Haakon Tjeldnes
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/ORFik |
| Branch: RELEASE_3_12 |
| Last Commit: 3f2976e |
| Last Changed Date: 2021-03-26 10:15:54 -0400 (Fri, 26 Mar 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:36:02 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the ORFik package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1278/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ORFik 1.10.13 (landing page) Haakon Tjeldnes
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ORFik |
| Version: 1.10.13 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ORFik.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ORFik_1.10.13.tar.gz |
| StartedAt: 2021-05-06 04:26:25 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 04:36:18 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 592.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ORFik.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ORFik.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ORFik_1.10.13.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/ORFik.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.10.13’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ORFik’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘GenomicFeatures:::.merge_seqinfo_and_infer_missing_seqlengths’
‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::normarg_mcols’
‘biomartr:::getENSEMBL.Seq’ ‘biomartr:::getENSEMBL.gtf’
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘findFa’ ‘find_url_ebi’ ‘hasHits’ ‘trimming.table’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DTEG.plot: no visible binding for global variable ‘rna’
DTEG.plot: no visible binding for global variable ‘rfp’
DTEG.plot: no visible binding for global variable ‘Regulation’
QC_count_tables: no visible binding for global variable ‘leaders’
QC_count_tables : <anonymous>: no visible binding for global variable
‘percentage_mrna_aligned’
QC_count_tables : <anonymous>: no visible binding for global variable
‘mRNA’
QC_count_tables : <anonymous>: no visible binding for global variable
‘ratio_cds_mrna’
QC_count_tables : <anonymous>: no visible binding for global variable
‘CDS’
QC_count_tables : <anonymous>: no visible binding for global variable
‘ratio_cds_leader’
QC_count_tables : <anonymous>: no visible binding for global variable
‘LEADERS’
QC_count_tables: no visible binding for global variable ‘tx’
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 : <anonymous>: no visible binding for global variable
‘fraction’
RiboQC.plot: no visible binding for global variable ‘percent’
RiboQC.plot: no visible binding for global variable ‘fraction’
RiboQC.plot: no visible binding for global variable ‘frame’
STAR.align.folder: no visible global function definition for
‘detectCores’
STAR.align.single: no visible global function definition for
‘detectCores’
STAR.index: no visible global function definition for ‘detectCores’
STAR.multiQC: no visible binding for global variable ‘sample_id’
STAR.multiQC: no visible binding for global variable ‘value’
TOP.Motif.ecdf: no visible binding for global variable ‘seq1’
TOP.Motif.ecdf: no visible binding for global variable ‘TOP’
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’
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 ‘.’
coverageHeatMap: no visible binding for global variable ‘position’
coverageHeatMap: no visible binding for global variable ‘fraction’
coveragePerTiling: no visible binding for global variable ‘ones’
coveragePerTiling: no visible binding for global variable ‘position’
coveragePerTiling: no visible binding for global variable ‘frame’
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’
detectRibosomeShifts: no visible global function definition for ‘.’
detectRibosomeShifts: no visible binding for global variable ‘size’
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 ‘fraction’
download.SRA.metadata: no visible binding for global variable ‘spots’
download.SRA.metadata: no visible binding for global variable ‘Run’
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’
filterTranscripts: no visible binding for global variable ‘tx_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’
floss: no visible binding for global variable ‘ORFGrouping’
floss: no visible binding for global variable ‘widths’
floss: no visible global function definition for ‘.’
floss: no visible binding for global variable ‘CDSGrouping’
floss: no visible binding for global variable ‘fraction.x’
floss: no visible binding for global variable ‘fraction.y’
gSort: no visible binding for global variable ‘grnames’
getNGenesCoverage: no visible global function definition for ‘.’
getNGenesCoverage: no visible binding for global variable ‘fraction’
initiationScore: no visible global function definition for ‘.’
initiationScore: no visible binding for global variable ‘dif’
initiationScore: no visible binding for global variable ‘fraction’
initiationScore: no visible binding for global variable ‘difPer’
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.experiments: no visible binding for global variable ‘name’
longestORFs: no visible global function definition for ‘.’
