Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-03-22 11:06:55 -0400 (Wed, 22 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4508
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4293
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4290
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 1422/2189HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.19.7  (landing page)
Haakon Tjeldnes
Snapshot Date: 2023-03-21 14:00:22 -0400 (Tue, 21 Mar 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 -0400 (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    OK    OK  UNNEEDED, same version is already published
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: 2023-03-22 04:40:25 -0400 (Wed, 22 Mar 2023)
EndedAt: 2023-03-22 05:03:28 -0400 (Wed, 22 Mar 2023)
EllapsedTime: 1383.3 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) (2023-03-16 r83985)
* 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 C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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             15.336  0.504  21.163
computeFeatures              9.047  0.063  12.026
codon_usage_plot             7.052  0.477  10.035
ribo_fft                     7.147  0.380  10.279
codon_usage                  6.545  0.058   8.840
ribo_fft_plot                5.452  0.048   7.584
shiftFootprintsByExperiment  2.279  0.082  13.643
download.SRA.metadata        0.457  0.021   7.737
* 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
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/ORFik.Rcheck/00check.log’
for details.



Installation output

ORFik.Rcheck/00install.out

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###
### 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) (2023-03-16 r83985) -- "Unsuffered Consequences"
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Platform: x86_64-apple-darwin17.0 (64-bit)

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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, 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.   :1.000  
 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  
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
In addition: Warning message:
call dbDisconnect() when finished working with a connection 
[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 
176.199   6.136 241.374 

