Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-24 13:08:05 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 machv2


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

raw results

Package 1349/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ORFik 1.14.7  (landing page)
Haakon Tjeldnes
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/ORFik
git_branch: RELEASE_3_14
git_last_commit: 3eb90dd
git_last_commit_date: 2022-01-17 04:54:42 -0500 (Mon, 17 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: ORFik
Version: 1.14.7
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_1.14.7.tar.gz
StartedAt: 2022-01-23 16:06:29 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 16:19:28 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 779.1 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_1.14.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ORFik.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ORFik/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ORFik’ version ‘1.14.7’
* 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
* 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’ ‘trimming.table’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DEG.plot.static: no visible binding for global variable ‘Regulation’
DEG.plot.static: no visible binding for global variable ‘meanCounts’
DEG.plot.static: no visible binding for global variable ‘LFC’
DTEG.plot: no visible binding for global variable ‘Regulation’
DTEG.plot: no visible binding for global variable ‘rna’
DTEG.plot: no visible binding for global variable ‘rfp’
QCplots: no visible binding for global variable ‘leaders’
QCplots: no visible binding for global variable ‘trailers’
QCstats.plot: no visible binding for global variable ‘variable’
QCstats.plot: no visible binding for global variable ‘sample_total’
QCstats.plot: no visible binding for global variable ‘value’
QCstats.plot: no visible global function definition for ‘.’
QCstats.plot: no visible binding for global variable ‘sample_id’
QCstats.plot: no visible binding for global variable ‘percentage’
QCstats.plot: no visible binding for global variable
  ‘perc_of_counts_per_sample’
QCstats.plot: no visible binding for global variable ‘read length’
RiboQC.plot: no visible binding for global variable ‘variable’
RiboQC.plot: no visible binding for global variable ‘sample_total’
RiboQC.plot: no visible binding for global variable ‘value’
RiboQC.plot: no visible global function definition for ‘.’
RiboQC.plot: no visible binding for global variable ‘sample_id’
RiboQC.plot: no visible binding for global variable ‘percentage’
RiboQC.plot: no visible binding for global variable ‘percent’
RiboQC.plot: no visible binding for global variable ‘frame’
STAR.multiQC: no visible binding for global variable ‘sample_id’
STAR.multiQC: no visible binding for global variable ‘value’
TOP.Motif.ecdf: no visible binding for global variable ‘seq1’
TOP.Motif.ecdf: no visible binding for global variable ‘TOP’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘percentage_mrna_aligned’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘mRNA’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘percentage_tx_aligned’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘Transcript’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘ratio_cds_mrna’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘CDS’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘ratio_cds_leader’
alignmentFeatureStatistics : <anonymous>: no visible binding for global
  variable ‘LEADERS’
allFeaturesHelper: no visible binding for global variable ‘te’
allFeaturesHelper: no visible binding for global variable ‘fpkmRFP’
allFeaturesHelper: no visible binding for global variable ‘fpkmRNA’
allFeaturesHelper: no visible binding for global variable ‘countRFP’
allFeaturesHelper: no visible binding for global variable ‘entropyRFP’
allFeaturesHelper: no visible binding for global variable
  ‘disengagementScores’
allFeaturesHelper: no visible binding for global variable ‘RRS’
allFeaturesHelper: no visible binding for global variable ‘RSS’
allFeaturesHelper: no visible binding for global variable ‘ORFScores’
allFeaturesHelper: no visible binding for global variable ‘ioScore’
allFeaturesHelper: no visible binding for global variable
  ‘startCodonCoverage’
allFeaturesHelper: no visible binding for global variable
  ‘startRegionRelative’
allFeaturesHelper: no visible binding for global variable ‘kozak’
allFeaturesHelper: no visible binding for global variable ‘StartCodons’
allFeaturesHelper: no visible binding for global variable ‘StopCodons’
allFeaturesHelper: no visible binding for global variable
  ‘fractionLengths’
allFeaturesHelper: no visible binding for global variable ‘distORFCDS’
allFeaturesHelper: no visible binding for global variable ‘inFrameCDS’
allFeaturesHelper: no visible binding for global variable
  ‘isOverlappingCds’
allFeaturesHelper: no visible binding for global variable ‘rankInTx’
appendZeroes: no visible binding for global variable ‘frame’
appendZeroes: no visible binding for global variable ‘position’
appendZeroes: no visible binding for global variable ‘count’
artificial.orfs: no visible binding for global variable ‘random’
artificial.orfs: no visible binding for global variable ‘pick’
artificial.orfs: no visible global function definition for ‘.’