metaWindow: no visible binding for global variable ‘position’
metaWindow: no visible binding for global variable ‘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’
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’
te.plot: no visible global function definition for ‘rowMin’
te.plot: no visible binding for global variable ‘variable’
te.plot: no visible binding for global variable ‘LFC_TE’
te.plot: no visible binding for global variable ‘rfp_log2’
te.plot: no visible binding for global variable ‘rna_log2’
te.plot: no visible binding for global variable ‘rna_log10’
te.table: no visible global function definition for ‘rowMin’
te.table: no visible binding for global variable ‘variable’
te.table: no visible binding for global variable ‘TE_log2’
te.table: no visible binding for global variable ‘rfp_log2’
te.table: no visible binding for global variable ‘rna_log2’
te_rna.plot: no visible binding for global variable ‘df.rfp’
te_rna.plot: no visible binding for global variable ‘df.rna’
te_rna.plot: no visible binding for global variable ‘subtitle’
te_rna.plot: no visible binding for global variable ‘rna_log10’
te_rna.plot: no visible binding for global variable ‘TE_log2’
topMotif: no visible binding for global variable ‘seq1’
topMotif: no visible binding for global variable ‘seq2’
topMotif: no visible binding for global variable ‘seq3’
topMotif: no visible binding for global variable ‘seq4’
topMotif: no visible binding for global variable ‘seq5’
transcriptWindow: no visible binding for global variable ‘fractions’
transcriptWindow1: no visible binding for global variable ‘leaders’
windowCoveragePlot: no visible binding for global variable ‘feature’
windowCoveragePlot: no visible binding for global variable ‘fraction’
windowCoveragePlot: no visible binding for global variable
‘fraction_min’
windowCoveragePlot: no visible binding for global variable ‘position’
collapseDuplicatedReads,GAlignmentPairs: no visible global function
definition for ‘.’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
variable ‘start1’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
variable ‘start2’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
variable ‘cigar1’
collapseDuplicatedReads,GAlignmentPairs: no visible binding for global
variable ‘cigar2’
collapseDuplicatedReads,GAlignments: no visible global function
definition for ‘.’
collapseDuplicatedReads,GRanges: no visible binding for global variable
‘size’
collapseDuplicatedReads,GRanges: no visible global function definition
for ‘.’
Undefined global functions or variables:
. CDS CDSGrouping Hx IR LEADERS LFC_TE ORFGrouping ORFScores RRS RSS
Regulation Run StartCodons StopCodons TE_log2 TOP chr cigar1 cigar2
codonSums count countRFP count_seq_pos_with_count counts_per_sample
detectCores df.rfp df.rna dif difPer disengagementScores distORFCDS
entropyRFP exon_rank feature forward fpkmRFP fpkmRNA fraction
fraction.x fraction.y fractionLengths fraction_min fractions frame
frame_one_RP frame_two_RP gene_id gene_sum grnames inFrameCDS ioScore
isOverlappingCds kozak leaders mRNA mean_IR mean_per_gene
median_per_gene median_score name ones pShifted
perc_of_counts_per_sample percent percentage percentage_mrna_aligned
pick position random rankInTx ranks ratio_cds_leader ratio_cds_mrna
read length rfp rfp_log2 rna rna_log10 rna_log2 rowMin rowSums2
sample_id sample_total scalingFactor sd_per_gene seq1 seq2 seq3 seq4
seq5 size spots start1 start2 startCodonCoverage startRegionRelative
subtitle sum.count sum_per_gene te trailers tx tx_len
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
shiftFootprintsByExperiment 5.913 0.058 6.021
computeFeatures 5.731 0.026 5.767
* 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-3.12-bioc/meat/ORFik.Rcheck/00check.log’
for details.
