Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-12-06 13:05:06 -0500 (Mon, 06 Dec 2021).

CHECK results for ORFik on nebbiolo2

To the developers/maintainers of the ORFik package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ORFik.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1349/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.14.5  (landing page)
Haakon Tjeldnes
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/ORFik
git_branch: RELEASE_3_14
git_last_commit: cdc337c
git_last_commit_date: 2021-11-04 04:48:24 -0500 (Thu, 04 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ORFik
Version: 1.14.5
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ORFik_1.14.5.tar.gz
StartedAt: 2021-12-05 09:00:44 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 09:09:35 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 531.7 seconds
RetCode: 0
Status:   OK  
CheckDir: ORFik.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings ORFik_1.14.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/ORFik.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ORFik/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ORFik’ version ‘1.14.5’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ORFik’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
* 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
* 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
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’
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_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 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 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
find_url_ebi 0.045  0.019   17.38
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/ORFik.Rcheck/00check.log’
for details.



Installation output

ORFik.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL ORFik
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘ORFik’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c findORFsHelpers.cpp -o findORFsHelpers.o
findORFsHelpers.cpp: In function ‘Rcpp::IntegerMatrix orfs_as_matrix(std::string&, std::string, std::string, int)’:
findORFsHelpers.cpp:214:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  214 |   for (int i = 0; i < uorfSize/2; i++) {
      |                   ~~^~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c findOrfs.cpp -o findOrfs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c findOrfsFasta.cpp -o findOrfsFasta.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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 unsigned int’} [-Wsign-compare]
  151 |   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 unsigned int’} [-Wsign-compare]
  155 |   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 unsigned int’} [-Wsign-compare]
  161 |   for(auto i = 1; i < indexSize; i++){
      |                   ~~^~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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]
   22 |   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]
   68 |   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 unsigned int’} [-Wsign-compare]
  126 |   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 unsigned int’} [-Wsign-compare]
  130 |   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 unsigned int’} [-Wsign-compare]
  136 |   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 unsigned int’} [-Wsign-compare]
  147 |   for (auto i = 1; i < 2 * xSize; i = i + 2) {
      |                    ~~^~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o ORFik.so RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o pmapToTranscripts.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-ORFik/00new/ORFik/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ORFik)

Tests output

ORFik.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

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> 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

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.   :1.000  
 1st Qu.: 9   1st Qu.:1.500  
 Median :12   Median :2.000  
 Mean   :12   Mean   :1.667  
 3rd Qu.:15   3rd Qu.:2.000  
 Max.   :18   Max.   :2.000  
[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"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 360 ]
> 
> proc.time()
   user  system elapsed 
 79.629   7.335  82.203 

