible binding for global variable 'RSS'
allFeaturesHelper: no visible binding for global variable 'ORFScores'
allFeaturesHelper: no visible binding for global variable 'ioScore'
allFeaturesHelper: no visible binding for global variable
  'startCodonCoverage'
allFeaturesHelper: no visible binding for global variable
  'startRegionRelative'
allFeaturesHelper: no visible binding for global variable 'kozak'
allFeaturesHelper: no visible binding for global variable 'StartCodons'
allFeaturesHelper: no visible binding for global variable 'StopCodons'
allFeaturesHelper: no visible binding for global variable
  'fractionLengths'
allFeaturesHelper: no visible binding for global variable 'distORFCDS'
allFeaturesHelper: no visible binding for global variable 'inFrameCDS'
allFeaturesHelper: no visible binding for global variable
  'isOverlappingCds'
allFeaturesHelper: no visible binding for global variable 'rankInTx'
appendZeroes: no visible binding for global variable 'frame'
appendZeroes: no visible binding for global variable 'position'
appendZeroes: no visible binding for global variable 'count'
artificial.orfs: no visible binding for global variable 'random'
artificial.orfs: no visible binding for global variable 'pick'
artificial.orfs: no visible global function definition for '.'
collapse.by.scores: no visible global function definition for '.'
collapse.fastq: no visible binding for global variable 'N'
coverageHeatMap: no visible binding for global variable 'position'
coverageHeatMap: no visible binding for global variable 'fraction'
coveragePerTiling: no visible binding for global variable 'frame'
coveragePerTiling: no visible binding for global variable 'position'
coverageScorings: no visible binding for global variable 'count'
coverageScorings: no visible binding for global variable 'zscore'
coverageScorings: no visible binding for global variable 'windowMean'
coverageScorings: no visible binding for global variable 'windowSD'
coverageScorings: no visible global function definition for '.'
coverageScorings: no visible binding for global variable 'gene_sum'
coverageScorings: no visible binding for global variable 'fraction'
detectRibosomeShifts: no visible global function definition for '.'
detectRibosomeShifts: no visible binding for global variable 'size'
detectRibosomeShifts: no visible binding for global variable 'fraction'
detectRibosomeShifts: no visible binding for global variable 'pShifted'
detectRibosomeShifts: no visible binding for global variable
  'sum.count'
detectRibosomeShifts: no visible binding for global variable 'count'
detectRibosomeShifts: no visible binding for global variable
  'frac.score'
download.SRA.metadata: no visible binding for global variable 'spots'
download.SRA.metadata: no visible binding for global variable 'MONTH'
download.SRA.metadata: no visible binding for global variable
  'ReleaseDate'
download.SRA.metadata: no visible binding for global variable 'YEAR'
download.SRA.metadata: no visible binding for global variable 'Run'
download.SRA.metadata: no visible binding for global variable
  'LIBRARYTYPE'
download.SRA.metadata: no visible binding for global variable
  'LibraryStrategy'
entropy: no visible binding for global variable 'Hx'
entropy: no visible binding for global variable 'codonSums'
entropy: no visible global function definition for '.'
filterExtremePeakGenes: no visible binding for global variable 'count'
filterExtremePeakGenes: no visible binding for global variable
  'median_per_gene'
filterExtremePeakGenes: no visible global function definition for '.'
filterTranscripts: no visible binding for global variable 'utr5_len'
filterTranscripts: no visible binding for global variable 'utr3_len'
findNGSPairs: no visible global function definition for '.'
findNGSPairs: no visible binding for global variable 'forward'
findPeaksPerGene: no visible binding for global variable 'sum_per_gene'
findPeaksPerGene: no visible binding for global variable 'count'
findPeaksPerGene: no visible binding for global variable
  'mean_per_gene'
findPeaksPerGene: no visible binding for global variable 'sd_per_gene'
findPeaksPerGene: no visible binding for global variable 'zscore'
findPeaksPerGene: no visible binding for global variable 'gene_id'
find_url_ebi_safe: no visible binding for global variable
  'run_accession'
flankPerGroup: no visible global function definition for '.'
flankPerGroup: no visible binding for global variable 'group_name'
floss: no visible binding for global variable 'ORFGrouping'
floss: no visible binding for global variable 'widths'
floss: no visible global function definition for '.'
floss: no visible binding for global variable 'CDSGrouping'
floss: no visible binding for global variable 'fraction.x'
floss: no visible binding for global variable 'fraction.y'
gSort: no visible binding for global variable 'grnames'
getNGenesCoverage: no visible global function definition for '.'
getNGenesCoverage: no visible binding for global variable 'fraction'
get_phix_genome: no visible binding for global variable 'phix.url'
initiationScore: no visible global function definition for '.'
initiationScore: no visible binding for global variable 'dif'
initiationScore: no visible binding for global variable 'fraction'
initiationScore: no visible binding for global variable 'difPer'
isPeriodic: no visible binding for global variable 'spec'
kozakHeatmap: no visible global function definition for '.'
kozakHeatmap: no visible binding for global variable 'variable'
kozakHeatmap: no visible binding for global variable 'value'
kozakHeatmap: no visible binding for global variable
  'count_seq_pos_with_count'
kozakHeatmap: no visible binding for global variable 'median_score'
kozak_IR_ranking: no visible global function definition for '.'
kozak_IR_ranking: no visible binding for global variable 'IR'
kozak_IR_ranking: no visible binding for global variable
  'upstream_kozak_strength'
kozak_IR_ranking: no visible binding for global variable 'count'
kozak_IR_ranking: no visible binding for global variable 'mean_IR'
list.genomes: no visible binding for global variable 'STAR_index'
longestORFs: no visible global function definition for '.'
