Kornel Labun
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/ORFik |
| Branch: RELEASE_3_7 |
| Last Commit: 74296f8 |
| Last Changed Date: 2018-04-30 10:35:53 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 09:00:10 -0400 (Wed, 17 Oct 2018).
| Package 1038/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ORFik 1.0.0 Kornel Labun
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: ORFik |
| Version: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2018-10-16 23:05:03 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 23:10:35 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 331.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ORFik.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ORFik.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * 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 ‘1.0.0’ * 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 ... OK * 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 * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.7-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/3.5/Resources/library’ * installing *source* package ‘ORFik’ ... ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -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/3.5/Resources/library/Rcpp/include" -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/3.5/Resources/library/Rcpp/include" -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/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c findOrfsFasta.cpp -o findOrfsFasta.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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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.
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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: 222 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
50.359 1.697 48.316
ORFik.Rcheck/ORFik-Ex.timings
| name | user | system | elapsed | |
| computeFeatures | 0.003 | 0.000 | 0.003 | |
| computeFeaturesCage | 0.005 | 0.000 | 0.005 | |
| coverageByWindow | 0.743 | 0.051 | 0.799 | |
| coveragePerTiling | 0.320 | 0.046 | 0.369 | |
| defineTrailer | 0.189 | 0.028 | 0.219 | |
| detectRibosomeShifts | 0.002 | 0.001 | 0.003 | |
| disengagementScore | 0.468 | 0.037 | 0.508 | |
| distToCds | 0.372 | 0.002 | 0.382 | |
| entropy | 1.002 | 0.004 | 1.013 | |
| extendLeaders | 0.788 | 0.011 | 0.815 | |
| findMapORFs | 0.725 | 0.002 | 0.731 | |
| findORFs | 0.052 | 0.001 | 0.052 | |
| findORFsFasta | 0.019 | 0.001 | 0.020 | |
| firstEndPerGroup | 0.087 | 0.000 | 0.088 | |
| firstExonPerGroup | 0.076 | 0.000 | 0.076 | |
| firstStartPerGroup | 0.064 | 0.000 | 0.065 | |
| floss | 0.164 | 0.001 | 0.165 | |
| fpkm | 0.065 | 0.000 | 0.065 | |
| fractionLength | 0.066 | 0.000 | 0.067 | |
| fread.bed | 0.048 | 0.009 | 0.059 | |
| getStartStopWindows | 4.592 | 0.342 | 3.886 | |
| groupGRangesBy | 0.044 | 0.001 | 0.046 | |
| insideOutsideORF | 0.786 | 0.002 | 0.792 | |
| isInFrame | 0.334 | 0.001 | 0.340 | |
| isOverlapping | 0.277 | 0.001 | 0.282 | |
| kozakSequenceScore | 0.455 | 0.001 | 0.467 | |
| lastExonEndPerGroup | 0.086 | 0.000 | 0.088 | |
| lastExonPerGroup | 0.080 | 0.000 | 0.081 | |
| lastExonStartPerGroup | 0.078 | 0.000 | 0.080 | |
| makeORFNames | 0.111 | 0.001 | 0.112 | |
| metaWindow | 0.203 | 0.003 | 0.206 | |
| numExonsPerGroup | 0.081 | 0.000 | 0.083 | |
| orfScore | 2.158 | 0.391 | 0.805 | |
| rankOrder | 0.258 | 0.085 | 0.104 | |
| reassignTSSbyCage | 0.363 | 0.002 | 0.372 | |
| reduceKeepAttr | 0.249 | 0.001 | 0.251 | |
| ribosomeReleaseScore | 0.226 | 0.001 | 0.228 | |
| ribosomeStallingScore | 0.351 | 0.001 | 0.355 | |
| seqnamesPerGroup | 0.089 | 0.001 | 0.092 | |
| shiftFootprints | 0.001 | 0.000 | 0.002 | |
| sortPerGroup | 0.328 | 0.001 | 0.335 | |
| startCodons | 0.625 | 0.002 | 0.629 | |
| startDefinition | 0.002 | 0.000 | 0.002 | |
| startSites | 0.419 | 0.000 | 0.423 | |
| stopCodons | 0.612 | 0.001 | 0.621 | |
| stopDefinition | 0.002 | 0.001 | 0.002 | |
| stopSites | 0.410 | 0.001 | 0.412 | |
| strandBool | 0.013 | 0.000 | 0.013 | |
| strandPerGroup | 0.101 | 0.000 | 0.102 | |
| tile1 | 0.258 | 0.002 | 0.262 | |
| translationalEff | 0.153 | 0.000 | 0.155 | |
| txNames | 0.047 | 0.000 | 0.048 | |
| txNamesWithLeaders | 1.196 | 0.009 | 1.203 | |
| uniqueGroups | 0.552 | 0.345 | 0.209 | |
| uniqueOrder | 0.363 | 0.001 | 0.372 | |
| unlistGrl | 0.050 | 0.001 | 0.052 | |
| widthPerGroup | 0.06 | 0.00 | 0.06 | |