collapse.by.scores: no visible global function definition for ‘.’
collapse.fastq: no visible binding for global variable ‘N’
coverageHeatMap: no visible binding for global variable ‘position’
coverageHeatMap: no visible binding for global variable ‘fraction’
coveragePerTiling: no visible binding for global variable ‘frame’
coveragePerTiling: no visible binding for global variable ‘position’
coverageScorings: no visible binding for global variable ‘count’
coverageScorings: no visible binding for global variable ‘zscore’
coverageScorings: no visible binding for global variable ‘windowMean’
coverageScorings: no visible binding for global variable ‘windowSD’
coverageScorings: no visible global function definition for ‘.’
coverageScorings: no visible binding for global variable ‘gene_sum’
coverageScorings: no visible binding for global variable ‘fraction’
detectRibosomeShifts: no visible global function definition for ‘.’
detectRibosomeShifts: no visible binding for global variable ‘size’
detectRibosomeShifts: no visible binding for global variable ‘fraction’
detectRibosomeShifts: no visible binding for global variable ‘pShifted’
detectRibosomeShifts: no visible binding for global variable
  ‘sum.count’
detectRibosomeShifts: no visible binding for global variable ‘count’
detectRibosomeShifts: no visible binding for global variable
  ‘frac.score’
download.SRA.metadata: no visible binding for global variable ‘spots’
download.SRA.metadata: no visible binding for global variable ‘MONTH’
download.SRA.metadata: no visible binding for global variable
  ‘ReleaseDate’
download.SRA.metadata: no visible binding for global variable ‘YEAR’
download.SRA.metadata: no visible binding for global variable ‘Run’
download.SRA.metadata: no visible binding for global variable
  ‘LIBRARYTYPE’
download.SRA.metadata: no visible binding for global variable
  ‘LibraryStrategy’
entropy: no visible binding for global variable ‘Hx’
entropy: no visible binding for global variable ‘codonSums’
entropy: no visible global function definition for ‘.’
filterExtremePeakGenes: no visible binding for global variable ‘count’
filterExtremePeakGenes: no visible binding for global variable
  ‘median_per_gene’
filterExtremePeakGenes: no visible global function definition for ‘.’
filterTranscripts: no visible binding for global variable ‘utr5_len’
filterTranscripts: no visible binding for global variable ‘utr3_len’
findNGSPairs: no visible global function definition for ‘.’
findNGSPairs: no visible binding for global variable ‘forward’
findPeaksPerGene: no visible binding for global variable ‘sum_per_gene’
findPeaksPerGene: no visible binding for global variable ‘count’
findPeaksPerGene: no visible binding for global variable
  ‘mean_per_gene’
findPeaksPerGene: no visible binding for global variable ‘sd_per_gene’
findPeaksPerGene: no visible binding for global variable ‘zscore’
findPeaksPerGene: no visible binding for global variable ‘gene_id’
find_url_ebi_safe: no visible binding for global variable
  ‘run_accession’
flankPerGroup: no visible global function definition for ‘.’
flankPerGroup: no visible binding for global variable ‘group_name’
floss: no visible binding for global variable ‘ORFGrouping’
floss: no visible binding for global variable ‘widths’
floss: no visible global function definition for ‘.’
floss: no visible binding for global variable ‘CDSGrouping’
floss: no visible binding for global variable ‘fraction.x’
floss: no visible binding for global variable ‘fraction.y’
gSort: no visible binding for global variable ‘grnames’
getNGenesCoverage: no visible global function definition for ‘.’
