Kornel Labun
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/ORFik |
| Branch: RELEASE_3_9 |
| Last Commit: 3ae9f3b |
| Last Changed Date: 2019-06-06 08:36:37 -0400 (Thu, 06 Jun 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:02:33 -0400 (Wed, 16 Oct 2019).
| Package 1150/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ORFik 1.4.1 Kornel Labun
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: ORFik |
| Version: 1.4.1 |
| 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_1.4.1.tar.gz |
| StartedAt: 2019-10-16 05:17:48 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:26:10 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 502.4 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_1.4.1.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ORFik.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.4.1’
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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
‘fractionLengths’
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 ‘ORFScores’
allFeaturesHelper: no visible binding for global variable ‘ioScore’
allFeaturesHelper: no visible binding for global variable ‘kozak’
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’
convertToOneBasedRanges: 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 ‘fraction’
entropy: no visible binding for global variable ‘Hx’
entropy: no visible binding for global variable ‘codonSums’
entropy: no visible global function definition for ‘.’
filterTranscripts: no visible binding for global variable ‘utr5_len’
filterTranscripts: no visible binding for global variable ‘utr3_len’
gSort: no visible binding for global variable ‘grnames’
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’
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 ‘position’
pSitePlot: no visible binding for global variable ‘frame’
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’
scaledWindowPositions: no visible binding for global variable
‘scalingFactor’
scaledWindowPositions: no visible binding for global variable
‘position’
scaledWindowPositions: no visible global function definition for ‘.’
windowCoveragePlot: no visible binding for global variable ‘feature’
windowCoveragePlot: no visible binding for global variable ‘fraction’
windowCoveragePlot: no visible binding for global variable ‘position’
windowCoveragePlot: no visible binding for global variable
‘fraction_min’
Undefined global functions or variables:
. Hx ORFScores RRS RSS chr codonSums count dif difPer
disengagementScores distORFCDS entropyRFP exon_rank feature fpkmRFP
fpkmRNA fraction fractionLengths fraction_min frame frame_one_RP
frame_two_RP gene_sum grnames inFrameCDS ioScore isOverlappingCds
kozak ones position rankInTx ranks scalingFactor te utr3_len utr5_len
windowMean windowSD zscore
Consider adding
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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
computeFeatures 14.375 4.64 9.324
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/ORFik.Rcheck/00check.log’
for details.
ORFik.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ORFik ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘ORFik’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c findORFsHelpers.cpp -o findORFsHelpers.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c findOrfs.cpp -o findOrfs.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c findOrfsFasta.cpp -o findOrfsFasta.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o clang++ -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, 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: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
