Kornel Labun
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ORFik |
| Branch: RELEASE_3_8 |
| Last Commit: 2e3a8c6 |
| Last Changed Date: 2019-01-04 13:42:32 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:53:32 -0400 (Tue, 16 Apr 2019).
| Package 1101/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ORFik 1.2.1 Kornel Labun
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: ORFik |
| Version: 1.2.1 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ORFik_1.2.1.tar.gz |
| StartedAt: 2019-04-16 01:54:43 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 01:59:58 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 314.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ORFik.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings ORFik_1.2.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/ORFik.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.2.1’
* 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
assignTSSByCage: no visible global function definition for ‘is’
computeFeatures: no visible global function definition for ‘is’
computeFeatures: no visible binding for global variable ‘entropyRFP’
computeFeatures: no visible binding for global variable
‘disengagementScores’
computeFeatures: no visible binding for global variable ‘RRS’
computeFeatures: no visible binding for global variable ‘RSS’
computeFeatures: no visible binding for global variable
‘fractionLengths’
computeFeatures: no visible binding for global variable ‘te’
computeFeatures: no visible binding for global variable ‘fpkmRFP’
computeFeatures: no visible binding for global variable ‘fpkmRNA’
computeFeatures: no visible binding for global variable ‘ORFScores’
computeFeatures: no visible binding for global variable ‘ioScore’
computeFeatures: no visible binding for global variable ‘inFrameCDS’
computeFeatures: no visible binding for global variable
‘isOverlappingCds’
computeFeatures: no visible binding for global variable ‘rankInTx’
computeFeaturesCage: no visible global function definition for ‘is’
computeFeaturesCage: no visible binding for global variable
‘entropyRFP’
computeFeaturesCage: no visible binding for global variable
‘disengagementScores’
computeFeaturesCage: no visible binding for global variable ‘RRS’
computeFeaturesCage: no visible binding for global variable ‘RSS’
computeFeaturesCage: no visible binding for global variable
‘fractionLengths’
computeFeaturesCage: no visible binding for global variable ‘te’
computeFeaturesCage: no visible binding for global variable ‘fpkmRFP’
computeFeaturesCage: no visible binding for global variable ‘fpkmRNA’
computeFeaturesCage: no visible binding for global variable ‘ORFScores’
computeFeaturesCage: no visible binding for global variable ‘ioScore’
computeFeaturesCage: no visible binding for global variable
‘inFrameCDS’
computeFeaturesCage: no visible binding for global variable
‘isOverlappingCds’
computeFeaturesCage: no visible binding for global variable ‘rankInTx’
convertToOneBasedRanges: no visible global function definition for ‘.’
disengagementScore: no visible global function definition for ‘is’
extendLeaders: no visible global function definition for ‘is’
findFa: no visible global function definition for ‘is’
findORFsFasta: no visible global function definition for ‘is’
groupGRangesBy: no visible global function definition for ‘is’
insideOutsideORF: no visible global function definition for ‘is’
kozakSequenceScore: no visible global function definition for ‘is’
longestORFs: no visible global function definition for ‘is’
longestORFs: no visible global function definition for ‘.’
mapToGRanges: no visible global function definition for ‘is’
readWidths: no visible global function definition for ‘is’
reassignTSSbyCage: no visible global function definition for ‘is’
reassignTxDbByCage: no visible global function definition for ‘is’
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’
ribosomeReleaseScore: no visible global function definition for ‘is’
strandBool: no visible global function definition for ‘is’
txNamesWithLeaders: no visible global function definition for ‘is’
txSeqsFromFa: no visible global function definition for ‘is’
Undefined global functions or variables:
. ORFScores RRS RSS chr disengagementScores entropyRFP exon_rank
fpkmRFP fpkmRNA fractionLengths inFrameCDS ioScore is
isOverlappingCds rankInTx ranks te
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 11.496 0.124 8.101
getStartStopWindows 6.376 0.064 4.816
* 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
‘/home/biocbuild/bbs-3.8-bioc/meat/ORFik.Rcheck/00check.log’
for details.