metaWindow: no visible binding for global variable 'position'
metaWindow: no visible binding for global variable 'frame'
orfFrameDistributions : <anonymous>: no visible binding for global
  variable 'fraction'
orfFrameDistributions: no visible binding for global variable 'percent'
orfFrameDistributions: no visible binding for global variable
  'fraction'
orfFrameDistributions: no visible binding for global variable
  'percent_length'
orfFrameDistributions: no visible global function definition for '.'
orfFrameDistributions: no visible binding for global variable
  'best_frame'
orfScore: no visible binding for global variable 'frame'
orfScore: no visible binding for global variable 'frame_one_RP'
orfScore: no visible binding for global variable 'frame_two_RP'
pSitePlot: no visible binding for global variable 'count'
pSitePlot: no visible binding for global variable 'frame'
pSitePlot: no visible binding for global variable 'position'
pcaExperiment: no visible binding for global variable 'PC1'
pcaExperiment: no visible binding for global variable 'PC2'
readLengthTable: no visible binding for global variable
  'counts_per_sample'
readLengthTable: no visible binding for global variable
  'perc_of_counts_per_sample'
regionPerReadLength : <anonymous>: no visible binding for global
  variable 'fraction'
remakeTxdbExonIds: no visible global function definition for '.'
remakeTxdbExonIds: no visible binding for global variable 'chr'
removeTxdbExons: no visible binding for global variable 'exon_rank'
removeTxdbExons: no visible binding for global variable 'ranks'
rnaNormalize: no visible binding for global variable 'feature'
scaledWindowPositions: no visible binding for global variable
  'scalingFactor'
scaledWindowPositions: no visible binding for global variable
  'position'
scaledWindowPositions: no visible global function definition for '.'
scoreSummarizedExperiment: no visible global function definition for
  'rowSums2'
shiftPlots : <anonymous>: no visible binding for global variable
  'frame'
shiftPlots : <anonymous>: no visible binding for global variable
  'position'
te.plot: no visible global function definition for 'rowMin'
te.plot: no visible binding for global variable 'variable'
te.plot: no visible binding for global variable 'LFC_TE'
te.plot: no visible binding for global variable 'rfp_log2'
te.plot: no visible binding for global variable 'rna_log2'
te.plot: no visible binding for global variable 'rna_log10'
te.table: no visible global function definition for 'rowMin'
te.table: no visible binding for global variable 'variable'
te.table: no visible binding for global variable 'TE_log2'
te.table: no visible binding for global variable 'rfp_log2'
te.table: no visible binding for global variable 'rna_log2'
te_rna.plot: no visible binding for global variable 'subtitle'
te_rna.plot: no visible binding for global variable 'rna_log10'
te_rna.plot: no visible binding for global variable 'TE_log2'
topMotif: no visible binding for global variable 'seq1'
topMotif: no visible binding for global variable 'seq2'
topMotif: no visible binding for global variable 'seq3'
topMotif: no visible binding for global variable 'seq4'
topMotif: no visible binding for global variable 'seq5'
transcriptWindow: no visible binding for global variable 'fractions'
transcriptWindow: no visible binding for global variable 'feature'
windowCoveragePlot: no visible binding for global variable 'feature'
windowCoveragePlot: no visible binding for global variable 'fraction'
windowCoveragePlot: no visible binding for global variable
  'fraction_min'
windowCoveragePlot: no visible binding for global variable 'position'
collapseDuplicatedReads,GAlignmentPairs: no visible global function
  definition for '.'
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable 'start1'
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable 'start2'
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable 'cigar1'
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable 'cigar2'
collapseDuplicatedReads,GAlignments: no visible global function
  definition for '.'
collapseDuplicatedReads,GRanges: no visible binding for global variable
  'size'
collapseDuplicatedReads,GRanges: no visible global function definition
  for '.'
design,experiment: no visible binding for global variable '..formula'
Undefined global functions or variables:
  . ..formula CDS CDSGrouping Hx IR LEADERS LFC LFC_TE LIBRARYTYPE
  LibraryStrategy MONTH N ORFGrouping ORFScores PC1 PC2 RRS RSS
  Regulation ReleaseDate Run STAR_index StartCodons StopCodons TE_log2
  TOP Transcript YEAR best_frame chr cigar1 cigar2 codonSums count
  countRFP count_seq_pos_with_count counts_per_sample dif difPer
  disengagementScores distORFCDS entropyRFP exon_rank feature forward
  fpkmRFP fpkmRNA frac.score fraction fraction.x fraction.y
  fractionLengths fraction_min fractions frame frame_one_RP
  frame_two_RP gene_id gene_sum grnames group_name inFrameCDS ioScore
  isOverlappingCds kozak leaders mRNA meanCounts mean_IR mean_per_gene
  median_per_gene median_score pShifted perc_of_counts_per_sample
  percent percent_length percentage percentage_mrna_aligned
  percentage_tx_aligned phix.url pick position random rankInTx ranks
  ratio_cds_leader ratio_cds_mrna read length rfp rfp_log2 rna
  rna_log10 rna_log2 rowMin rowSums2 run_accession sample_id
  sample_total scalingFactor sd_per_gene seq1 seq2 seq3 seq4 seq5 size
  spec spots start1 start2 startCodonCoverage startRegionRelative
  subtitle sum.count sum_per_gene te trailers upstream_kozak_strength
  utr3_len utr5_len value variable widths windowMean windowSD zscore
Consider adding
  importFrom("base", "length")
  importFrom("graphics", "frame")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/ORFik/libs/i386/ORFik.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/ORFik/libs/x64/ORFik.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
computeFeatures             5.09   0.05    5.17
orfFrameDistributions       3.44   0.00   33.70
regionPerReadLength         2.55   0.04   41.74
shiftFootprintsByExperiment 2.19   0.00   29.78
outputLibs                  1.47   0.03   24.50
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                            user system elapsed
computeFeatures             5.92   0.00    5.94
orfFrameDistributions       4.27   0.07   42.62
regionPerReadLength         2.61   0.02   38.50
shiftFootprintsByExperiment 2.47   0.02   24.85
outputLibs                  1.90   0.05   26.74
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/ORFik.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/ORFik_1.14.7.tar.gz && rm -rf ORFik.buildbin-libdir && mkdir ORFik.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ORFik.buildbin-libdir ORFik_1.14.7.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ORFik_1.14.7.zip && rm ORFik_1.14.7.tar.gz ORFik_1.14.7.zip
###
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install for i386

* installing *source* package 'ORFik' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c findORFsHelpers.cpp -o findORFsHelpers.o
findORFsHelpers.cpp: In function 'Rcpp::IntegerMatrix orfs_as_matrix(std::__cxx11::string&, std::__cxx11::string, std::__cxx11::string, int)':
findORFsHelpers.cpp:214:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (int i = 0; i < uorfSize/2; i++) {
                   ~~^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c findOrfs.cpp -o findOrfs.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c findOrfsFasta.cpp -o findOrfsFasta.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o
pmapFromTranscripts.cpp: In function 'Rcpp::List pmapFromTranscriptsCPP(const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const char&, bool)':
pmapFromTranscripts.cpp:151:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(auto i = 0;i < xSize; i++){
