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 12:14:43 -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: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ORFik_1.4.1.tar.gz |
| StartedAt: 2019-10-16 03:42:18 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:48:17 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 358.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ORFik.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:ORFik.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings ORFik_1.4.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ORFik.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.1’
* 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 14.325 0.103 12.475
* 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-3.9-bioc/meat/ORFik.Rcheck/00check.log’
for details.
ORFik.Rcheck/00install.out
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### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ORFik
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘ORFik’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c findORFsHelpers.cpp -o findORFsHelpers.o
findORFsHelpers.cpp: In function ‘void calc_z(const string&, vi&)’:
findORFsHelpers.cpp:57:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
for (z[i] = r - i; r < len; ++r, ++z[i])
^~~
findORFsHelpers.cpp:60:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
--r;
^~
findORFsHelpers.cpp: In function ‘Rcpp::IntegerMatrix orfs_as_matrix(std::__cxx11::string&, std::__cxx11::string, std::__cxx11::string, int)’:
findORFsHelpers.cpp:212:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i = 0; i < uorfSize/2; i++) {
~~^~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c findOrfsFasta.cpp -o findOrfsFasta.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o
pmapFromTranscripts.cpp: In function ‘Rcpp::List pmapFromTranscriptsCPP(const std::vector&, const std::vector&, const std::vector&, const std::vector&, const std::vector&, const char&, bool)’:
pmapFromTranscripts.cpp:151:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0;i < xSize; i++){
~~^~~~~~~
pmapFromTranscripts.cpp:155:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 0; i < indexSize; i++){
~~^~~~~~~~~~~
pmapFromTranscripts.cpp:161:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(auto i = 1; i < indexSize; i++){
~~^~~~~~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o ORFik.so RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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-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, 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
55.888 0.767 46.645
ORFik.Rcheck/ORFik-Ex.timings
| name | user | system | elapsed | |
| assignTSSByCage | 0 | 0 | 0 | |
| computeFeatures | 14.325 | 0.103 | 12.475 | |
| computeFeaturesCage | 0 | 0 | 0 | |
| coverageHeatMap | 1.605 | 0.014 | 1.420 | |
| coveragePerTiling | 0.342 | 0.000 | 0.344 | |
| coverageScorings | 0.137 | 0.000 | 0.022 | |
| defineTrailer | 0.164 | 0.000 | 0.163 | |
| detectRibosomeShifts | 0.001 | 0.000 | 0.001 | |
| disengagementScore | 0.452 | 0.000 | 0.465 | |
| distToCds | 0.218 | 0.000 | 0.218 | |
| distToTSS | 0.238 | 0.000 | 0.238 | |
| entropy | 2.059 | 0.005 | 0.983 | |
| extendLeaders | 1.348 | 0.004 | 0.850 | |
| filterTranscripts | 2.151 | 0.007 | 1.424 | |
| findMapORFs | 1.651 | 0.000 | 0.806 | |
| findORFs | 0.671 | 0.000 | 0.209 | |
| findORFsFasta | 0.320 | 0.000 | 0.095 | |
| firstEndPerGroup | 0.064 | 0.000 | 0.064 | |
| firstExonPerGroup | 0.054 | 0.000 | 0.054 | |
| firstStartPerGroup | 0.075 | 0.000 | 0.075 | |
| floss | 0.229 | 0.000 | 0.229 | |
| fpkm | 0.063 | 0.000 | 0.063 | |
| fractionLength | 0.054 | 0.000 | 0.054 | |
| fread.bed | 0.027 | 0.056 | 0.092 | |
| gcContent | 1.305 | 0.056 | 0.924 | |
| groupGRangesBy | 0.057 | 0.012 | 0.069 | |
| groupings | 0.059 | 0.000 | 0.117 | |
| initiationScore | 1.992 | 0.028 | 2.056 | |
| insideOutsideORF | 1.952 | 0.005 | 2.297 | |
| isInFrame | 0.248 | 0.004 | 0.393 | |
| isOverlapping | 0.228 | 0.000 | 0.396 | |
| kozakSequenceScore | 1.163 | 0.011 | 1.655 | |
| lastExonEndPerGroup | 0.066 | 0.004 | 0.086 | |
| lastExonPerGroup | 0.069 | 0.000 | 0.104 | |
| lastExonStartPerGroup | 0.069 | 0.000 | 0.113 | |
| loadTxdb | 0.173 | 0.003 | 0.317 | |
| longestORFs | 0.317 | 0.000 | 0.253 | |
| makeORFNames | 0.098 | 0.000 | 0.099 | |
| metaWindow | 0.955 | 0.009 | 0.558 | |
| numExonsPerGroup | 0.048 | 0.000 | 0.049 | |
| orfScore | 3.528 | 0.020 | 1.410 | |
| overlapsToCoverage | 0.063 | 0.000 | 0.049 | |
| pSitePlot | 0.427 | 0.004 | 0.432 | |
| pmapFromTranscriptF | 0.115 | 0.004 | 0.119 | |
| rankOrder | 0.067 | 0.000 | 0.067 | |
| readWidths | 0.019 | 0.000 | 0.019 | |
| reassignTSSbyCage | 1.314 | 0.012 | 0.726 | |
| reassignTxDbByCage | 0.001 | 0.000 | 0.000 | |
| reduceKeepAttr | 0.501 | 0.008 | 0.272 | |
| ribosomeReleaseScore | 0.162 | 0.004 | 0.170 | |
| ribosomeStallingScore | 0.325 | 0.000 | 0.325 | |
| scaledWindowPositions | 1.391 | 0.018 | 0.694 | |
| seqnamesPerGroup | 0.094 | 0.000 | 0.096 | |
| shiftFootprints | 0 | 0 | 0 | |
| sortPerGroup | 0.868 | 0.011 | 0.440 | |
| startCodons | 1.211 | 0.000 | 0.737 | |
| startDefinition | 0.001 | 0.000 | 0.000 | |
| startSites | 1.068 | 0.002 | 0.627 | |
| stopCodons | 0.889 | 0.001 | 0.601 | |
| stopDefinition | 0.001 | 0.000 | 0.000 | |
| stopSites | 0.958 | 0.001 | 0.471 | |
| strandBool | 0.008 | 0.000 | 0.009 | |
| strandPerGroup | 0.082 | 0.000 | 0.082 | |
| tile1 | 0.271 | 0.004 | 0.275 | |
| translationalEff | 0.110 | 0.004 | 0.114 | |
| txNames | 0.047 | 0.000 | 0.048 | |
| uORFSearchSpace | 1.185 | 0.004 | 0.742 | |
| uniqueGroups | 0.125 | 0.000 | 0.125 | |
| uniqueOrder | 0.468 | 0.000 | 0.306 | |
| unlistGrl | 0.031 | 0.000 | 0.031 | |
| widthPerGroup | 0.045 | 0.000 | 0.045 | |
| windowCoveragePlot | 0.783 | 0.011 | 0.492 | |
| windowPerGroup | 0.293 | 0.000 | 0.293 | |