Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:55 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the trackViewer package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/trackViewer.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1942/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
trackViewer 1.28.1 (landing page) Jianhong Ou
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: trackViewer |
Version: 1.28.1 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings trackViewer_1.28.1.tar.gz |
StartedAt: 2021-10-14 11:54:47 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 12:02:57 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 489.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: trackViewer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings trackViewer_1.28.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/trackViewer.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘trackViewer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘trackViewer’ version ‘1.28.1’ * 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 ‘trackViewer’ 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 use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed trackViewer-package 29.717 0.195 29.914 viewTracks 22.777 0.020 22.798 parseWIG 20.742 0.059 20.844 browseTracks 20.014 0.247 20.270 importGInteractions 8.869 1.260 10.134 geneModelFromTxdb 6.134 0.376 6.511 viewGene 6.094 0.047 6.142 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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 ‘/home/biocbuild/bbs-3.13-bioc/meat/trackViewer.Rcheck/00check.log’ for details.
trackViewer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL trackViewer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘trackViewer’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c hic.cpp -o hic.o hic.cpp: In member function ‘void HicFileHead::readHeader(std::ifstream&)’: hic.cpp:247:16: warning: unused variable ‘nviPosition’ [-Wunused-variable] 247 | long nviPosition = readLong(ifile); | ^~~~~~~~~~~ hic.cpp:248:16: warning: unused variable ‘nviLength’ [-Wunused-variable] 248 | long nviLength = readLong(ifile); | ^~~~~~~~~ hic.cpp: In function ‘std::vector<cellData> getByCoor(std::string, int, int, std::string, int, int, int, std::string, std::string, HicFileHead&, HicFileFoot&, std::ifstream&)’: hic.cpp:751:19: warning: ‘*((void*)(& bd)+8).resolutions::nResolutions’ may be used uninitialized in this function [-Wmaybe-uninitialized] 751 | for(int i=0; i<data.nResolutions; i++){ | ~^~~~~~~~~~~~~~~~~~ hic.cpp:797:10: note: ‘*((void*)(& bd)+8).resolutions::nResolutions’ was declared here 797 | body bd; | ^~ hic.cpp:797:10: warning: ‘*((void*)(& bd)+8).resolutions::res’ may be used uninitialized in this function [-Wmaybe-uninitialized] g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o trackViewer.so RcppExports.o hic.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-trackViewer/00new/trackViewer/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 (trackViewer)
trackViewer.Rcheck/tests/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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. > require("trackViewer") || stop("unable to load Package:trackViewer") Loading required package: trackViewer Loading required package: GenomicRanges Loading required package: stats4 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.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: grid Loading required package: Rcpp [1] TRUE > require("RUnit") || stop("unable to load Package:RUnit") Loading required package: RUnit [1] TRUE > BiocGenerics:::testPackage("trackViewer") RUNIT TEST PROTOCOL -- Thu Oct 14 12:02:53 2021 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : trackViewer RUnit Tests - 2 test functions, 0 errors, 0 failures Number of test functions: 2 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 17.937 0.502 18.430
trackViewer.Rcheck/trackViewer-Ex.timings
name | user | system | elapsed | |
GRoperator | 2.927 | 0.285 | 3.211 | |
addArrowMark | 0.008 | 0.000 | 0.007 | |
addGuideLine | 0.005 | 0.000 | 0.004 | |
browseTracks | 20.014 | 0.247 | 20.270 | |
coverageGR | 0.290 | 0.024 | 0.314 | |
dandelion.plot | 3.426 | 0.044 | 3.469 | |
geneModelFromTxdb | 6.134 | 0.376 | 6.511 | |
geneTrack | 3.964 | 0.072 | 4.038 | |
getCurTrackViewport | 0.003 | 0.000 | 0.003 | |
getGeneIDsFromTxDb | 0.950 | 0.028 | 0.978 | |
getLocation | 1.320 | 0.028 | 1.348 | |
gi2track | 0.091 | 0.000 | 0.091 | |
gieStain | 0.006 | 0.000 | 0.007 | |
ideogramPlot | 0 | 0 | 0 | |
importBam | 0.453 | 0.000 | 0.453 | |
importData | 4.197 | 0.344 | 4.541 | |
importGInteractions | 8.869 | 1.260 | 10.134 | |
importScSeqScore | 0 | 0 | 0 | |
importScore | 1.996 | 0.034 | 2.030 | |
listChromosomes | 0.425 | 0.008 | 0.433 | |
listResolutions | 0.003 | 0.000 | 0.003 | |
loadIdeogram | 0 | 0 | 0 | |
lolliplot | 1.299 | 0.064 | 1.363 | |
optimizeStyle | 0.615 | 0.037 | 0.652 | |
parse2GRanges | 0.020 | 0.000 | 0.019 | |
parseWIG | 20.742 | 0.059 | 20.844 | |
plotGInteractions | 1.423 | 0.072 | 1.494 | |
plotGRanges | 2.021 | 0.000 | 2.022 | |
plotIdeo | 0.000 | 0.000 | 0.001 | |
plotOneIdeo | 0.000 | 0.000 | 0.001 | |
trackStyle-class | 0.072 | 0.001 | 0.074 | |
trackViewer-package | 29.717 | 0.195 | 29.914 | |
trackViewerStyle-class | 0 | 0 | 0 | |
viewGene | 6.094 | 0.047 | 6.142 | |
viewTracks | 22.777 | 0.020 | 22.798 | |