Haakon Tjeldnes
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/ORFik |
| git_branch: RELEASE_3_13 |
| git_last_commit: b86b7a7 |
| git_last_commit_date: 2021-09-29 10:33:24 -0400 (Wed, 29 Sep 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:47 -0400 (Fri, 15 Oct 2021).
|
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. |
| Package 1323/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ORFik 1.12.13 (landing page) Haakon Tjeldnes
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ORFik |
| Version: 1.12.13 |
| Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ORFik_1.12.13.tar.gz |
| StartedAt: 2021-10-14 10:54:01 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 11:02:32 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 511.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ORFik.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ORFik_1.12.13.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ORFik.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.12.13’
* 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 ... OK
* 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:
‘coverageByTranscriptW’ ‘find_url_ebi’ ‘groupings’ ‘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.align.folder: no visible global function definition for
‘detectCores’
STAR.align.single: no visible global function definition for
‘detectCores’
STAR.index: no visible global function definition for ‘detectCores’
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’
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 ‘df.rfp’
te_rna.plot: no visible binding for global variable ‘df.rna’
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’
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 ‘.’
Undefined global functions or variables:
. 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 detectCores df.rfp df.rna
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 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
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.13-bioc/meat/ORFik.Rcheck/00check.log’
for details.
ORFik.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ORFik
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘ORFik’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-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-3.13-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-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-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)
ORFik.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
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.
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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
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>
> test_check("ORFik")
widths group.size
Min. : 6 Min. :1.000
1st Qu.: 9 1st Qu.:1.000
Median :12 Median :1.000
Mean :12 Mean :1.667
3rd Qu.:15 3rd Qu.:2.000
Max. :18 Max. :3.000
[1] "CAGE_heart"
[1] "RFP_heart"
[1] "RFP"
[1] "RNA_heart"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 359 ]
>
> proc.time()
user system elapsed
83.923 4.680 83.791
ORFik.Rcheck/ORFik-Ex.timings
| name | user | system | elapsed | |
| DTEG.analysis | 0.001 | 0.000 | 0.000 | |
| DTEG.plot | 0.001 | 0.000 | 0.000 | |
| ORFik.template.experiment | 0.138 | 0.004 | 0.142 | |
| ORFikQC | 0.076 | 0.004 | 0.080 | |
| QCreport | 0.058 | 0.008 | 0.066 | |
| QCstats | 0.043 | 0.032 | 0.074 | |
| QCstats.plot | 0.066 | 0.008 | 0.074 | |
| RiboQC.plot | 0.052 | 0.020 | 0.073 | |