                  ~~^~~~~~~
pmapFromTranscripts.cpp:155:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(auto i = 0; i < indexSize; i++){
                   ~~^~~~~~~~~~~
pmapFromTranscripts.cpp:161:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(auto i = 1; i < indexSize; i++){
                   ~~^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pmapToTranscripts.cpp -o pmapToTranscripts.o
pmapToTranscripts.cpp: In function 'void pmapToPositive(vi&, const int&, int&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&)':
pmapToTranscripts.cpp:22:7: warning: variable 'currentWidth' set but not used [-Wunused-but-set-variable]
   int currentWidth = 0;
       ^~~~~~~~~~~~
pmapToTranscripts.cpp: In function 'void pmapToNegative(vi&, const int&, int&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&)':
pmapToTranscripts.cpp:68:7: warning: variable 'currentWidth' set but not used [-Wunused-but-set-variable]
   int currentWidth = 0;
       ^~~~~~~~~~~~
pmapToTranscripts.cpp: In function 'Rcpp::List pmapToTranscriptsCPP(const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const char&, const std::vector<int>&)':
pmapToTranscripts.cpp:126:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(auto i = 0;i < xSize; i++){ // Width per exon in x
                  ~~^~~~~~~
pmapToTranscripts.cpp:130:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(auto i = 0; i < indexSize; i++){ // Width per exon in tx
                   ~~^~~~~~~~~~~
pmapToTranscripts.cpp:136:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for(auto i = 1; i < indexSize; i++){
                   ~~^~~~~~~~~~~
pmapToTranscripts.cpp:147:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
   for (auto i = 1; i < 2 * xSize; i = i + 2) {
                    ~~^~~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o ORFik.dll tmp.def RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o pmapToTranscripts.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/ORFik.buildbin-libdir/00LOCK-ORFik/00new/ORFik/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ORFik'
    finding HTML links ... done
    DEG.analysis                            html  
    DEG.plot.static                         html  
    DTEG.analysis                           html  
    finding level-2 HTML links ... done

    DTEG.plot                               html  
    ORFik-package                           html  
    ORFik.template.experiment               html  
    ORFik.template.experiment.zf            html  
    ORFikQC                                 html  
    QC_count_tables                         html  
    QCfolder-experiment-method              html  
    QCfolder                                html  
    QCplots                                 html  
    QCreport                                html  
    QCstats                                 html  
    QCstats.plot                            html  
    RiboQC.plot                             html  
    STAR.align.folder                       html  
    STAR.align.single                       html  
    STAR.allsteps.multiQC                   html  
    STAR.index                              html  
    STAR.install                            html  
    STAR.multiQC                            html  
    STAR.remove.crashed.genome              html  
    TOP.Motif.ecdf                          html  
    addCdsOnLeaderEnds                      html  
    addNewTSSOnLeaders                      html  
    alignmentFeatureStatistics              html  
    allFeaturesHelper                       html  
    appendZeroes                            html  
    artificial.orfs                         html  
    asTX                                    html  
    assignAnnotations                       html  
    assignFirstExonsStartSite               html  
    assignLastExonsStopSite                 html  
    assignTSSByCage                         html  
    bamVarName                              html  
    bamVarNamePicker                        html  
    batchNames                              html  
    bedToGR                                 html  
    cellLineNames                           html  
    changePointAnalysis                     html  
    checkRFP                                html  
    checkRNA                                html  
    codonSumsPerGroup                       html  
    collapse.by.scores                      html  
    collapse.fastq                          html  
    collapseDuplicatedReads-GAlignmentPairs-method
                                            html  
    collapseDuplicatedReads-GAlignments-method
                                            html  
    collapseDuplicatedReads-GRanges-method
                                            html  
    collapseDuplicatedReads                 html  
    combn.pairs                             html  
    computeFeatures                         html  
    computeFeaturesCage                     html  
    conditionNames                          html  
    config                                  html  
    config.exper                            html  
    config.save                             html  
    convertLibs                             html  
    convertToOneBasedRanges                 html  
    correlation.plots                       html  
    countOverlapsW                          html  
    countTable                              html  
    countTable_regions                      html  
    coverageByTranscriptW                   html  
    coverageGroupings                       html  
    coverageHeatMap                         html  
    coveragePerTiling                       html  
    coverageScorings                        html  
    create.experiment                       html  
    defineIsoform                           html  
    defineTrailer                           html  
    design-experiment-method                html  
    detectRibosomeShifts                    html  
    disengagementScore                      html  
    distToCds                               html  
    distToTSS                               html  
    download.SRA                            html  
    download.SRA.metadata                   html  
    download.ebi                            html  
    downstreamFromPerGroup                  html  
    downstreamN                             html  
    downstreamOfPerGroup                    html  
    entropy                                 html  
    envExp-experiment-method                html  
    envExp-set-experiment-method            html  
    envExp-set                              html  
    envExp                                  html  
    exists.ftp.dir.fast                     html  
    exists.ftp.file.fast                    html  
    experiment-class                        html  
    experiment.colors                       html  
    export.bed12                            html  
    export.bedo                             html  
    export.bedoc                            html  
    export.bigWig                           html  
    export.ofst-GAlignmentPairs-method      html  
    export.ofst-GAlignments-method          html  
    export.ofst-GRanges-method              html  
    export.ofst                             html  
    export.wiggle                           html  
    extendLeaders                           html  
    extendTrailers                          html  
    extendsTSSexons                         html  
    filepath                                html  
    filterCage                              html  
    filterExtremePeakGenes                  html  
    filterTranscripts                       html  