ORFik.Rcheck/00install.out
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ORFik
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c findORFsHelpers.cpp -o findORFsHelpers.o
In file included from findORFsHelpers.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c findOrfs.cpp -o findOrfs.o
In file included from findOrfs.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c findOrfsFasta.cpp -o findOrfsFasta.o
In file included from findOrfsFasta.cpp:10:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o
In file included from pmapFromTranscripts.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c pmapToTranscripts.cpp -o pmapToTranscripts.o
In file included from pmapToTranscripts.cpp:9:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
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/4.0/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)
ORFik.Rcheck/tests/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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 object is masked from 'package:base':
expand.grid
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
>
> test_check("ORFik")
widths group.size
Min. : 6 Min. :2.00
1st Qu.: 9 1st Qu.:2.25
Median :12 Median :2.50
Mean :12 Mean :2.50
3rd Qu.:15 3rd Qu.:2.75
Max. :18 Max. :3.00
Error in x$.self$finalize() : attempt to apply non-function
[1] "CAGE_heart"
[1] "RFP_heart"
[1] "RFP"
[1] "RNA_heart"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 331 ]
Warning message:
call dbDisconnect() when finished working with a connection
>
> proc.time()
user system elapsed
94.347 3.288 96.921
ORFik.Rcheck/ORFik-Ex.timings
| name | user | system | elapsed | |
| DTEG.analysis | 0.000 | 0.001 | 0.001 | |
| DTEG.plot | 0.001 | 0.000 | 0.001 | |
| ORFik.template.experiment | 0.438 | 0.017 | 0.455 | |
| ORFikQC | 0.307 | 0.034 | 0.341 | |
| QCreport | 0.308 | 0.034 | 0.343 | |
| QCstats | 0.975 | 0.028 | 1.006 | |
| QCstats.plot | 0.278 | 0.001 | 0.279 | |
| RiboQC.plot | 0.312 | 0.004 | 0.316 | |
| STAR.align.folder | 0 | 0 | 0 | |
| STAR.align.single | 0.000 | 0.000 | 0.001 | |
| STAR.index | 0.001 | 0.000 | 0.001 | |
| STAR.install | 0.000 | 0.000 | 0.001 | |
| STAR.remove.crashed.genome | 0 | 0 | 0 | |
| TOP.Motif.ecdf | 0.001 | 0.000 | 0.001 | |
| assignTSSByCage | 0.002 | 0.000 | 0.002 | |
| bamVarName | 0.605 | 0.025 | 0.631 | |
| collapse.by.scores | 0.233 | 0.002 | 0.236 | |
| collapse.fastq | 0 | 0 | 0 | |
| collapseDuplicatedReads-GAlignmentPairs-method | 0.073 | 0.001 | 0.074 | |
| collapseDuplicatedReads-GAlignments-method | 0.034 | 0.001 | 0.035 | |
| collapseDuplicatedReads-GRanges-method | 0.034 | 0.001 | 0.035 | |
| collapseDuplicatedReads | 0.031 | 0.001 | 0.032 | |
| computeFeatures | 5.731 | 0.026 | 5.767 | |
| computeFeaturesCage | 0.000 | 0.001 | 0.001 | |