| STAR.align.folder | 0.000 | 0.000 | 0.001 | |
| STAR.align.single | 0 | 0 | 0 | |
| STAR.index | 0 | 0 | 0 | |
| STAR.install | 0 | 0 | 0 | |
| STAR.remove.crashed.genome | 0.000 | 0.000 | 0.001 | |
| TOP.Motif.ecdf | 0.001 | 0.000 | 0.001 | |
| artificial.orfs | 0.068 | 0.004 | 0.072 | |
| asTX | 0.810 | 0.043 | 0.854 | |
| assignTSSByCage | 0.002 | 0.000 | 0.002 | |
| bamVarName | 0.093 | 0.000 | 0.093 | |
| collapse.by.scores | 0.152 | 0.000 | 0.133 | |
| collapse.fastq | 0.000 | 0.000 | 0.001 | |
| collapseDuplicatedReads-GAlignmentPairs-method | 0.068 | 0.000 | 0.069 | |
| collapseDuplicatedReads-GAlignments-method | 0.036 | 0.000 | 0.036 | |
| collapseDuplicatedReads-GRanges-method | 0.036 | 0.000 | 0.036 | |
| collapseDuplicatedReads | 0.035 | 0.003 | 0.039 | |
| combn.pairs | 0.085 | 0.001 | 0.085 | |
| computeFeatures | 4.755 | 0.004 | 4.730 | |
| computeFeaturesCage | 0 | 0 | 0 | |
| config | 0.000 | 0.000 | 0.001 | |
| config.exper | 0 | 0 | 0 | |
| config.save | 0 | 0 | 0 | |
| convertLibs | 0.065 | 0.000 | 0.064 | |
| convertToOneBasedRanges | 0.161 | 0.003 | 0.164 | |
| countOverlapsW | 0.084 | 0.000 | 0.083 | |
| countTable | 0.075 | 0.004 | 0.078 | |
| countTable_regions | 0.064 | 0.000 | 0.063 | |
| coverageHeatMap | 1.194 | 0.008 | 1.201 | |
| coveragePerTiling | 0.882 | 0.000 | 0.882 | |
| coverageScorings | 0.009 | 0.000 | 0.008 | |
| create.experiment | 0.065 | 0.000 | 0.059 | |
| defineTrailer | 0.134 | 0.000 | 0.134 | |
| detectRibosomeShifts | 0.001 | 0.000 | 0.002 | |
| disengagementScore | 0.499 | 0.000 | 0.500 | |
| distToCds | 0.244 | 0.000 | 0.245 | |
| distToTSS | 0.238 | 0.000 | 0.237 | |
| download.SRA | 0 | 0 | 0 | |
| download.SRA.metadata | 0.211 | 0.084 | 1.348 | |
| entropy | 0.989 | 0.068 | 1.041 | |
| experiment-class | 0.082 | 0.000 | 0.082 | |
| export.bed12 | 0.049 | 0.000 | 0.049 | |
| export.bigWig | 0.043 | 0.000 | 0.043 | |
| export.ofst-GAlignmentPairs-method | 0.068 | 0.000 | 0.068 | |
| export.ofst-GAlignments-method | 0.063 | 0.000 | 0.063 | |
| export.ofst-GRanges-method | 0.06 | 0.00 | 0.06 | |
| export.ofst | 0.066 | 0.000 | 0.066 | |
| export.wiggle | 0.043 | 0.000 | 0.043 | |
| extendLeaders | 1.294 | 0.004 | 1.299 | |
| extendTrailers | 0.765 | 0.032 | 0.792 | |
| filepath | 0.074 | 0.002 | 0.076 | |
| filterTranscripts | 1.462 | 0.092 | 1.554 | |
| fimport | 0.313 | 0.040 | 0.355 | |
| findFa | 0.005 | 0.000 | 0.006 | |
| findMapORFs | 0.641 | 0.032 | 0.673 | |
| findORFs | 0.180 | 0.008 | 0.187 | |
| findORFsFasta | 0.103 | 0.008 | 0.101 | |
| findPeaksPerGene | 2.205 | 0.272 | 2.477 | |
| findUORFs | 0.001 | 0.000 | 0.001 | |
| find_url_ebi | 0.046 | 0.008 | 3.618 | |
| firstEndPerGroup | 0.132 | 0.008 | 0.140 | |
| firstExonPerGroup | 0.090 | 0.012 | 0.103 | |
| firstStartPerGroup | 0.065 | 0.008 | 0.073 | |
| floss | 0.375 | 0.024 | 0.372 | |
| fpkm | 0.136 | 0.024 | 0.157 | |
| fractionLength | 0.072 | 0.008 | 0.080 | |
| fread.bed | 0.040 | 0.012 | 0.053 | |
| gcContent | 0.485 | 0.016 | 0.501 | |
| getGenomeAndAnnotation | 0.001 | 0.000 | 0.001 | |
| get_genome_fasta | 0.001 | 0.000 | 0.001 | |
| get_genome_gtf | 0.001 | 0.000 | 0.000 | |
| get_noncoding_rna | 0 | 0 | 0 | |
| get_phix_genome | 0.001 | 0.000 | 0.001 | |
| get_silva_rRNA | 0 | 0 | 0 | |
| groupGRangesBy | 0.071 | 0.000 | 0.071 | |
| groupings | 0.043 | 0.012 | 0.055 | |
| heatMapRegion | 0.08 | 0.00 | 0.08 | |
| import.ofst | 0.066 | 0.004 | 0.071 | |
| initiationScore | 1.180 | 0.076 | 1.256 | |