>
> test_check("ORFik")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 262 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
116.358 31.960 73.096
ORFik.Rcheck/ORFik-Ex.timings
| name | user | system | elapsed | |
| assignTSSByCage | 0.000 | 0.000 | 0.001 | |
| computeFeatures | 14.375 | 4.640 | 9.324 | |
| computeFeaturesCage | 0.001 | 0.001 | 0.002 | |
| coverageHeatMap | 1.985 | 0.697 | 1.372 | |
| coveragePerTiling | 0.339 | 0.002 | 0.341 | |
| coverageScorings | 0.035 | 0.030 | 0.022 | |
| defineTrailer | 0.514 | 0.293 | 0.230 | |
| detectRibosomeShifts | 0.001 | 0.001 | 0.001 | |
| disengagementScore | 0.659 | 0.004 | 0.663 | |
| distToCds | 0.320 | 0.003 | 0.324 | |
| distToTSS | 0.303 | 0.005 | 0.309 | |
| entropy | 3.043 | 0.993 | 1.376 | |
| extendLeaders | 2.739 | 0.418 | 1.075 | |
| filterTranscripts | 1.741 | 0.116 | 1.649 | |
| findMapORFs | 2.490 | 0.664 | 0.936 | |
| findORFs | 0.391 | 0.208 | 0.165 | |
| findORFsFasta | 0.213 | 0.133 | 0.089 | |
| firstEndPerGroup | 0.285 | 0.161 | 0.110 | |
| firstExonPerGroup | 0.147 | 0.033 | 0.112 | |
| firstStartPerGroup | 0.113 | 0.001 | 0.114 | |
| floss | 0.250 | 0.002 | 0.251 | |
| fpkm | 0.049 | 0.000 | 0.050 | |
| fractionLength | 0.045 | 0.000 | 0.045 | |
| fread.bed | 0.045 | 0.012 | 0.060 | |
| gcContent | 1.759 | 0.410 | 0.801 | |
| groupGRangesBy | 0.060 | 0.001 | 0.061 | |
| groupings | 0.040 | 0.000 | 0.041 | |
| initiationScore | 1.754 | 0.415 | 1.360 | |
| insideOutsideORF | 1.893 | 0.706 | 1.231 | |
| isInFrame | 0.536 | 0.206 | 0.344 | |
| isOverlapping | 0.300 | 0.001 | 0.302 | |
| kozakSequenceScore | 1.365 | 0.395 | 0.968 | |
| lastExonEndPerGroup | 0.104 | 0.000 | 0.104 | |
| lastExonPerGroup | 0.111 | 0.001 | 0.113 | |
| lastExonStartPerGroup | 0.112 | 0.000 | 0.113 | |
| loadTxdb | 0.258 | 0.009 | 0.267 | |
| longestORFs | 0.261 | 0.044 | 0.218 | |
| makeORFNames | 0.363 | 0.244 | 0.121 | |
| metaWindow | 1.001 | 0.499 | 0.498 | |
| numExonsPerGroup | 0.201 | 0.135 | 0.069 | |
| orfScore | 2.364 | 1.177 | 0.994 | |
| overlapsToCoverage | 0.227 | 0.153 | 0.075 | |
| pSitePlot | 0.846 | 0.267 | 0.649 | |
| pmapFromTranscriptF | 0.150 | 0.001 | 0.152 | |
| rankOrder | 0.107 | 0.000 | 0.108 | |
| readWidths | 0.029 | 0.000 | 0.030 | |
| reassignTSSbyCage | 1.643 | 0.420 | 0.896 | |
| reassignTxDbByCage | 0.000 | 0.001 | 0.001 | |
| reduceKeepAttr | 0.640 | 0.356 | 0.295 | |
| ribosomeReleaseScore | 0.244 | 0.002 | 0.245 | |
| ribosomeStallingScore | 0.420 | 0.003 | 0.422 | |
| scaledWindowPositions | 1.272 | 0.545 | 0.666 | |
| seqnamesPerGroup | 1.309 | 0.005 | 0.125 | |
| shiftFootprints | 0.000 | 0.000 | 0.001 | |
| sortPerGroup | 1.407 | 0.565 | 0.400 | |
| startCodons | 1.508 | 0.778 | 0.779 | |
| startDefinition | 0.001 | 0.000 | 0.001 | |
| startSites | 1.210 | 0.792 | 0.493 | |
| stopCodons | 1.931 | 0.463 | 0.770 | |
| stopDefinition | 0.001 | 0.000 | 0.001 | |
| stopSites | 1.166 | 0.680 | 0.460 | |
| strandBool | 0.006 | 0.000 | 0.007 | |
| strandPerGroup | 0.109 | 0.001 | 0.109 | |
| tile1 | 0.373 | 0.069 | 0.441 | |
| translationalEff | 0.190 | 0.001 | 0.192 | |
| txNames | 0.060 | 0.000 | 0.061 | |
| uORFSearchSpace | 2.079 | 0.383 | 0.904 | |
| uniqueGroups | 0.132 | 0.006 | 0.137 | |
| uniqueOrder | 0.841 | 0.425 | 0.451 | |
| unlistGrl | 0.187 | 0.131 | 0.064 | |
| widthPerGroup | 0.270 | 0.168 | 0.087 | |
| windowCoveragePlot | 0.946 | 0.449 | 0.545 | |
| windowPerGroup | 0.429 | 0.002 | 0.430 | |