| config.exper | 0.000 | 0.001 | 0.000 | |
| convertLibs | 0.329 | 0.002 | 0.331 | |
| convertToOneBasedRanges | 0.162 | 0.002 | 0.164 | |
| countOverlapsW | 0.109 | 0.000 | 0.109 | |
| countTable | 0.340 | 0.002 | 0.342 | |
| coverageHeatMap | 1.571 | 0.011 | 1.584 | |
| coveragePerTiling | 0.852 | 0.005 | 0.858 | |
| coverageScorings | 0.009 | 0.000 | 0.009 | |
| create.experiment | 0.357 | 0.001 | 0.359 | |
| defineTrailer | 0.226 | 0.001 | 0.228 | |
| detectRibosomeShifts | 0.001 | 0.001 | 0.003 | |
| disengagementScore | 0.732 | 0.007 | 0.742 | |
| distToCds | 0.340 | 0.001 | 0.343 | |
| distToTSS | 0.329 | 0.001 | 0.330 | |
| download.SRA | 0.000 | 0.001 | 0.001 | |
| download.SRA.metadata | 0.001 | 0.001 | 0.001 | |
| entropy | 0.967 | 0.002 | 0.969 | |
| experiment-class | 0.270 | 0.002 | 0.271 | |
| export.bed12 | 0.027 | 0.000 | 0.027 | |
| export.ofst-GAlignmentPairs-method | 0.080 | 0.001 | 0.080 | |
| export.ofst-GAlignments-method | 0.094 | 0.001 | 0.094 | |
| export.ofst-GRanges-method | 0.092 | 0.001 | 0.093 | |
| export.ofst | 0.101 | 0.001 | 0.102 | |
| export.wiggle | 0.056 | 0.001 | 0.057 | |
| extendLeaders | 1.591 | 0.017 | 1.610 | |
| extendTrailers | 0.939 | 0.015 | 0.956 | |
| filepath | 0.361 | 0.002 | 0.363 | |
| filterTranscripts | 1.940 | 0.007 | 1.950 | |
| fimport | 0.444 | 0.015 | 0.462 | |
| findFa | 0.008 | 0.001 | 0.009 | |
| findMapORFs | 0.964 | 0.008 | 0.975 | |
| findORFs | 0.252 | 0.003 | 0.256 | |
| findORFsFasta | 0.142 | 0.009 | 0.152 | |
| findPeaksPerGene | 2.009 | 0.014 | 2.029 | |
| findUORFs | 0.001 | 0.000 | 0.001 | |
| firstEndPerGroup | 0.112 | 0.001 | 0.113 | |
| firstExonPerGroup | 0.124 | 0.003 | 0.128 | |
| firstStartPerGroup | 0.111 | 0.002 | 0.114 | |
| floss | 0.419 | 0.004 | 0.425 | |
| fpkm | 0.175 | 0.003 | 0.179 | |
| fractionLength | 0.085 | 0.001 | 0.084 | |
| fread.bed | 0.058 | 0.009 | 0.068 | |
| gcContent | 0.768 | 0.006 | 0.776 | |
| getGenomeAndAnnotation | 0 | 0 | 0 | |
| get_genome_fasta | 0.000 | 0.000 | 0.001 | |
| get_genome_gtf | 0.001 | 0.000 | 0.000 | |
| get_noncoding_rna | 0.001 | 0.000 | 0.000 | |
| get_phix_genome | 0.000 | 0.000 | 0.001 | |
| get_silva_rRNA | 0 | 0 | 0 | |
| groupGRangesBy | 0.117 | 0.001 | 0.118 | |
| groupings | 0.080 | 0.001 | 0.082 | |
| heatMapRegion | 0.421 | 0.003 | 0.425 | |
| import.ofst | 0.072 | 0.000 | 0.072 | |
| initiationScore | 1.232 | 0.007 | 1.243 | |
| insideOutsideORF | 1.227 | 0.004 | 1.232 | |
| install.fastp | 0 | 0 | 0 | |
| install.sratoolkit | 0.001 | 0.000 | 0.001 | |
| isInFrame | 0.284 | 0.002 | 0.286 | |
| isOverlapping | 0.297 | 0.001 | 0.299 | |
| kozakHeatmap | 0.000 | 0.000 | 0.001 | |
| kozakSequenceScore | 0.599 | 0.002 | 0.601 | |
| lastExonEndPerGroup | 0.104 | 0.001 | 0.106 | |
| lastExonPerGroup | 0.101 | 0.001 | 0.103 | |
