Back to Multiple platform build/check report for BioC 3.17:   simplified   long
ABCDEFGHIJKLMN[O]PQRSTUVWXYZ

This page was generated on 2023-02-07 11:07:06 -0500 (Tue, 07 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for ORFik on merida1


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? 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 1402/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.19.7  (landing page)
Haakon Tjeldnes
Snapshot Date: 2023-02-06 14:00:21 -0500 (Mon, 06 Feb 2023)
git_url: https://git.bioconductor.org/packages/ORFik
git_branch: master
git_last_commit: d3ee070
git_last_commit_date: 2023-01-30 03:23:09 -0500 (Mon, 30 Jan 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ORFik
Version: 1.19.7
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ORFik.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ORFik_1.19.7.tar.gz
StartedAt: 2023-02-07 04:37:14 -0500 (Tue, 07 Feb 2023)
EndedAt: 2023-02-07 04:59:51 -0500 (Tue, 07 Feb 2023)
EllapsedTime: 1357.2 seconds
RetCode: 0
Status:   OK  
CheckDir: ORFik.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ORFik.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ORFik_1.19.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/ORFik.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ORFik/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ORFik’ version ‘1.19.7’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ORFik’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
* used SDK: ‘’
* 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:
  ‘find_url_ebi’ ‘revElementsF’ ‘save.fstwig’ ‘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 ‘.’
codon_usage: no visible binding for global variable ‘merged’
codon_usage: no visible binding for global variable ‘AA’
codon_usage: no visible binding for global variable ‘codon’
codon_usage_plot: no visible binding for global variable ‘seqs’
collapse.by.scores: no visible global function definition for ‘.’
collapse.fastq.internal: no visible binding for global variable ‘N’
cor_plot: no visible binding for global variable ‘Var2’
cor_plot: no visible binding for global variable ‘Var1’
cor_plot: no visible binding for global variable ‘Cor’
cor_table: no visible binding for global variable ‘Var1’
cor_table: no visible binding for global variable ‘Var2’
cor_table: no visible binding for global variable ‘Cor’
coverageHeatMap: no visible binding for global variable ‘position’
coverageHeatMap: no visible binding for global variable ‘fraction’
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’
coverage_random_access_file: no visible binding for global variable
  ‘position’
coverage_random_access_file: no visible binding for global variable
  ‘frame’
coverage_to_dt: no visible binding for global variable ‘frame’
coverage_to_dt: no visible binding for global variable ‘position’
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’
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’
geneToSymbol: no visible binding for global variable ‘ensembl_gene_id’
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’
metadata.autnaming: no visible binding for global variable
  ‘LIBRARYTYPE’
metadata.autnaming: no visible binding for global variable
  ‘LibraryStrategy’
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’
ribo_fft: no visible binding for global variable ‘fraction’
ribo_fft_plot: no visible binding for global variable ‘periods’
ribo_fft_plot: no visible binding for global variable ‘amplitude’
rnaNormalize: no visible binding for global variable ‘feature’
sample_info_append_SRA: no visible binding for global variable ‘Run’