    filterUORFs                             html  
    fimport                                 html  
    findFa                                  html  
    findFromPath                            html  
    findLibrariesInFolder                   html  
    findMapORFs                             html  
    findMaxPeaks                            html  
    findNGSPairs                            html  
    findNewTSS                              html  
    findORFs                                html  
    findORFsFasta                           html  
    findPeaksPerGene                        html  
    findUORFs                               html  
    find_url_ebi                            html  
    find_url_ebi_safe                       html  
    firstEndPerGroup                        html  
    firstExonPerGroup                       html  
    firstStartPerGroup                      html  
    flankPerGroup                           html  
    floss                                   html  
    footprints.analysis                     html  
    fpkm                                    html  
    fpkm_calc                               html  
    fractionLength                          html  
    fractionNames                           html  
    fread.bed                               html  
    gSort                                   html  
    gcContent                               html  
    getGAlignments                          html  
    getGAlignmentsPairs                     html  
    getGRanges                              html  
    getGenomeAndAnnotation                  html  
    getGtfPathFromTxdb                      html  
    getNGenesCoverage                       html  
    getWeights                              html  
    get_genome_fasta                        html  
    get_genome_gtf                          html  
    get_noncoding_rna                       html  
    get_phix_genome                         html  
    get_silva_rRNA                          html  
    groupGRangesBy                          html  
    groupings                               html  
    hasHits                                 html  
    heatMapL                                html  
    heatMapRegion                           html  
    heatMap_single                          html  
    import.bedo                             html  
    import.bedoc                            html  
    import.ofst                             html  
    importGtfFromTxdb                       html  
    inhibitorNames                          html  
    initiationScore                         html  
    insideOutsideORF                        html  
    install.fastp                           html  
    install.sratoolkit                      html  
    is.ORF                                  html  
    is.gr_or_grl                            html  
    is.grl                                  html  
    is.range                                html  
    isInFrame                               html  
    isOverlapping                           html  
    isPeriodic                              html  
    kozakHeatmap                            html  
    kozakSequenceScore                      html  
    kozak_IR_ranking                        html  
    lastExonEndPerGroup                     html  
    lastExonPerGroup                        html  
    lastExonStartPerGroup                   html  
    libNames                                html  
    libraryTypes                            html  
    list.experiments                        html  
    list.genomes                            html  
    loadRegion                              html  
    loadRegions                             html  
    loadTranscriptType                      html  
    loadTxdb                                html  
    longestORFs                             html  
    mainNames                               html  
    makeExonRanks                           html  
    makeORFNames                            html  
    makeSummarizedExperimentFromBam         html  
    makeTxdbFromGenome                      html  
    mapToGRanges                            html  
    matchColors                             html  
    matchNaming                             html  
    matchSeqStyle                           html  
    mergeFastq                              html  
    metaWindow                              html  
    name-experiment-method                  html  
    name                                    html  
    nrow-experiment-method                  html  
    numCodons                               html  
    numExonsPerGroup                        html  
    optimizeReads                           html  
    optimizedTranscriptLengths              html  
    optimized_txdb_path                     html  
    orfFrameDistributions                   html  
    orfID                                   html  
    orfScore                                html  
    organism-experiment-method              html  
    outputLibs                              html  
    pSitePlot                               html  
    pasteDir                                html  
    pcaExperiment                           html  
    percentage_to_ratio                     html  
    plotHelper                              html  
    pmapFromTranscriptF                     html  
    pmapToTranscriptF                       html  
    prettyScoring                           html  
    pseudo.transform                        html  
    rankOrder                               html  
    read.experiment                         html  
    readBam                                 html  
    readBigWig                              html  
    readLengthTable                         html  
    readWidths                              html  
    readWig                                 html  
    reassignTSSbyCage                       html  
    reassignTxDbByCage                      html  
    reduceKeepAttr                          html  
    regionPerReadLength                     html  
    remakeTxdbExonIds                       html  
    remove.experiments                      html  
    remove.file_ext                         html  
    removeMetaCols                          html  
    removeORFsWithSameStartAsCDS            html  
    removeORFsWithSameStopAsCDS             html  
    removeORFsWithStartInsideCDS            html  
    removeORFsWithinCDS                     html  
    removeTxdbExons                         html  
    removeTxdbTranscripts                   html  
    rename.SRA.files                        html  
    repNames                                html  
    restrictTSSByUpstreamLeader             html  
    revElementsF                            html  
    reverseMinusStrandPerGroup              html  
    ribosomeReleaseScore                    html  
    ribosomeStallingScore                   html  
    rnaNormalize                            html  
    save.experiment                         html  
    savePlot                                html  
    scaledWindowPositions                   html  
    scoreSummarizedExperiment               html  
    seqnamesPerGroup                        html  
    shiftFootprints                         html  
    shiftFootprintsByExperiment             html  
    shiftPlots                              html  
    shifts.load                             html  
    show-experiment-method                  html  
    simpleLibs                              html  
    sortPerGroup                            html  
    splitIn3Tx                              html  