| lastExonStartPerGroup | 0.089 | 0.002 | 0.091 | |
| list.experiments | 0.043 | 0.001 | 0.045 | |
| loadRegion | 1.744 | 0.012 | 1.759 | |
| loadRegions | 1.181 | 0.004 | 1.187 | |
| loadTxdb | 0.151 | 0.004 | 0.155 | |
| longestORFs | 0.242 | 0.001 | 0.243 | |
| makeORFNames | 0.142 | 0.001 | 0.144 | |
| makeSummarizedExperimentFromBam | 0.347 | 0.003 | 0.380 | |
| mergeFastq | 0.000 | 0.001 | 0.001 | |
| metaWindow | 0.279 | 0.001 | 0.281 | |
| numExonsPerGroup | 0.084 | 0.001 | 0.085 | |
| orfScore | 0.991 | 0.003 | 0.995 | |
| organism.df | 0.340 | 0.002 | 0.344 | |
| outputLibs | 0.330 | 0.001 | 0.332 | |
| pSitePlot | 0.408 | 0.002 | 0.410 | |
| pmapFromTranscriptF | 0.131 | 0.001 | 0.133 | |
| pmapToTranscriptF | 0.110 | 0.001 | 0.111 | |
| rankOrder | 0.090 | 0.001 | 0.091 | |
| read.experiment | 0.265 | 0.001 | 0.266 | |
| readBam | 0.172 | 0.006 | 0.178 | |
| readWidths | 0.02 | 0.00 | 0.02 | |
| reassignTSSbyCage | 0.822 | 0.006 | 0.831 | |
| reassignTxDbByCage | 0.000 | 0.001 | 0.000 | |
| reduceKeepAttr | 0.185 | 0.001 | 0.187 | |
| regionPerReadLength | 2.229 | 0.035 | 2.267 | |
| remove.experiments | 0.295 | 0.001 | 0.296 | |
| ribosomeReleaseScore | 0.233 | 0.001 | 0.233 | |
| ribosomeStallingScore | 0.512 | 0.012 | 0.525 | |
| save.experiment | 0.393 | 0.023 | 0.417 | |
| scaledWindowPositions | 0.435 | 0.003 | 0.438 | |
| seqnamesPerGroup | 0.081 | 0.001 | 0.081 | |
| shiftFootprints | 0.001 | 0.001 | 0.002 | |
| shiftFootprintsByExperiment | 5.913 | 0.058 | 6.021 | |
| shiftPlots | 0.347 | 0.002 | 0.350 | |
| shifts.load | 0.353 | 0.002 | 0.354 | |
| simpleLibs | 0.361 | 0.002 | 0.363 | |
| sortPerGroup | 0.436 | 0.003 | 0.440 | |
| startCodons | 0.948 | 0.004 | 0.953 | |
| startDefinition | 0.001 | 0.000 | 0.001 | |
| startRegion | 0.768 | 0.012 | 0.781 | |
| startSites | 0.520 | 0.001 | 0.522 | |
| stopCodons | 0.980 | 0.003 | 0.985 | |
| stopDefinition | 0.001 | 0.000 | 0.001 | |
| stopRegion | 0.771 | 0.008 | 0.784 | |
| stopSites | 0.579 | 0.002 | 0.581 | |
| strandBool | 0.009 | 0.000 | 0.010 | |
| strandPerGroup | 0.077 | 0.001 | 0.078 | |
| te.plot | 0.000 | 0.000 | 0.001 | |
| te.table | 0.000 | 0.001 | 0.000 | |
| te_rna.plot | 0.000 | 0.001 | 0.001 | |
| tile1 | 0.365 | 0.003 | 0.368 | |
| topMotif | 0.000 | 0.001 | 0.001 | |
| transcriptWindow | 1.653 | 0.012 | 1.672 | |
| translationalEff | 0.152 | 0.000 | 0.153 | |
| txNames | 0.057 | 0.000 | 0.057 | |
| txNamesToGeneNames | 1.037 | 0.003 | 1.040 | |
| uORFSearchSpace | 0.903 | 0.007 | 0.911 | |
| uniqueGroups | 0.253 | 0.002 | 0.254 | |
| uniqueOrder | 0.336 | 0.001 | 0.338 | |
| unlistGrl | 0.068 | 0.000 | 0.069 | |
| widthPerGroup | 0.089 | 0.001 | 0.090 | |
| windowCoveragePlot | 0.906 | 0.006 | 0.913 | |
| windowPerGroup | 0.557 | 0.003 | 0.560 | |
| windowPerReadLength | 1.448 | 0.006 | 1.461 | |