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’
seq_usage: no visible binding for global variable ‘variable’
seq_usage: no visible binding for global variable ‘codon_sum’
seq_usage: no visible global function definition for ‘.’
seq_usage: no visible binding for global variable ‘gene_sum’
seq_usage: no visible binding for global variable
  ‘N_AA_of_type_per_gene’
seq_usage: no visible binding for global variable ‘as_prob_normalized’
seq_usage: no visible binding for global variable ‘N_total’
seq_usage: no visible binding for global variable ‘N’
seq_usage: no visible binding for global variable ‘mean_txNorm’
seq_usage: no visible binding for global variable ‘sum_txNorm’
seq_usage: no visible binding for global variable ‘dispersion’
seq_usage: no visible binding for global variable ‘dispersion_txNorm’
seq_usage: no visible binding for global variable ‘var_txNorm’
seq_usage: no visible binding for global variable ‘mean_percentage’
seq_usage: no visible binding for global variable ‘mean_txNorm_prob’
seq_usage: no visible binding for global variable
  ‘mean_txNorm_percentage’
seq_usage: no visible binding for global variable
  ‘relative_to_max_score’
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 ‘.’
collapseDuplicatedReads,data.table: no visible global function
  definition for ‘.’
collapseDuplicatedReads,data.table: no visible binding for global
  variable ‘size’
design,experiment: no visible binding for global variable ‘..formula’
seqlevels,experiment: no visible binding for global variable ‘df’
show,covRleList: no visible global function definition for ‘head’
Undefined global functions or variables:
  . ..formula AA CDS CDSGrouping Cor Hx IR LEADERS LFC LFC_TE
  LIBRARYTYPE LibraryStrategy MONTH N N_AA_of_type_per_gene N_total
  ORFGrouping ORFScores PC1 PC2 RRS RSS Regulation ReleaseDate Run
  STAR_index StartCodons StopCodons TE_log2 TOP Transcript Var1 Var2
  YEAR amplitude as_prob_normalized best_frame chr cigar1 cigar2 codon
  codonSums codon_sum count countRFP count_seq_pos_with_count
  counts_per_sample df dif difPer disengagementScores dispersion
  dispersion_txNorm distORFCDS ensembl_gene_id 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 head inFrameCDS
  ioScore isOverlappingCds kozak leaders mRNA meanCounts mean_IR
  mean_per_gene mean_percentage mean_txNorm mean_txNorm_percentage
  mean_txNorm_prob median_per_gene median_score merged pShifted
  perc_of_counts_per_sample percent percent_length percentage
  percentage_mrna_aligned percentage_tx_aligned periods phix.url pick
  position random rankInTx ranks ratio_cds_leader ratio_cds_mrna read
  length relative_to_max_score 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 seqs size spec spots start1
  start2 startCodonCoverage startRegionRelative subtitle sum.count
  sum_per_gene sum_txNorm te trailers upstream_kozak_strength utr3_len
  utr5_len value var_txNorm variable widths windowMean windowSD zscore
Consider adding
  importFrom("base", "length")
  importFrom("graphics", "frame")
  importFrom("stats", "df")
  importFrom("utils", "head")
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
codon_usage_exp             15.511  0.570  21.250
shiftFootprintsByExperiment  9.287  1.410  13.353
computeFeatures              9.076  0.054  12.199
codon_usage_plot             7.145  0.585  10.285
codon_usage                  6.464  0.063   8.948
ribo_fft                     5.808  0.250   7.477
ribo_fft_plot                5.550  0.041   7.095
find_url_ebi                 0.054  0.008   6.454
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/ORFik.Rcheck/00check.log’
for details.



