Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:22 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 2072/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
trackViewer 1.34.0 (landing page) Jianhong Ou
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
Package: trackViewer |
Version: 1.34.0 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings trackViewer_1.34.0.tar.gz |
StartedAt: 2023-04-11 00:36:28 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 00:55:41 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 1153.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: trackViewer.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings trackViewer_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/trackViewer.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘trackViewer/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘trackViewer’ version ‘1.34.0’ * 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 ... NOTE installed size is 7.1Mb sub-directories of 1Mb or more: extdata 2.9Mb libs 2.8Mb * 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 loading without being on the library search path ... 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 21.710 0.264 21.974 viewTracks 16.144 0.163 16.311 browseTracks 15.450 0.352 15.805 parseWIG 14.901 0.211 15.113 geneModelFromTxdb 5.574 0.255 5.831 viewGene 5.281 0.063 5.345 * 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 ... ‘changeTracksStyles.Rmd’ using ‘UTF-8’... OK ‘dandelionPlot.Rmd’ using ‘UTF-8’... OK ‘lollipopPlot.Rmd’ using ‘UTF-8’... OK ‘plotInteractionData.Rmd’ using ‘UTF-8’... OK ‘trackViewer.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.16-bioc/meat/trackViewer.Rcheck/00check.log’ for details.
trackViewer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL trackViewer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘trackViewer’ ... ** using staged installation ** libs g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-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-3.16-bioc/R/lib -L/usr/local/lib -o trackViewer.so RcppExports.o hic.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.16-bioc/R/site-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 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 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 Attaching package: 'BiocGenerics' 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, aperm, 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 -- Tue Apr 11 00:44:31 2023 *********************************************** 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 17.401 0.908 18.295
trackViewer.Rcheck/trackViewer-Ex.timings
name | user | system | elapsed | |
GRoperator | 2.295 | 0.200 | 2.494 | |
addArrowMark | 0.005 | 0.003 | 0.009 | |
addGuideLine | 0.004 | 0.000 | 0.005 | |
browseTracks | 15.450 | 0.352 | 15.805 | |
coverageGR | 0.196 | 0.000 | 0.196 | |
dandelion.plot | 2.152 | 0.028 | 2.180 | |
geneModelFromTxdb | 5.574 | 0.255 | 5.831 | |
geneTrack | 1.961 | 0.039 | 2.001 | |
getCurTrackViewport | 0.003 | 0.000 | 0.003 | |
getGeneIDsFromTxDb | 0.839 | 0.024 | 0.863 | |
getLocation | 1.305 | 0.020 | 1.325 | |
gi2track | 0.042 | 0.000 | 0.042 | |
gieStain | 0.000 | 0.004 | 0.005 | |
ideogramPlot | 0 | 0 | 0 | |
importBam | 0.282 | 0.002 | 0.283 | |
importData | 2.856 | 0.065 | 2.920 | |
importGInteractions | 1.497 | 0.015 | 1.518 | |
importScSeqScore | 0 | 0 | 0 | |
importScore | 0.627 | 0.017 | 0.643 | |
listChromosomes | 0.417 | 0.003 | 0.420 | |
listResolutions | 0.003 | 0.001 | 0.002 | |
loadIdeogram | 0 | 0 | 0 | |
lolliplot | 0.731 | 0.007 | 0.739 | |
optimizeStyle | 0.506 | 0.029 | 0.534 | |
parse2GRanges | 0.010 | 0.000 | 0.011 | |
parseWIG | 14.901 | 0.211 | 15.113 | |
plotGInteractions | 1.193 | 0.021 | 1.213 | |
plotGRanges | 1.559 | 0.012 | 1.570 | |
plotIdeo | 0 | 0 | 0 | |
plotOneIdeo | 0 | 0 | 0 | |
trackStyle-class | 0.042 | 0.000 | 0.043 | |
trackViewer-package | 21.710 | 0.264 | 21.974 | |
trackViewerStyle-class | 0.000 | 0.000 | 0.001 | |
viewGene | 5.281 | 0.063 | 5.345 | |
viewTracks | 16.144 | 0.163 | 16.311 | |