getNGenesCoverage: no visible binding for global variable ‘fraction’
get_phix_genome: no visible binding for global variable ‘phix.url’
initiationScore: no visible global function definition for ‘.’
initiationScore: no visible binding for global variable ‘dif’
initiationScore: no visible binding for global variable ‘fraction’
initiationScore: no visible binding for global variable ‘difPer’
isPeriodic: no visible binding for global variable ‘spec’
kozakHeatmap: no visible global function definition for ‘.’
kozakHeatmap: no visible binding for global variable ‘variable’
kozakHeatmap: no visible binding for global variable ‘value’
kozakHeatmap: no visible binding for global variable
  ‘count_seq_pos_with_count’
kozakHeatmap: no visible binding for global variable ‘median_score’
kozak_IR_ranking: no visible global function definition for ‘.’
kozak_IR_ranking: no visible binding for global variable ‘IR’
kozak_IR_ranking: no visible binding for global variable
  ‘upstream_kozak_strength’
kozak_IR_ranking: no visible binding for global variable ‘count’
kozak_IR_ranking: no visible binding for global variable ‘mean_IR’
list.genomes: no visible binding for global variable ‘STAR_index’
longestORFs: no visible global function definition for ‘.’
metaWindow: no visible binding for global variable ‘position’
metaWindow: no visible binding for global variable ‘frame’
orfFrameDistributions : <anonymous>: no visible binding for global
  variable ‘fraction’
orfFrameDistributions: no visible binding for global variable ‘percent’
orfFrameDistributions: no visible binding for global variable
  ‘fraction’
orfFrameDistributions: no visible binding for global variable
  ‘percent_length’
orfFrameDistributions: no visible global function definition for ‘.’
orfFrameDistributions: no visible binding for global variable
  ‘best_frame’
orfScore: no visible binding for global variable ‘frame’
orfScore: no visible binding for global variable ‘frame_one_RP’
orfScore: no visible binding for global variable ‘frame_two_RP’
pSitePlot: no visible binding for global variable ‘count’
pSitePlot: no visible binding for global variable ‘frame’
pSitePlot: no visible binding for global variable ‘position’
pcaExperiment: no visible binding for global variable ‘PC1’
pcaExperiment: no visible binding for global variable ‘PC2’
readLengthTable: no visible binding for global variable
  ‘counts_per_sample’
readLengthTable: no visible binding for global variable
  ‘perc_of_counts_per_sample’
regionPerReadLength : <anonymous>: no visible binding for global
  variable ‘fraction’
remakeTxdbExonIds: no visible global function definition for ‘.’
remakeTxdbExonIds: no visible binding for global variable ‘chr’
removeTxdbExons: no visible binding for global variable ‘exon_rank’
removeTxdbExons: no visible binding for global variable ‘ranks’
rnaNormalize: no visible binding for global variable ‘feature’
scaledWindowPositions: no visible binding for global variable
  ‘scalingFactor’
scaledWindowPositions: no visible binding for global variable
  ‘position’
scaledWindowPositions: no visible global function definition for ‘.’