| insideOutsideORF | 1.004 | 0.024 | 1.014 | |
| install.fastp | 0 | 0 | 0 | |
| install.sratoolkit | 0.001 | 0.000 | 0.000 | |
| isInFrame | 0.299 | 0.020 | 0.318 | |
| isOverlapping | 0.266 | 0.024 | 0.290 | |
| kozakHeatmap | 0.000 | 0.000 | 0.001 | |
| kozakSequenceScore | 0.601 | 0.024 | 0.625 | |
| lastExonEndPerGroup | 0.071 | 0.000 | 0.072 | |
| lastExonPerGroup | 0.094 | 0.000 | 0.095 | |
| lastExonStartPerGroup | 0.084 | 0.000 | 0.084 | |
| libraryTypes | 0.075 | 0.008 | 0.083 | |
| list.experiments | 0.056 | 0.000 | 0.055 | |
| list.genomes | 0.001 | 0.000 | 0.001 | |
| loadRegion | 1.314 | 0.060 | 1.374 | |
| loadRegions | 0.973 | 0.036 | 1.010 | |
| loadTranscriptType | 0.001 | 0.000 | 0.000 | |
| loadTxdb | 0.109 | 0.008 | 0.117 | |
| longestORFs | 0.154 | 0.003 | 0.157 | |
| makeORFNames | 0.1 | 0.0 | 0.1 | |
| makeSummarizedExperimentFromBam | 0.102 | 0.000 | 0.101 | |
| makeTxdbFromGenome | 0 | 0 | 0 | |
| mergeFastq | 0.001 | 0.000 | 0.000 | |
| metaWindow | 0.231 | 0.020 | 0.250 | |
| numExonsPerGroup | 0.062 | 0.000 | 0.050 | |
| orfFrameDistributions | 3.548 | 0.672 | 3.738 | |
| orfScore | 0.862 | 0.096 | 0.944 | |
| organism-experiment-method | 0.088 | 0.005 | 0.089 | |
| outputLibs | 0.497 | 0.379 | 0.438 | |
| pSitePlot | 0.327 | 0.048 | 0.376 | |
| pmapFromTranscriptF | 0.120 | 0.012 | 0.131 | |
| pmapToTranscriptF | 0.977 | 0.060 | 1.037 | |
| rankOrder | 0.105 | 0.010 | 0.115 | |
| read.experiment | 0.065 | 0.008 | 0.073 | |
| readBam | 0.133 | 0.012 | 0.145 | |
| readWidths | 0.022 | 0.000 | 0.023 | |
| reassignTSSbyCage | 0.672 | 0.016 | 0.689 | |
| reassignTxDbByCage | 0.001 | 0.000 | 0.000 | |
| reduceKeepAttr | 0.157 | 0.004 | 0.160 | |
| regionPerReadLength | 0.456 | 0.004 | 0.454 | |
| remove.experiments | 0.06 | 0.00 | 0.06 | |
| ribosomeReleaseScore | 0.209 | 0.008 | 0.218 | |
| ribosomeStallingScore | 0.301 | 0.012 | 0.314 | |
| save.experiment | 0.064 | 0.004 | 0.069 | |
| scaledWindowPositions | 0.364 | 0.012 | 0.373 | |
| seqnamesPerGroup | 0.070 | 0.001 | 0.067 | |
| shiftFootprints | 0.002 | 0.000 | 0.001 | |
| shiftFootprintsByExperiment | 4.116 | 0.148 | 4.216 | |
| shiftPlots | 0.060 | 0.003 | 0.064 | |
| shifts.load | 0.064 | 0.000 | 0.064 | |
| simpleLibs | 0.064 | 0.000 | 0.064 | |
| sortPerGroup | 0.292 | 0.000 | 0.292 | |
| startCodons | 0.589 | 0.016 | 0.605 | |
| startDefinition | 0 | 0 | 0 | |
| startRegion | 0.693 | 0.020 | 0.713 | |
| startSites | 0.333 | 0.004 | 0.337 | |
| stopCodons | 0.573 | 0.011 | 0.584 | |
| stopDefinition | 0.001 | 0.000 | 0.001 | |
| stopRegion | 0.656 | 0.012 | 0.668 | |
| stopSites | 0.341 | 0.000 | 0.341 | |
| strandBool | 0.012 | 0.000 | 0.012 | |
| strandPerGroup | 0.066 | 0.000 | 0.066 | |
| subsetToFrame | 0.022 | 0.000 | 0.022 | |
| te.plot | 0 | 0 | 0 | |
| te.table | 0 | 0 | 0 | |
| te_rna.plot | 0 | 0 | 0 | |
| tile1 | 0.254 | 0.000 | 0.254 | |
| topMotif | 0 | 0 | 0 | |
| transcriptWindow | 1.120 | 0.016 | 1.136 | |
| translationalEff | 0.167 | 0.000 | 0.167 | |
| trimming.table | 0.001 | 0.000 | 0.000 | |
| txNames | 0.047 | 0.000 | 0.048 | |
| txNamesToGeneNames | 0.915 | 0.012 | 0.927 | |
| uORFSearchSpace | 0.689 | 0.016 | 0.705 | |
| uniqueGroups | 0.168 | 0.008 | 0.175 | |
| uniqueOrder | 0.233 | 0.024 | 0.257 | |
| unlistGrl | 0.057 | 0.004 | 0.060 | |
| widthPerGroup | 0.056 | 0.000 | 0.055 | |
| windowCoveragePlot | 0.544 | 0.032 | 0.561 | |
| windowPerGroup | 0.521 | 0.000 | 0.521 | |
| windowPerReadLength | 1.062 | 0.032 | 1.079 | |