Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-07 11:46:36 -0400 (Sun, 07 Apr 2019).
Package 1127/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ORFik 1.3.13 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 | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: ORFik |
Version: 1.3.13 |
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_1.3.13.tar.gz |
StartedAt: 2019-04-07 02:57:37 -0400 (Sun, 07 Apr 2019) |
EndedAt: 2019-04-07 03:03:21 -0400 (Sun, 07 Apr 2019) |
EllapsedTime: 344.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ORFik.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.3.13.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/ORFik.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * 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 ‘1.3.13’ * 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 ... 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 ‘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 ‘.’ 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 entropyRFP exon_rank feature fpkmRFP fpkmRNA fraction fractionLengths fraction_min frame frame_one_RP frame_two_RP gene_sum grnames inFrameCDS ioScore isOverlappingCds ones position rankInTx ranks scalingFactor te 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 19.334 0.178 7.310 orfScore 6.975 0.057 3.876 entropy 6.339 0.037 3.664 * 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
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL ORFik ### ############################################################################## ############################################################################## * 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<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, const std::vector<int>&, 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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences" 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, 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, 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: 255 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 141.513 0.989 62.680
ORFik.Rcheck/ORFik-Ex.timings
name | user | system | elapsed | |
assignTSSByCage | 0 | 0 | 0 | |
computeFeatures | 19.334 | 0.178 | 7.310 | |
computeFeaturesCage | 0.001 | 0.000 | 0.000 | |
coverageHeatMap | 2.447 | 0.009 | 1.979 | |
coveragePerTiling | 0.423 | 0.000 | 0.920 | |
coverageScorings | 1.345 | 0.007 | 0.773 | |
defineTrailer | 0.167 | 0.000 | 0.217 | |
detectRibosomeShifts | 0 | 0 | 0 | |
disengagementScore | 0.481 | 0.000 | 0.488 | |
distToCds | 0.249 | 0.000 | 0.284 | |
distToTSS | 0.276 | 0.000 | 0.312 | |
entropy | 6.339 | 0.037 | 3.664 | |
extendLeaders | 2.841 | 0.020 | 0.937 | |
filterTranscripts | 3.026 | 0.000 | 1.200 | |
findMapORFs | 3.062 | 0.011 | 0.824 | |
findORFs | 1.296 | 0.001 | 0.218 | |
findORFsFasta | 0.650 | 0.000 | 0.171 | |
firstEndPerGroup | 0.084 | 0.000 | 0.084 | |
firstExonPerGroup | 0.079 | 0.000 | 0.079 | |
firstStartPerGroup | 0.075 | 0.000 | 0.075 | |
floss | 0.152 | 0.000 | 0.152 | |
fpkm | 0.036 | 0.000 | 0.037 | |
fractionLength | 0.045 | 0.000 | 0.045 | |
fread.bed | 0.018 | 0.054 | 0.087 | |
gcContent | 2.054 | 0.029 | 0.829 | |
groupGRangesBy | 0.066 | 0.003 | 0.069 | |
groupings | 0.048 | 0.008 | 0.056 | |
initiationScore | 2.772 | 0.043 | 1.390 | |
insideOutsideORF | 2.785 | 0.001 | 1.104 | |
isInFrame | 0.235 | 0.000 | 0.235 | |
isOverlapping | 0.223 | 0.000 | 0.223 | |
kozakSequenceScore | 1.712 | 0.004 | 1.088 | |
lastExonEndPerGroup | 0.079 | 0.000 | 0.201 | |
lastExonPerGroup | 0.082 | 0.000 | 0.164 | |
lastExonStartPerGroup | 0.080 | 0.000 | 0.177 | |
loadTxdb | 0.165 | 0.004 | 0.380 | |
longestORFs | 0.567 | 0.000 | 0.532 | |
makeORFNames | 0.09 | 0.00 | 0.15 | |
metaWindow | 1.705 | 0.005 | 1.040 | |
numExonsPerGroup | 0.051 | 0.000 | 0.051 | |
orfScore | 6.975 | 0.057 | 3.876 | |
overlapsToCoverage | 0.072 | 0.000 | 0.058 | |
pSitePlot | 0.488 | 0.000 | 0.546 | |
pmapFromTranscriptF | 0.127 | 0.000 | 0.159 | |
rankOrder | 0.079 | 0.003 | 0.134 | |
reassignTSSbyCage | 2.387 | 0.004 | 0.950 | |
reassignTxDbByCage | 0 | 0 | 0 | |
reduceKeepAttr | 0.910 | 0.008 | 0.356 | |
ribosomeReleaseScore | 0.107 | 0.008 | 0.115 | |
ribosomeStallingScore | 0.258 | 0.000 | 0.258 | |
scaledWindowPositions | 2.441 | 0.016 | 0.834 | |
seqnamesPerGroup | 0.095 | 0.000 | 0.084 | |
shiftFootprints | 0.001 | 0.000 | 0.000 | |
sortPerGroup | 1.520 | 0.021 | 0.462 | |
startCodons | 1.849 | 0.008 | 0.667 | |
startDefinition | 0 | 0 | 0 | |
startSites | 1.655 | 0.008 | 0.493 | |
stopCodons | 2.005 | 0.004 | 0.686 | |
stopDefinition | 0 | 0 | 0 | |
stopSites | 1.711 | 0.020 | 0.451 | |
strandBool | 0.008 | 0.000 | 0.008 | |
strandPerGroup | 0.076 | 0.000 | 0.076 | |
tile1 | 0.153 | 0.002 | 0.156 | |
translationalEff | 0.084 | 0.000 | 0.084 | |
txNames | 0.032 | 0.000 | 0.032 | |
uORFSearchSpace | 2.242 | 0.004 | 0.632 | |
uniqueGroups | 0.104 | 0.000 | 0.104 | |
uniqueOrder | 1.560 | 0.084 | 1.236 | |
unlistGrl | 0.037 | 0.000 | 0.038 | |
widthPerGroup | 0.05 | 0.00 | 0.05 | |
windowCoveragePlot | 1.234 | 0.004 | 0.519 | |
windowPerGroup | 0.290 | 0.004 | 0.295 | |