scoreSummarizedExperiment: no visible global function definition for
  ‘rowSums2’
shiftPlots : <anonymous>: no visible binding for global variable
  ‘frame’
shiftPlots : <anonymous>: no visible binding for global variable
  ‘position’
te.plot: no visible global function definition for ‘rowMin’
te.plot: no visible binding for global variable ‘variable’
te.plot: no visible binding for global variable ‘LFC_TE’
te.plot: no visible binding for global variable ‘rfp_log2’
te.plot: no visible binding for global variable ‘rna_log2’
te.plot: no visible binding for global variable ‘rna_log10’
te.table: no visible global function definition for ‘rowMin’
te.table: no visible binding for global variable ‘variable’
te.table: no visible binding for global variable ‘TE_log2’
te.table: no visible binding for global variable ‘rfp_log2’
te.table: no visible binding for global variable ‘rna_log2’
te_rna.plot: no visible binding for global variable ‘subtitle’
te_rna.plot: no visible binding for global variable ‘rna_log10’
te_rna.plot: no visible binding for global variable ‘TE_log2’
topMotif: no visible binding for global variable ‘seq1’
topMotif: no visible binding for global variable ‘seq2’
topMotif: no visible binding for global variable ‘seq3’
topMotif: no visible binding for global variable ‘seq4’
topMotif: no visible binding for global variable ‘seq5’
transcriptWindow: no visible binding for global variable ‘fractions’
transcriptWindow: no visible binding for global variable ‘feature’
windowCoveragePlot: no visible binding for global variable ‘feature’
windowCoveragePlot: no visible binding for global variable ‘fraction’
windowCoveragePlot: no visible binding for global variable
  ‘fraction_min’
windowCoveragePlot: no visible binding for global variable ‘position’
collapseDuplicatedReads,GAlignmentPairs: no visible global function
  definition for ‘.’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable ‘start1’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable ‘start2’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable ‘cigar1’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
  variable ‘cigar2’
collapseDuplicatedReads,GAlignments: no visible global function
  definition for ‘.’
collapseDuplicatedReads,GRanges: no visible binding for global variable
  ‘size’
collapseDuplicatedReads,GRanges: no visible global function definition
  for ‘.’
design,experiment: no visible binding for global variable ‘..formula’
Undefined global functions or variables:
  . ..formula CDS CDSGrouping Hx IR LEADERS LFC LFC_TE LIBRARYTYPE
  LibraryStrategy MONTH N ORFGrouping ORFScores PC1 PC2 RRS RSS
  Regulation ReleaseDate Run STAR_index StartCodons StopCodons TE_log2
  TOP Transcript YEAR best_frame chr cigar1 cigar2 codonSums count
  countRFP count_seq_pos_with_count counts_per_sample dif difPer
  disengagementScores distORFCDS entropyRFP exon_rank feature forward
  fpkmRFP fpkmRNA frac.score fraction fraction.x fraction.y
  fractionLengths fraction_min fractions frame frame_one_RP
  frame_two_RP gene_id gene_sum grnames group_name inFrameCDS ioScore
  isOverlappingCds kozak leaders mRNA meanCounts mean_IR mean_per_gene
  median_per_gene median_score pShifted perc_of_counts_per_sample
  percent percent_length percentage percentage_mrna_aligned
  percentage_tx_aligned phix.url pick position random rankInTx ranks
  ratio_cds_leader ratio_cds_mrna read length rfp rfp_log2 rna
  rna_log10 rna_log2 rowMin rowSums2 run_accession sample_id
  sample_total scalingFactor sd_per_gene seq1 seq2 seq3 seq4 seq5 size
  spec spots start1 start2 startCodonCoverage startRegionRelative