Installation output

ORFik.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ORFik
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/Resources/library’
* installing *source* package ‘ORFik’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 11.0.0 (clang-1100.0.33.17)’
using C++11
using SDK: ‘’
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c findORFsHelpers.cpp -o findORFsHelpers.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c findOrfs.cpp -o findOrfs.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c findOrfsFasta.cpp -o findOrfsFasta.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3/Resources/library/Rcpp/include' -I/usr/local/include    -fPIC  -Wall -g -O2  -c pmapToTranscripts.cpp -o pmapToTranscripts.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ORFik.so RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o pmapToTranscripts.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3/Resources/library/00LOCK-ORFik/00new/ORFik/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘symbols’ in package ‘ORFik’
** 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 Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following 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

Attaching package: 'ORFik'

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

    symbols

> 
> test_check("ORFik")
Regulation
No change 
        6 
     widths     group.size  
 Min.   : 6   Min.   :1.00  
 1st Qu.: 9   1st Qu.:1.75  
 Median :12   Median :2.50  
 Mean   :12   Mean   :2.50  
 3rd Qu.:15   3rd Qu.:3.25  
 Max.   :18   Max.   :4.00  
[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 407 ]
> 
> proc.time()
   user  system elapsed 
175.507   5.741 243.955 

Example timings

ORFik.Rcheck/ORFik-Ex.timings

nameusersystemelapsed
DEG.analysis1.1920.0231.520
DEG.plot.static0.9580.0901.400
DTEG.analysis0.8940.0051.210
DTEG.plot0.8680.0051.177
ORFik.template.experiment0.9050.0061.199
ORFik.template.experiment.zf0.1260.0020.170
ORFikQC0.8340.0051.105
QCreport0.8860.0051.194
QCstats0.8280.0031.147
QCstats.plot1.8350.0062.530
RiboQC.plot0.8140.0031.132
STAR.align.folder0.0000.0000.002
STAR.align.single0.0010.0000.001
STAR.index000
STAR.install000
STAR.remove.crashed.genome000
TOP.Motif.ecdf000
artificial.orfs0.8060.0031.111
asTX1.4660.1192.216
assignTSSByCage0.0020.0020.008
bamVarName1.6790.0372.381
codon_usage6.4640.0638.948
codon_usage_exp15.511 0.57021.250
codon_usage_plot 7.145 0.58510.285
collapse.by.scores0.2240.0180.316
collapse.fastq000
collapseDuplicatedReads-GAlignmentPairs-method0.1690.0020.224
collapseDuplicatedReads-GAlignments-method0.0540.0000.073
collapseDuplicatedReads-GRanges-method0.0550.0000.070
collapseDuplicatedReads-data.table-method0.0560.0010.072
collapseDuplicatedReads0.0510.0010.067
combn.pairs0.8360.0061.119
computeFeatures 9.076 0.05412.199
computeFeaturesCage000
config0.0010.0010.000
config.exper000
config.save000
convertLibs0.8460.0041.136
convertToOneBasedRanges0.2780.0020.382
convert_bam_to_ofst0.3160.0140.500
convert_to_bigWig1.8790.0152.502
convert_to_covRle1.0850.0081.479
convert_to_covRleList1.6430.0152.422
countOverlapsW0.1490.0010.210
countTable0.8030.0041.099
countTable_regions0.8350.0041.100
covRle0.1120.0010.173
covRleFromGR0.1960.0020.296
covRleList0.0380.0000.048
coverageHeatMap2.4620.0143.377
coveragePerTiling1.5670.0052.135
coverageScorings0.0150.0000.016
create.experiment0.8560.0041.152
defineTrailer0.3520.0020.479
design-experiment-method0.8930.0051.215
detectRibosomeShifts0.0020.0010.008
disengagementScore1.0520.0041.485
distToCds0.4790.0020.657
distToTSS0.4490.0020.644
download.SRA0.0000.0000.001
download.SRA.metadata0.4290.0181.605
entropy1.6510.0062.195
experiment-class0.9280.0051.264