Example timings

ORFik.Rcheck/ORFik-Ex.timings

nameusersystemelapsed
DEG.analysis1.2390.1301.804
DEG.plot.static0.9690.0571.379
DTEG.analysis0.8810.0031.174
DTEG.plot0.8580.0041.123
ORFik.template.experiment0.9050.0051.170
ORFik.template.experiment.zf0.1270.0020.175
ORFikQC0.8490.0031.158
QCreport0.8560.0041.134
QCstats0.8520.0041.126
QCstats.plot0.8570.0041.132
RiboQC.plot0.8400.0061.102
STAR.align.folder0.0000.0000.001
STAR.align.single000
STAR.index000
STAR.install0.0000.0000.001
STAR.remove.crashed.genome0.0010.0000.001
TOP.Motif.ecdf000
artificial.orfs0.8550.0051.125
asTX1.4650.0101.940
assignTSSByCage0.0020.0010.003
bamVarName1.7230.0092.363
codon_usage6.5450.0588.840
codon_usage_exp15.336 0.50421.163
codon_usage_plot 7.052 0.47710.035
collapse.by.scores0.2110.0040.288
collapse.fastq0.0010.0000.001
collapseDuplicatedReads-GAlignmentPairs-method0.1370.0010.178
collapseDuplicatedReads-GAlignments-method0.0570.0010.077
collapseDuplicatedReads-GRanges-method0.0530.0010.074
collapseDuplicatedReads-data.table-method0.0530.0000.073
collapseDuplicatedReads0.0500.0000.065
combn.pairs0.8310.0071.094
computeFeatures 9.047 0.06312.026
computeFeaturesCage0.0000.0000.001
config000
config.exper000
config.save0.0000.0000.001
convertLibs0.8260.0041.121
convertToOneBasedRanges0.2610.0010.331
convert_bam_to_ofst0.2990.0150.424
convert_to_bigWig1.8680.0212.457
convert_to_covRle1.1100.0091.462
convert_to_covRleList1.6080.0112.245
countOverlapsW0.1570.0010.219
countTable0.8720.0041.189
countTable_regions0.8370.0041.171
covRle0.1050.0010.144
covRleFromGR0.1910.0020.262
covRleList0.0380.0010.049
coverageHeatMap2.4390.0103.155
coveragePerTiling1.4930.0041.915
coverageScorings0.0140.0010.021
create.experiment0.8610.0031.155
defineTrailer0.3360.0010.451
design-experiment-method0.9070.0041.186
detectRibosomeShifts0.0020.0010.003
disengagementScore1.0480.0031.339
distToCds0.4880.0010.651
distToTSS0.4310.0010.555
download.SRA000
download.SRA.metadata0.4570.0217.737
entropy1.6750.0052.284
experiment-class0.9520.0051.249
export.bed120.0430.0000.057
export.bigWig0.070.000.09
export.fstwig0.1260.0010.162
export.ofst-GAlignmentPairs-method0.1420.0010.180
export.ofst-GAlignments-method0.1390.0010.177
export.ofst-GRanges-method0.1420.0010.185
export.ofst0.1430.0010.188
export.wiggle0.0700.0010.092
extendLeaders2.2640.0232.998
extendTrailers1.3830.0151.837
filepath0.9390.0051.241
filterTranscripts2.9300.0153.842
fimport0.5560.0200.739
findFa0.0050.0010.009
findMapORFs1.1740.0051.534
findORFs0.3650.0030.456
findORFsFasta0.1310.0030.177
findPeaksPerGene2.3490.0193.191
findUORFs0.0020.0010.002
find_url_ebi0.0540.0084.368
firstEndPerGroup0.1170.0000.124
firstExonPerGroup0.1380.0000.175
firstStartPerGroup0.1180.0000.150
flankPerGroup0.1870.0010.241
floss0.6090.0030.801
fpkm0.2460.0010.337
fractionLength0.1090.0000.148
fread.bed0.0610.0110.107
gcContent0.7960.0031.161
geneToSymbol0.0010.0000.000
getGenomeAndAnnotation0.0000.0010.000
get_bioproject_candidates0.0000.0000.001
get_genome_fasta0.0010.0000.001
get_genome_gtf0.0000.0010.001
get_noncoding_rna000
get_phix_genome0.0000.0000.001
get_silva_rRNA000
groupGRangesBy0.1260.0010.181
groupings0.0850.0010.120
heatMapRegion0.9180.0031.318
import.ofst0.1450.0000.203
initiationScore2.1550.0053.080
insideOutsideORF1.7700.0062.513
install.fastp0.0010.0000.000
install.sratoolkit0.0000.0010.001
isInFrame0.4690.0010.665
isOverlapping0.4650.0010.656
kozakHeatmap0.0000.0010.003
kozakSequenceScore1.1530.0051.678
lastExonEndPerGroup0.1230.0010.184
lastExonPerGroup0.1390.0010.202
lastExonStartPerGroup0.1220.0010.173
libraryTypes0.8440.0031.266
list.experiments0.5650.0020.838
list.genomes0.0010.0000.001
loadRegion1.2240.0181.734
loadRegions1.4270.0192.162
loadTranscriptType000
loadTxdb0.2380.0070.371
longestORFs0.2770.0010.429
makeORFNames0.1660.0010.245
makeSummarizedExperimentFromBam0.9170.0041.296
makeTxdbFromGenome0.0000.0000.001
mergeFastq0.0000.0010.001
mergeLibs0.8630.0051.308
metaWindow0.4340.0010.651
numExonsPerGroup0.0850.0000.123
optimizedTranscriptLengths2.0100.0172.998
orfFrameDistributions2.3090.5393.970
orfScore1.8280.1813.043
organism-experiment-method0.8520.0241.236
outputLibs2.2540.4203.083
pSitePlot0.7580.0861.089
pcaExperiment2.7440.1073.771
pmapFromTranscriptF0.2470.0030.353
pmapToTranscriptF1.8360.0192.516
rankOrder0.1910.0000.257
read.experiment0.8250.0051.113
readBam0.2840.0140.404
readWidths0.0290.0000.039
reassignTSSbyCage1.2390.0121.690
reassignTxDbByCage0.0000.0000.001
reduceKeepAttr0.2560.0020.342
regionPerReadLength1.2190.5872.266
remove.experiments0.9320.0981.400
ribo_fft 7.147 0.38010.279
ribo_fft_plot5.4520.0487.584
ribosomeReleaseScore0.4190.0010.582
ribosomeStallingScore0.6060.0020.818
save.experiment0.8360.0051.168
scaledWindowPositions0.6420.0040.876
seqnamesPerGroup0.1270.0010.168
shiftFootprints0.0030.0010.003
shiftFootprintsByExperiment 2.279 0.08213.643
shiftPlots0.1090.0360.151
shifts.load0.9240.0841.310
simpleLibs0.9030.0671.279
sortPerGroup0.5680.0500.853
startCodons1.0370.0081.424
startDefinition0.0010.0000.001
startRegion1.1600.0101.648
startSites0.5870.0020.799
stopCodons0.9800.0031.321
stopDefinition0.0010.0000.001
stopRegion1.1520.0051.565
stopSites0.6140.0020.824
strandBool0.0200.0000.028
strandPerGroup0.1300.0010.183
subsetToFrame0.0380.0000.050
te.plot0.0000.0000.001
te.table0.8780.0041.195
te_rna.plot0.8700.0051.166
tile10.4300.0020.582
topMotif000
transcriptWindow2.2700.0333.173
translationalEff0.2980.0020.402
trimming.table000
txNames0.1050.0020.147
txNamesToGeneNames1.8770.0132.510
uORFSearchSpace1.2340.0111.668
uniqueGroups0.2940.0050.398
uniqueOrder0.4470.0020.597
unlistGrl0.1050.0010.146
widthPerGroup0.0890.0010.117
windowCoveragePlot1.2620.0131.739
windowPerGroup0.8670.0031.193
windowPerReadLength1.8520.0062.487