    stageNames                              html  
    startCodons                             html  
    startDefinition                         html  
    startRegion                             html  
    startRegionCoverage                     html  
    startRegionString                       html  
    startSites                              html  
    stopCodons                              html  
    stopDefinition                          html  
    stopRegion                              html  
    stopSites                               html  
    strandBool                              html  
    strandPerGroup                          html  
    subsetCoverage                          html  
    subsetToFrame                           html  
    te.plot                                 html  
    te.table                                html  
    te_rna.plot                             html  
    tile1                                   html  
    tissueNames                             html  
    topMotif                                html  
    transcriptWindow                        html  
    transcriptWindow1                       html  
    transcriptWindowPer                     html  
    translationalEff                        html  
    trim_detection                          html  
    trimming.table                          html  
    txNames                                 html  
    txNamesToGeneNames                      html  
    txSeqsFromFa                            html  
    uORFSearchSpace                         html  
    uniqueGroups                            html  
    uniqueOrder                             html  
    unlistGrl                               html  
    updateTxdbRanks                         html  
    updateTxdbStartSites                    html  
    upstreamFromPerGroup                    html  
    upstreamOfPerGroup                      html  
    validGRL                                html  
    validSeqlevels                          html  
    validateExperiments                     html  
    widthPerGroup                           html  
    windowCoveragePlot                      html  
    windowPerGroup                          html  
    windowPerReadLength                     html  
    windowPerTranscript                     html  
    xAxisScaler                             html  
    yAxisScaler                             html  
** 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

install for x64

* installing *source* package 'ORFik' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c findORFsHelpers.cpp -o findORFsHelpers.o
findORFsHelpers.cpp: In function 'Rcpp::IntegerMatrix orfs_as_matrix(std::__cxx11::string&, std::__cxx11::string, std::__cxx11::string, int)':
findORFsHelpers.cpp:214:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for (int i = 0; i < uorfSize/2; i++) {
                   ~~^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c findOrfs.cpp -o findOrfs.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c findOrfsFasta.cpp -o findOrfsFasta.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o
pmapFromTranscripts.cpp: In function 'Rcpp::List pmapFromTranscriptsCPP(const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const char&, bool)':
pmapFromTranscripts.cpp:151:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(auto i = 0;i < xSize; i++){
                  ~~^~~~~~~
pmapFromTranscripts.cpp:155:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(auto i = 0; i < indexSize; i++){
                   ~~^~~~~~~~~~~
pmapFromTranscripts.cpp:161:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(auto i = 1; i < indexSize; i++){
                   ~~^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pmapToTranscripts.cpp -o pmapToTranscripts.o
pmapToTranscripts.cpp: In function 'void pmapToPositive(vi&, const int&, int&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&)':
pmapToTranscripts.cpp:22:7: warning: variable 'currentWidth' set but not used [-Wunused-but-set-variable]
   int currentWidth = 0;
       ^~~~~~~~~~~~
pmapToTranscripts.cpp: In function 'void pmapToNegative(vi&, const int&, int&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&, const vi&)':
pmapToTranscripts.cpp:68:7: warning: variable 'currentWidth' set but not used [-Wunused-but-set-variable]
   int currentWidth = 0;
       ^~~~~~~~~~~~
pmapToTranscripts.cpp: In function 'Rcpp::List pmapToTranscriptsCPP(const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const char&, const std::vector<int>&)':
pmapToTranscripts.cpp:126:20: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(auto i = 0;i < xSize; i++){ // Width per exon in x
                  ~~^~~~~~~
pmapToTranscripts.cpp:130:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(auto i = 0; i < indexSize; i++){ // Width per exon in tx
                   ~~^~~~~~~~~~~
pmapToTranscripts.cpp:136:21: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for(auto i = 1; i < indexSize; i++){
                   ~~^~~~~~~~~~~
pmapToTranscripts.cpp:147:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long long unsigned int'} [-Wsign-compare]
   for (auto i = 1; i < 2 * xSize; i = i + 2) {
                    ~~^~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o ORFik.dll tmp.def RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o pmapToTranscripts.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/ORFik.buildbin-libdir/ORFik/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ORFik' as ORFik_1.14.7.zip
* DONE (ORFik)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ORFik' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(testthat)
> library(ORFik)
Loading required package: IRanges
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, 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 objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
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: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: Rsamtools
> 
> test_check("ORFik")
     widths     group.size  
 Min.   : 6   Min.   :2.00  
 1st Qu.: 9   1st Qu.:2.25  
 Median :12   Median :2.50  
 Mean   :12   Mean   :2.50  
 3rd Qu.:15   3rd Qu.:2.75  
 Max.   :18   Max.   :3.00  
Warning message:
In coveragePerTiling(grl, reads[rWidth == l], as.data.table = TRUE,  :
  No coverage found, Returning empty data.table!
[1] "CAGE_Mutant_r1"
[1] "CAGE_Mutant_r2"
[1] "CAGE_WT_r1"
[1] "CAGE_WT_r2"
[1] "PAS_Mutant_r1"
[1] "PAS_Mutant_r2"
[1] "PAS_WT_r1"
[1] "PAS_WT_r2"
[1] "RFP_Mutant_r1"
[1] "RFP_Mutant_r2"
[1] "RFP_WT_r1"
[1] "RFP_WT_r2"
[1] "RNA_Mutant_r1"
[1] "RNA_Mutant_r2"
[1] "RNA_WT_r1"
[1] "RNA_WT_r2"
[1] "RFP"
[1] "RFP"
[1] "RFP"
[1] "RFP"
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
Error in x$.self$finalize() : attempt to apply non-function
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 361 ]
> 
> proc.time()
   user  system elapsed 
  81.35    2.00  174.21


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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(testthat)
> library(ORFik)
Loading required package: IRanges
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, 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 objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
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: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: Rsamtools
> 
> test_check("ORFik")
     widths     group.size  
 Min.   : 6   Min.   :2.00  
 1st Qu.: 9   1st Qu.:2.25  
 Median :12   Median :2.50  
 Mean   :12   Mean   :2.50  
 3rd Qu.:15   3rd Qu.:2.75  
 Max.   :18   Max.   :3.00  
Warning message:
In coveragePerTiling(grl, reads[rWidth == l], as.data.table = TRUE,  :
  No coverage found, Returning empty data.table!