  subtitle sum.count sum_per_gene te trailers upstream_kozak_strength
  utr3_len utr5_len value variable widths windowMean windowSD zscore
Consider adding
  importFrom("base", "length")
  importFrom("graphics", "frame")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
computeFeatures             7.874  0.032   7.915
orfFrameDistributions       3.972  0.696   7.904
shiftFootprintsByExperiment 2.290  0.089  16.311
find_url_ebi                0.043  0.008   6.491
* 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-3.14-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/4.1/Resources/library’
* installing *source* package ‘ORFik’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/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/4.1/Resources/library/00LOCK-ORFik/00new/ORFik/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ORFik)

Tests output

ORFik.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-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, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

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

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: Rsamtools
> 
> test_check("ORFik")
     widths       group.size  
 Min.   : 6.0   Min.   :2.00  
 1st Qu.: 7.5   1st Qu.:2.25  
 Median : 9.0   Median :2.50  
 Mean   : 9.0   Mean   :2.50  
 3rd Qu.:10.5   3rd Qu.:2.75  
 Max.   :12.0   Max.   :3.00  
Error in x$.self$finalize() : attempt to apply non-function
[1] "CAGE_Mutant_r1"
[1] "CAGE_Mutant_r2"
[1] "CAGE_WT_r1"
[1] "CAGE_WT_r2"
[1] "PAS_Mutant_r1"
[1] "PAS_Mutant_r2"
[1] "PAS_WT_r1"
[1] "PAS_WT_r2"
[1] "RFP_Mutant_r1"
[1] "RFP_Mutant_r2"
[1] "RFP_WT_r1"
[1] "RFP_WT_r2"
[1] "RNA_Mutant_r1"
[1] "RNA_Mutant_r2"
[1] "RNA_WT_r1"
[1] "RNA_WT_r2"
[1] "RFP"
[1] "RFP"
[1] "RFP"
[1] "RFP"
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 361 ]
> 
> proc.time()
   user  system elapsed 
130.601   4.187 135.018 

Example timings

ORFik.Rcheck/ORFik-Ex.timings

nameusersystemelapsed
DEG.analysis0.7000.0430.747
DEG.plot.static0.5960.0100.607
DTEG.analysis0.5480.0050.554
DTEG.plot1.4190.0381.456
ORFik.template.experiment0.4960.0030.500
ORFik.template.experiment.zf0.0650.0010.066
ORFikQC0.4070.0030.411
QCreport0.4490.0270.476
QCstats0.4140.0390.452
QCstats.plot0.5130.0450.560
RiboQC.plot0.5780.0420.621
STAR.align.folder0.0000.0010.001
STAR.align.single0.0000.0010.001
STAR.index000
STAR.install000
STAR.remove.crashed.genome0.0000.0000.001
TOP.Motif.ecdf0.0000.0010.001
artificial.orfs0.5520.0040.557
asTX1.4340.0131.451
assignTSSByCage0.0010.0000.002
bamVarName0.7340.0080.743
collapse.by.scores0.2240.0020.227
collapse.fastq0.0000.0000.001
collapseDuplicatedReads-GAlignmentPairs-method0.1510.0000.152
collapseDuplicatedReads-GAlignments-method0.0740.0010.074
collapseDuplicatedReads-GRanges-method0.0650.0020.068
collapseDuplicatedReads0.0690.0010.070
combn.pairs0.5810.0020.583
computeFeatures7.8740.0327.915
computeFeaturesCage0.0000.0000.001
config0.0010.0000.000
config.exper000
config.save0.0000.0010.001
convertLibs0.4830.0030.486
convertToOneBasedRanges0.2720.0030.276
countOverlapsW0.1500.0010.151
countTable0.5230.0050.528
countTable_regions0.6020.0020.604
coverageHeatMap2.0460.0132.060
coveragePerTiling1.2670.0031.271
coverageScorings0.0120.0010.013
create.experiment0.4160.0030.418
defineTrailer0.1930.0010.193
design-experiment-method0.4630.0030.467
detectRibosomeShifts0.0020.0010.002
disengagementScore0.9000.0020.903
distToCds0.3250.0010.326
distToTSS0.4330.0010.435
download.SRA0.0010.0000.001
download.SRA.metadata0.4130.0161.480