export.bed120.0420.0000.060
export.bigWig0.0690.0010.098
export.fstwig0.1250.0010.165
export.ofst-GAlignmentPairs-method0.1490.0010.188
export.ofst-GAlignments-method0.1400.0010.173
export.ofst-GRanges-method0.1380.0010.168
export.ofst0.1430.0010.185
export.wiggle0.0700.0010.087
extendLeaders2.2690.0242.980
extendTrailers1.4040.0172.015
filepath0.9100.0051.283
filterTranscripts2.7640.0103.810
fimport0.5620.0250.801
findFa0.0060.0010.011
findMapORFs1.1650.0061.640
findORFs0.3990.0060.581
findORFsFasta0.1330.0030.184
findPeaksPerGene2.3470.0163.268
findUORFs0.0020.0000.002
find_url_ebi0.0540.0086.454
firstEndPerGroup0.1260.0010.138
firstExonPerGroup0.1410.0010.193
firstStartPerGroup0.1240.0010.176
flankPerGroup0.2200.0020.307
floss0.5470.0020.763
fpkm0.2370.0010.314
fractionLength0.1080.0000.146
fread.bed0.0600.0100.103
gcContent0.7780.0051.081
geneToSymbol0.0000.0000.001
getGenomeAndAnnotation0.0010.0010.000
get_bioproject_candidates000
get_genome_fasta000
get_genome_gtf0.0010.0010.001
get_noncoding_rna0.0000.0000.001
get_phix_genome0.0010.0000.001
get_silva_rRNA000
groupGRangesBy0.1170.0000.164
groupings0.0810.0000.118
heatMapRegion0.9300.0041.361
import.ofst0.1430.0010.201
initiationScore2.1110.0073.003
insideOutsideORF1.7010.0062.498
install.fastp0.0010.0000.000
install.sratoolkit0.0010.0010.000
isInFrame0.4760.0020.735
isOverlapping0.4740.0020.706
kozakHeatmap0.0000.0000.001
kozakSequenceScore1.1300.0041.622
lastExonEndPerGroup0.1220.0010.180
lastExonPerGroup0.1390.0010.216
lastExonStartPerGroup0.1220.0010.186
libraryTypes0.8460.0041.272
list.experiments0.5340.0030.776
list.genomes0.0020.0010.002
loadRegion1.2810.0201.938
loadRegions1.3690.0162.075
loadTranscriptType000
loadTxdb0.2390.0070.365
longestORFs0.2700.0010.393
makeORFNames0.1750.0010.268
makeSummarizedExperimentFromBam0.8700.0051.265
makeTxdbFromGenome000
mergeFastq0.0010.0000.001
mergeLibs0.8760.0041.201
metaWindow0.4260.0010.571
numExonsPerGroup0.0800.0000.108
optimizedTranscriptLengths1.9770.0202.749
orfFrameDistributions2.1830.5333.434
orfScore1.9380.2242.861
organism-experiment-method0.8730.0551.259
outputLibs2.1680.4733.021
pSitePlot0.7810.1011.210
pcaExperiment2.7270.1674.008
pmapFromTranscriptF0.1960.0010.287
pmapToTranscriptF1.7440.0162.412
rankOrder0.1620.0020.219
read.experiment0.8670.0081.158
readBam0.2770.0140.392
readWidths0.0290.0010.040
reassignTSSbyCage1.1730.0121.612
reassignTxDbByCage0.0010.0000.000
reduceKeepAttr0.2660.0010.354
regionPerReadLength1.2050.5932.003
remove.experiments0.9390.1091.282
ribo_fft5.8080.2507.477
ribo_fft_plot5.5500.0417.095
ribosomeReleaseScore0.4360.0020.576
ribosomeStallingScore0.6430.0030.821
save.experiment0.8350.0031.057
scaledWindowPositions0.6570.0040.798
seqnamesPerGroup0.1240.0010.164
shiftFootprints0.0030.0010.007
shiftFootprintsByExperiment 9.287 1.41013.353
shiftPlots0.1080.0360.158
shifts.load0.9100.0801.271
simpleLibs0.9220.0851.328
sortPerGroup0.5350.0430.748
startCodons1.0620.0721.500
startDefinition0.0010.0000.001
startRegion1.1940.0101.516
startSites0.6000.0020.772
stopCodons1.0080.0031.312
stopDefinition0.0010.0000.000
stopRegion1.1830.0041.527
stopSites0.6110.0020.787
strandBool0.0190.0000.026
strandPerGroup0.1240.0010.157
subsetToFrame0.0320.0010.042
te.plot000
te.table0.8320.0051.105
te_rna.plot0.8560.0061.100
tile10.4170.0030.515
topMotif000
transcriptWindow2.2240.0282.902
translationalEff0.3020.0010.374
trimming.table0.0010.0010.000
txNames0.0890.0010.114
txNamesToGeneNames1.9700.0152.505
uORFSearchSpace1.2180.0111.549
uniqueGroups0.3110.0050.396
uniqueOrder0.4820.0020.637
unlistGrl0.0850.0010.113
widthPerGroup0.0890.0010.121
windowCoveragePlot1.2630.0121.673
windowPerGroup0.8650.0041.157
windowPerReadLength1.8320.0082.553