[1] "CAGE_Mutant_r1"
[1] "CAGE_Mutant_r2"
[1] "CAGE_WT_r1"
[1] "CAGE_WT_r2"
[1] "PAS_Mutant_r1"
[1] "PAS_Mutant_r2"
[1] "PAS_WT_r1"
[1] "PAS_WT_r2"
[1] "RFP_Mutant_r1"
[1] "RFP_Mutant_r2"
[1] "RFP_WT_r1"
[1] "RFP_WT_r2"
[1] "RNA_Mutant_r1"
[1] "RNA_Mutant_r2"
[1] "RNA_WT_r1"
[1] "RNA_WT_r2"
[1] "RFP"
[1] "RFP"
[1] "RFP"
[1] "RFP"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 361 ]
> 
> proc.time()
   user  system elapsed 
  87.07    1.01  182.14

name	user	system	elapsed
DEG.analysis	0.57	0.08	0.64
DEG.plot.static	0.40	0.14	0.55
DTEG.analysis	1.05	0.04	1.07
DTEG.plot	0.42	0.00	0.43
ORFik.template.experiment	0.38	0.00	0.37
ORFik.template.experiment.zf	0.06	0.01	0.08
ORFikQC	0.5	0.2	0.7
QCreport	0.34	0.04	0.37
QCstats	0.42	0.01	0.44
QCstats.plot	0.34	0.00	0.34
RiboQC.plot	0.32	0.02	0.33
STAR.align.folder	0	0	0
STAR.align.single	0	0	0
STAR.index	0	0	0
STAR.install	0	0	0
STAR.remove.crashed.genome	0	0	0
TOP.Motif.ecdf	0	0	0
artificial.orfs	0.35	0.03	0.37
asTX	1.11	0.08	1.19
assignTSSByCage	0.01	0.00	0.02
bamVarName	0.77	0.01	0.79
collapse.by.scores	0.25	0.00	0.25
collapse.fastq	0	0	0
collapseDuplicatedReads-GAlignmentPairs-method	0.11	0.00	0.11
collapseDuplicatedReads-GAlignments-method	0.06	0.00	0.07
collapseDuplicatedReads-GRanges-method	0.05	0.00	0.04
collapseDuplicatedReads	0.04	0.00	0.05
combn.pairs	0.33	0.00	0.33
computeFeatures	5.09	0.05	5.17
computeFeaturesCage	0	0	0
config	0	0	0
config.exper	0	0	0
config.save	0	0	0
convertLibs	0.25	0.00	0.25
convertToOneBasedRanges	0.19	0.00	0.19
countOverlapsW	0.08	0.00	0.08
countTable	0.28	0.01	0.30
countTable_regions	0.34	0.00	0.34
coverageHeatMap	1.50	0.02	1.52
coveragePerTiling	0.75	0.02	0.76
coverageScorings	0.02	0.00	0.02
create.experiment	0.4	0.0	0.4
defineTrailer	0.27	0.00	0.27
design-experiment-method	0.48	0.00	0.48
detectRibosomeShifts	0.02	0.00	0.02
disengagementScore	0.61	0.00	0.61
distToCds	0.44	0.00	0.44
distToTSS	0.42	0.00	0.42
download.SRA	0	0	0
download.SRA.metadata	0.23	0.07	1.73
entropy	1.3	0.0	1.3
experiment-class	0.33	0.00	0.33
export.bed12	0.04	0.00	0.04
export.bigWig	0.08	0.00	0.08
export.ofst-GAlignmentPairs-method	0.1	0.0	0.1
export.ofst-GAlignments-method	0.09	0.00	0.09
export.ofst-GRanges-method	0.08	0.00	0.08
export.ofst	0.09	0.00	0.09
export.wiggle	0.05	0.00	0.05
extendLeaders	1.56	0.02	1.58
extendTrailers	0.92	0.02	0.93
filepath	0.33	0.01	0.35
filterTranscripts	2.27	0.00	2.26
fimport	0.42	0.02	0.61
findFa	0.01	0.00	0.02
findMapORFs	0.71	0.00	0.70
findORFs	0.20	0.00	0.21
findORFsFasta	0.08	0.01	0.09
findPeaksPerGene	1.20	0.03	1.26
findUORFs	0	0	0
find_url_ebi	0.03	0.03	1.80
firstEndPerGroup	0.14	0.00	0.14
firstExonPerGroup	0.13	0.00	0.13
firstStartPerGroup	0.1	0.0	0.1
flankPerGroup	0.15	0.00	0.15
floss	0.41	0.00	0.41
fpkm	0.16	0.00	0.16
fractionLength	0.09	0.00	0.09
fread.bed	0.08	0.00	0.09
gcContent	0.54	0.00	0.55
getGenomeAndAnnotation	0	0	0
get_genome_fasta	0	0	0
get_genome_gtf	0	0	0
get_noncoding_rna	0	0	0
get_phix_genome	0	0	0
get_silva_rRNA	0	0	0
groupGRangesBy	0.08	0.00	0.08
groupings	0.05	0.00	0.04
heatMapRegion	0.34	0.02	0.36
import.ofst	0.1	0.0	0.1
initiationScore	1.31	0.00	1.31
insideOutsideORF	0.89	0.00	0.89
install.fastp	0	0	0
install.sratoolkit	0	0	0
isInFrame	0.25	0.00	0.25
isOverlapping	0.25	0.00	0.25
kozakHeatmap	0	0	0
kozakSequenceScore	0.58	0.02	0.59
lastExonEndPerGroup	0.08	0.00	0.08
lastExonPerGroup	0.11	0.00	0.11
lastExonStartPerGroup	0.06	0.00	0.06
libraryTypes	0.25	0.00	0.25
list.experiments	0.19	0.00	0.19
list.genomes	0	0	0