Example timings

ORFik.Rcheck/ORFik-Ex.timings

nameusersystemelapsed
DTEG.analysis0.280.000.28
DTEG.plot000
ORFik.template.experiment0.2400.0560.296
ORFik.template.experiment.zf0.9530.0160.969
ORFikQC0.2130.0000.213
QCreport0.2110.0000.211
QCstats0.2280.0120.240
QCstats.plot0.2300.0240.254
RiboQC.plot0.2060.0440.250
STAR.align.folder000
STAR.align.single0.0000.0000.001
STAR.index000
STAR.install000
STAR.remove.crashed.genome000
TOP.Motif.ecdf0.0000.0000.001
artificial.orfs0.2200.0310.252
asTX0.7270.0230.752
assignTSSByCage0.0020.0000.002
bamVarName0.3480.0040.351
collapse.by.scores0.1580.0000.138
collapse.fastq0.0010.0010.001
collapseDuplicatedReads-GAlignmentPairs-method0.0640.0080.073
collapseDuplicatedReads-GAlignments-method0.040.000.04
collapseDuplicatedReads-GRanges-method0.040.000.04
collapseDuplicatedReads0.040.000.04
combn.pairs0.2810.0000.281
computeFeatures4.4530.0714.510
computeFeaturesCage000
config000
config.exper000
config.save000
convertLibs0.2170.0320.249
convertToOneBasedRanges0.1640.0080.172
countOverlapsW0.0760.0080.084
countTable0.2380.0160.254
countTable_regions0.2350.0120.247
coverageHeatMap1.0900.0481.138
coveragePerTiling0.7200.0120.732
coverageScorings0.0070.0000.007
create.experiment0.2370.0040.227
defineTrailer0.1510.0000.151
design-experiment-method0.2820.0000.282
detectRibosomeShifts0.0010.0000.001
disengagementScore0.5380.0000.538
distToCds0.2580.0000.259
distToTSS0.2130.0000.213
download.SRA000
download.SRA.metadata0.1840.0451.234
entropy0.8640.2081.051
experiment-class0.2740.0520.326
export.bed120.0310.0000.031
export.bigWig0.0450.0000.044
export.ofst-GAlignmentPairs-method0.0620.0120.074
export.ofst-GAlignments-method0.0630.0080.071
export.ofst-GRanges-method0.0590.0120.071
export.ofst0.0710.0120.083
export.wiggle0.0410.0120.053
extendLeaders1.1940.2761.470
extendTrailers0.6650.0360.695
filepath0.2270.0080.236
filterTranscripts1.3890.0761.466
fimport0.3650.0160.383
findFa0.0050.0000.005
findMapORFs0.5990.0040.602
findORFs0.1920.0000.192
findORFsFasta0.0880.0080.091
findPeaksPerGene0.9770.0120.978
findUORFs0.0010.0000.001
find_url_ebi 0.045 0.01917.380
firstEndPerGroup0.1130.0080.121
firstExonPerGroup0.0710.0000.072
firstStartPerGroup0.0540.0080.062
flankPerGroup0.1140.0040.111
floss0.3160.0040.296
fpkm0.1290.0080.135
fractionLength0.0670.0000.066
fread.bed0.0440.0030.048
gcContent0.4470.0200.468
getGenomeAndAnnotation000
get_genome_fasta0.0000.0000.001
get_genome_gtf000
get_noncoding_rna0.0000.0000.001
get_phix_genome000
get_silva_rRNA000
groupGRangesBy0.0710.0000.071
groupings0.0500.0000.049
heatMapRegion0.2280.0120.240
import.ofst0.0700.0040.074
initiationScore1.0270.0321.058
insideOutsideORF0.8790.0560.926
install.fastp000
install.sratoolkit000
isInFrame0.2800.0280.309
isOverlapping0.2410.0120.253
kozakHeatmap000
kozakSequenceScore0.5650.0160.581
lastExonEndPerGroup0.0690.0000.070
lastExonPerGroup0.0980.0000.099
lastExonStartPerGroup0.0710.0000.071
libraryTypes0.2280.0040.233
list.experiments0.1950.0080.202
list.genomes0.0010.0000.001
loadRegion0.5970.0200.617
loadRegions0.6800.0160.695
loadTranscriptType000
loadTxdb0.1140.0060.120
longestORFs0.1710.0120.183
makeORFNames0.0980.0000.098
makeSummarizedExperimentFromBam0.2440.0040.248
makeTxdbFromGenome000
mergeFastq0.0000.0000.001
metaWindow0.2060.0120.217
numExonsPerGroup0.0540.0040.052
orfFrameDistributions2.7560.3173.457
orfScore0.9970.3470.816
organism-experiment-method0.2650.0080.264
outputLibs0.9320.4920.889
pSitePlot0.3040.0400.345
pcaExperiment1.0790.0641.143
pmapFromTranscriptF0.1040.0040.108
pmapToTranscriptF0.9170.0240.941
rankOrder0.1200.0040.124
read.experiment0.2270.0000.227
readBam0.1240.0280.152
readWidths0.0230.0000.023
reassignTSSbyCage0.6410.0160.657
reassignTxDbByCage000
reduceKeepAttr0.1410.0120.153
regionPerReadLength0.3730.2040.873
remove.experiments0.5140.2120.324
ribosomeReleaseScore0.2060.0200.226
ribosomeStallingScore0.3070.0350.343
save.experiment0.2220.0320.254
scaledWindowPositions0.3390.0240.363
seqnamesPerGroup0.0880.0000.073
shiftFootprints0.0010.0000.001
shiftFootprintsByExperiment1.0440.0484.495
shiftPlots2.8930.6390.059
shifts.load0.2770.0320.309
simpleLibs0.2680.0160.284
sortPerGroup0.3130.0120.325
startCodons0.5700.0240.595
startDefinition000
startRegion0.6220.0080.631
startSites0.3050.0000.306
stopCodons0.5420.0000.543
stopDefinition0.0000.0000.001
stopRegion0.6320.0000.632
stopSites0.3160.0000.315
strandBool0.0120.0000.011
strandPerGroup0.0700.0000.071
subsetToFrame0.0210.0000.022
te.plot000
te.table000
te_rna.plot000
tile10.2120.0040.216
topMotif000
transcriptWindow0.9170.0040.920
translationalEff0.1570.0000.156
trimming.table000
txNames0.0540.0000.053
txNamesToGeneNames0.9120.0000.911
uORFSearchSpace0.6330.0080.641
uniqueGroups0.1760.0000.176
uniqueOrder0.2400.0000.239
unlistGrl0.0590.0000.059
widthPerGroup0.0610.0000.062
windowCoveragePlot0.5510.0080.554
windowPerGroup0.4370.0000.438
windowPerReadLength0.9450.0000.931