ORFik.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL ORFik ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘ORFik’ ... ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c findORFsHelpers.cpp -o findORFsHelpers.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c findOrfs.cpp -o findOrfs.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c findOrfsFasta.cpp -o findOrfsFasta.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o ORFik.so RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.8-bioc/R/library/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 * DONE (ORFik)
ORFik.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, 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
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: 236 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
87.840 0.576 55.426
ORFik.Rcheck/ORFik-Ex.timings
| name | user | system | elapsed | |
| assignTSSByCage | 0.000 | 0.000 | 0.001 | |
| computeFeatures | 11.496 | 0.124 | 8.101 | |
| computeFeaturesCage | 0.004 | 0.000 | 0.000 | |
| coverageByWindow | 1.348 | 0.008 | 1.260 | |
| coveragePerTiling | 0.252 | 0.000 | 0.504 | |
| defineTrailer | 0.180 | 0.000 | 0.361 | |
| detectRibosomeShifts | 0 | 0 | 0 | |
| disengagementScore | 0.612 | 0.000 | 1.082 | |
| distToCds | 0.384 | 0.000 | 0.766 | |
| distToTSS | 0.336 | 0.000 | 0.449 | |
| entropy | 1.260 | 0.000 | 1.137 | |
| extendLeaders | 1.804 | 0.008 | 0.994 | |
| findMapORFs | 2.208 | 0.004 | 1.218 | |
| findORFs | 0.836 | 0.004 | 0.284 | |
| findORFsFasta | 0.332 | 0.000 | 0.126 | |
| firstEndPerGroup | 0.064 | 0.000 | 0.065 | |
| firstExonPerGroup | 0.052 | 0.000 | 0.054 | |
| firstStartPerGroup | 0.044 | 0.004 | 0.050 | |
| floss | 0.208 | 0.000 | 0.212 | |
| fpkm | 0.056 | 0.000 | 0.058 | |
| fractionLength | 0.044 | 0.000 | 0.043 | |
| fread.bed | 0.032 | 0.040 | 0.087 | |
| getStartStopWindows | 6.376 | 0.064 | 4.816 | |
| groupGRangesBy | 0.064 | 0.000 | 0.127 | |
| initiationScore | 1.908 | 0.000 | 3.036 | |
| insideOutsideORF | 2.056 | 0.000 | 2.005 | |
| isInFrame | 0.18 | 0.00 | 0.18 | |
| isOverlapping | 0.196 | 0.000 | 0.194 | |
| kozakSequenceScore | 0.492 | 0.004 | 0.515 | |
| lastExonEndPerGroup | 0.052 | 0.000 | 0.049 | |
| lastExonPerGroup | 0.048 | 0.000 | 0.050 | |
| lastExonStartPerGroup | 0.048 | 0.000 | 0.048 | |
| longestORFs | 0.328 | 0.000 | 0.180 | |
| makeORFNames | 0.144 | 0.000 | 0.144 | |
| metaWindow | 0.736 | 0.000 | 0.304 | |
| numExonsPerGroup | 0.092 | 0.000 | 0.092 | |
| orfScore | 3.216 | 0.004 | 1.201 | |
| overlapsToCoverage | 0.060 | 0.004 | 0.066 | |
| rankOrder | 0.128 | 0.000 | 0.125 | |
| reassignTSSbyCage | 1.608 | 0.012 | 0.976 | |
| reassignTxDbByCage | 0 | 0 | 0 | |
| reduceKeepAttr | 0.532 | 0.000 | 0.298 | |
| ribosomeReleaseScore | 0.192 | 0.000 | 0.196 | |
| ribosomeStallingScore | 0.320 | 0.000 | 0.321 | |
| seqnamesPerGroup | 0.088 | 0.000 | 0.087 | |
| shiftFootprints | 0 | 0 | 0 | |
| sortPerGroup | 0.932 | 0.004 | 0.474 | |
| startCodons | 1.208 | 0.004 | 0.634 | |
| startDefinition | 0 | 0 | 0 | |
| startSites | 1.028 | 0.004 | 0.489 | |
| stopCodons | 1.172 | 0.000 | 0.645 | |
| stopDefinition | 0.000 | 0.000 | 0.001 | |
| stopSites | 1.020 | 0.012 | 0.502 | |
| strandBool | 0.000 | 0.004 | 0.006 | |
| strandPerGroup | 0.056 | 0.000 | 0.054 | |
| tile1 | 0.144 | 0.000 | 0.144 | |
| translationalEff | 0.092 | 0.004 | 0.093 | |
| txNames | 0.044 | 0.000 | 0.045 | |
| txNamesWithLeaders | 1.820 | 0.000 | 1.083 | |
| uORFSearchSpace | 1.528 | 0.000 | 0.834 | |
| uniqueGroups | 0.116 | 0.000 | 0.115 | |
| uniqueOrder | 0.456 | 0.000 | 0.277 | |
| unlistGrl | 0.028 | 0.000 | 0.029 | |
| widthPerGroup | 0.040 | 0.000 | 0.036 | |