loadRegion	0.70	0.00	0.71
loadRegions	0.69	0.00	0.68
loadTranscriptType	0	0	0
loadTxdb	0.11	0.01	0.13
longestORFs	0.18	0.00	0.19
makeORFNames	0.10	0.00	0.09
makeSummarizedExperimentFromBam	0.26	0.00	0.26
makeTxdbFromGenome	0	0	0
mergeFastq	0	0	0
metaWindow	0.22	0.00	0.22
numExonsPerGroup	0.06	0.00	0.07
orfFrameDistributions	3.44	0.00	33.70
orfScore	1.06	0.00	1.06
organism-experiment-method	0.25	0.00	0.25
outputLibs	1.47	0.03	24.50
pSitePlot	0.5	0.0	0.5
pcaExperiment	2.28	0.02	3.28
pmapFromTranscriptF	0.23	0.00	0.50
pmapToTranscriptF	1.83	0.00	2.05
rankOrder	0.16	0.00	0.15
read.experiment	0.44	0.00	0.44
readBam	0.25	0.01	0.26
readWidths	0.04	0.00	0.05
reassignTSSbyCage	1.05	0.04	1.08
reassignTxDbByCage	0	0	0
reduceKeepAttr	0.26	0.00	0.26
regionPerReadLength	2.55	0.04	41.74
remove.experiments	0.42	0.00	0.42
ribosomeReleaseScore	0.30	0.00	0.29
ribosomeStallingScore	0.36	0.00	0.36
save.experiment	0.28	0.00	0.28
scaledWindowPositions	0.38	0.00	0.38
seqnamesPerGroup	0.17	0.00	0.17
shiftFootprints	0	0	0
shiftFootprintsByExperiment	2.19	0.00	29.78
shiftPlots	0.08	0.00	0.08
shifts.load	0.37	0.00	0.37
simpleLibs	0.29	0.00	0.29
sortPerGroup	0.33	0.00	0.33
startCodons	0.58	0.00	0.58
startDefinition	0	0	0
startRegion	0.59	0.00	0.59
startSites	0.3	0.0	0.3
stopCodons	0.47	0.00	0.47
stopDefinition	0	0	0
stopRegion	0.55	0.00	0.54
stopSites	0.3	0.0	0.3
strandBool	0.01	0.00	0.01
strandPerGroup	0.07	0.00	0.07
subsetToFrame	0.03	0.00	0.03
te.plot	0	0	0
te.table	0.22	0.00	0.22
te_rna.plot	0.32	0.00	0.34
tile1	0.34	0.00	0.45
topMotif	0	0	0
transcriptWindow	0.91	0.02	0.92
translationalEff	0.17	0.00	0.17
trimming.table	0	0	0
txNames	0.06	0.00	0.07
txNamesToGeneNames	1.14	0.00	1.14
uORFSearchSpace	0.90	0.03	0.92
uniqueGroups	0.21	0.00	0.22
uniqueOrder	0.43	0.00	0.42
unlistGrl	0.11	0.00	0.11
widthPerGroup	0.09	0.00	0.09
windowCoveragePlot	0.53	0.00	0.53
windowPerGroup	0.48	0.00	0.48
windowPerReadLength	1.07	0.00	1.07

name	user	system	elapsed
DEG.analysis	0.64	0.00	1.15
DEG.plot.static	0.50	0.01	0.77
DTEG.analysis	0.59	0.03	0.96
DTEG.plot	0.49	0.02	2.11
ORFik.template.experiment	0.48	0.00	0.48
ORFik.template.experiment.zf	0.06	0.01	0.08
ORFikQC	1.47	0.00	1.47
QCreport	0.42	0.00	0.42
QCstats	0.36	0.00	0.36
QCstats.plot	0.25	0.02	0.27
RiboQC.plot	0.37	0.06	0.45
STAR.align.folder	0.00	0.02	0.02
STAR.align.single	0	0	0
STAR.index	0	0	0
STAR.install	0	0	0
STAR.remove.crashed.genome	0	0	0
TOP.Motif.ecdf	0	0	0
artificial.orfs	0.44	0.03	0.75
asTX	1.41	0.00	1.62
assignTSSByCage	0	0	0
bamVarName	0.76	0.00	1.11
collapse.by.scores	0.30	0.00	3.69
collapse.fastq	0.00	0.00	0.05
collapseDuplicatedReads-GAlignmentPairs-method	0.12	0.00	0.82
collapseDuplicatedReads-GAlignments-method	0.07	0.01	0.88
collapseDuplicatedReads-GRanges-method	0.08	0.00	0.85
collapseDuplicatedReads	0.07	0.00	0.82
combn.pairs	0.47	0.00	0.64
computeFeatures	5.92	0.00	5.94
computeFeaturesCage	0	0	0
config	0	0	0
config.exper	0	0	0
config.save	0	0	0
convertLibs	0.27	0.00	0.26
convertToOneBasedRanges	0.19	0.00	0.19
countOverlapsW	0.09	0.00	0.09
countTable	0.25	0.00	0.25
countTable_regions	0.25	0.00	0.25
coverageHeatMap	1.59	0.00	1.60
coveragePerTiling	0.94	0.00	0.93
coverageScorings	0.02	0.00	0.02
create.experiment	0.26	0.00	0.26
defineTrailer	0.21	0.00	0.21
design-experiment-method	0.28	0.00	0.28
detectRibosomeShifts	0	0	0
disengagementScore	0.61	0.00	0.61
distToCds	0.26	0.00	0.26
distToTSS	0.28	0.00	0.29
download.SRA	0	0	0
download.SRA.metadata	0.35	0.03	1.68
entropy	1.44	0.02	1.46
experiment-class	0.31	0.00	0.31