entropy1.4070.0091.420
experiment-class0.5650.0060.574
export.bed120.0530.0000.053
export.bigWig0.0660.0000.066
export.ofst-GAlignmentPairs-method0.1320.0010.132
export.ofst-GAlignments-method0.1400.0010.141
export.ofst-GRanges-method0.1460.0010.146
export.ofst0.1500.0010.151
export.wiggle0.0870.0010.087
extendLeaders2.0510.0242.099
extendTrailers1.2630.0141.279
filepath0.5480.0040.552
filterTranscripts2.3910.0092.402
fimport0.5400.0230.563
findFa0.0090.0010.009
findMapORFs1.0690.0071.078
findORFs0.2990.0040.304
findORFsFasta0.1330.0050.139
findPeaksPerGene1.8130.0111.829
findUORFs0.0010.0010.002
find_url_ebi0.0430.0086.491
firstEndPerGroup0.1320.0010.133
firstExonPerGroup0.1580.0020.160
firstStartPerGroup0.1440.0010.144
flankPerGroup0.2170.0020.218
floss0.4540.0020.456
fpkm0.2050.0010.207
fractionLength0.1030.0000.103
fread.bed0.0710.0080.081
gcContent0.7130.0030.715
getGenomeAndAnnotation0.0000.0010.001
get_genome_fasta0.0000.0010.001
get_genome_gtf0.0000.0010.001
get_noncoding_rna0.0000.0010.000
get_phix_genome0.0010.0000.001
get_silva_rRNA000
groupGRangesBy0.0870.0010.088
groupings0.070.000.07
heatMapRegion0.4530.0010.456
import.ofst0.1190.0010.119
initiationScore1.9710.0041.978
insideOutsideORF1.4830.0061.493
install.fastp0.0010.0000.000
install.sratoolkit000
isInFrame0.4660.0010.468
isOverlapping0.4630.0020.465
kozakHeatmap0.0000.0010.001
kozakSequenceScore1.1290.0071.138
lastExonEndPerGroup0.1420.0010.143
lastExonPerGroup0.1220.0010.123
lastExonStartPerGroup0.1350.0010.135
libraryTypes0.5020.0010.504
list.experiments0.4060.0020.410
list.genomes0.0010.0010.001
loadRegion1.2680.0181.673
loadRegions1.4080.0151.830
loadTranscriptType000
loadTxdb0.2260.0070.362
longestORFs0.3250.0080.609
makeORFNames0.2320.0020.389
makeSummarizedExperimentFromBam0.6730.0041.299
makeTxdbFromGenome0.0000.0010.002
mergeFastq0.0000.0010.002
metaWindow0.4820.0030.889
numExonsPerGroup0.1390.0020.266
orfFrameDistributions3.9720.6967.904
orfScore1.9210.1912.953
organism-experiment-method0.6050.0490.668
outputLibs2.2440.8993.494
pSitePlot0.6260.0690.696
pcaExperiment2.1250.1422.269
pmapFromTranscriptF0.2010.0030.203
pmapToTranscriptF1.7240.0201.747
rankOrder0.1740.0000.174
read.experiment0.4200.0030.424
readBam0.2700.0130.284
readWidths0.0370.0010.037
reassignTSSbyCage1.3520.0121.758
reassignTxDbByCage000
reduceKeepAttr0.3170.0030.381
regionPerReadLength1.2710.6532.453
remove.experiments0.6510.0771.229
ribosomeReleaseScore0.5320.0531.090
ribosomeStallingScore0.7370.0651.462
save.experiment0.6530.0461.246
scaledWindowPositions0.8280.0711.634
seqnamesPerGroup0.1610.0060.298
shiftFootprints0.0020.0010.004
shiftFootprintsByExperiment 2.290 0.08916.311
shiftPlots0.0700.0220.091
shifts.load0.6840.0771.405
simpleLibs0.6350.0461.293
sortPerGroup0.6750.0631.453
startCodons1.2020.0972.374
startDefinition0.0000.0010.002
startRegion1.3650.0232.550
startSites0.6960.0021.306
stopCodons1.1240.0072.030
stopDefinition0.0010.0000.001
stopRegion1.2670.0071.882
stopSites0.6590.0040.987
strandBool0.0270.0010.050
strandPerGroup0.1610.0020.232
subsetToFrame0.0520.0010.164
te.plot0.0000.0000.001
te.table0.5990.0041.085
te_rna.plot0.6200.0051.160
tile10.5070.0050.928
topMotif0.0000.0010.001
transcriptWindow1.9940.0273.609
translationalEff0.3480.0020.623
trimming.table0.0000.0000.001
txNames0.1100.0010.201
txNamesToGeneNames1.9810.0133.564
uORFSearchSpace1.3630.0112.600
uniqueGroups0.3850.0060.746
uniqueOrder0.4970.0020.758
unlistGrl0.1110.0010.112
widthPerGroup0.1090.0010.110
windowCoveragePlot1.0950.0131.110
windowPerGroup0.9490.0050.955
windowPerReadLength1.9240.0081.933