export.bed12	0.03	0.00	0.03
export.bigWig	0.06	0.00	0.06
export.ofst-GAlignmentPairs-method	0.1	0.0	0.1
export.ofst-GAlignments-method	0.07	0.00	0.07
export.ofst-GRanges-method	0.08	0.00	0.08
export.ofst	0.08	0.00	0.08
export.wiggle	0.04	0.00	0.04
extendLeaders	2.05	0.01	2.07
extendTrailers	1.33	0.02	1.34
filepath	0.47	0.00	0.47
filterTranscripts	2	0	2
fimport	0.36	0.00	0.36
findFa	0.01	0.00	0.01
findMapORFs	0.69	0.00	0.69
findORFs	0.25	0.00	0.25
findORFsFasta	0.15	0.01	0.20
findPeaksPerGene	1.36	0.00	1.36
findUORFs	0.02	0.00	0.02
find_url_ebi	0.00	0.02	2.42
firstEndPerGroup	0.16	0.00	0.16
firstExonPerGroup	0.15	0.00	0.15
firstStartPerGroup	0.11	0.00	0.11
flankPerGroup	0.17	0.00	0.17
floss	0.39	0.01	0.41
fpkm	0.16	0.00	0.16
fractionLength	0.07	0.00	0.08
fread.bed	0.10	0.00	0.09
gcContent	0.54	0.00	0.55
getGenomeAndAnnotation	0	0	0
get_genome_fasta	0	0	0
get_genome_gtf	0	0	0
get_noncoding_rna	0	0	0
get_phix_genome	0	0	0
get_silva_rRNA	0	0	0
groupGRangesBy	0.08	0.00	0.08
groupings	0.06	0.00	0.06
heatMapRegion	0.24	0.00	0.24
import.ofst	0.07	0.00	0.08
initiationScore	1.21	0.00	1.20
insideOutsideORF	0.95	0.00	0.95
install.fastp	0	0	0
install.sratoolkit	0	0	0
isInFrame	0.28	0.00	0.28
isOverlapping	0.27	0.00	0.27
kozakHeatmap	0	0	0
kozakSequenceScore	0.65	0.00	0.65
lastExonEndPerGroup	0.1	0.0	0.1
lastExonPerGroup	0.09	0.00	0.09
lastExonStartPerGroup	0.09	0.00	0.10
libraryTypes	0.24	0.00	0.23
list.experiments	0.19	0.00	0.19
list.genomes	0	0	0
loadRegion	0.70	0.05	0.75
loadRegions	0.76	0.03	0.79
loadTranscriptType	0	0	0
loadTxdb	0.13	0.02	0.15
longestORFs	0.2	0.0	0.2
makeORFNames	0.14	0.00	0.14
makeSummarizedExperimentFromBam	0.35	0.00	0.34
makeTxdbFromGenome	0	0	0
mergeFastq	0	0	0
metaWindow	0.31	0.00	0.32
numExonsPerGroup	0.06	0.00	0.06
orfFrameDistributions	4.27	0.07	42.62
orfScore	1.22	0.00	1.28
organism-experiment-method	0.23	0.00	0.24
outputLibs	1.90	0.05	26.74
pSitePlot	0.57	0.00	0.56
pcaExperiment	2.15	0.02	2.17
pmapFromTranscriptF	0.22	0.00	0.22
pmapToTranscriptF	1.73	0.01	2.23
rankOrder	0.23	0.00	0.47
read.experiment	0.46	0.00	0.52
readBam	0.26	0.00	0.26
readWidths	0.03	0.00	0.03
reassignTSSbyCage	1.27	0.00	1.28
reassignTxDbByCage	0	0	0
reduceKeepAttr	0.31	0.00	0.32
regionPerReadLength	2.61	0.02	38.50
remove.experiments	0.41	0.00	0.40
ribosomeReleaseScore	0.31	0.00	0.32
ribosomeStallingScore	0.34	0.00	0.34
save.experiment	0.25	0.01	0.26
scaledWindowPositions	0.41	0.00	0.41
seqnamesPerGroup	0.09	0.00	0.09
shiftFootprints	0	0	0
shiftFootprintsByExperiment	2.47	0.02	24.85
shiftPlots	0.05	0.00	0.05
shifts.load	0.40	0.00	0.41
simpleLibs	0.30	0.00	0.29
sortPerGroup	0.34	0.00	0.35
startCodons	0.60	0.00	0.59
startDefinition	0	0	0
startRegion	0.67	0.00	0.67
startSites	0.33	0.00	0.33
stopCodons	0.54	0.00	0.55
stopDefinition	0	0	0
stopRegion	0.66	0.00	0.65
stopSites	0.34	0.00	0.35
strandBool	0.02	0.00	0.01
strandPerGroup	0.08	0.00	0.08
subsetToFrame	0.01	0.00	0.02
te.plot	0	0	0
te.table	0.24	0.00	0.23
te_rna.plot	0.23	0.00	0.24
tile1	0.22	0.00	0.22
topMotif	0	0	0
transcriptWindow	0.95	0.01	0.97
translationalEff	0.19	0.00	0.19
trimming.table	0	0	0
txNames	0.06	0.00	0.06
txNamesToGeneNames	0.94	0.00	0.94
uORFSearchSpace	0.93	0.00	0.93
uniqueGroups	0.18	0.00	0.18
uniqueOrder	0.26	0.00	0.26
unlistGrl	0.06	0.00	0.06
widthPerGroup	0.07	0.00	0.07
windowCoveragePlot	0.61	0.00	0.61
windowPerGroup	0.47	0.00	0.47
windowPerReadLength	0.97	0.00	0.97

CHECK results for ORFik on tokay2

Summary

Command output

Installation output

Tests output

Example timings