| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:45 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
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To the developers/maintainers of the trackViewer package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 2089/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| trackViewer 1.37.4 (landing page) Jianhong Ou
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: trackViewer |
| Version: 1.37.4 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings trackViewer_1.37.4.tar.gz |
| StartedAt: 2023-05-30 21:35:14 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 22:02:07 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 1613.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: trackViewer.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings trackViewer_1.37.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/trackViewer.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘trackViewer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trackViewer’ version ‘1.37.4’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
trackViewer-package 31.254 0.284 31.540
parseWIG 22.579 0.208 22.789
viewTracks 22.059 0.248 22.308
browseTracks 20.830 0.435 21.274
geneModelFromTxdb 8.296 0.287 8.585
viewGene 7.984 0.100 8.084
* 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: OK
trackViewer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL trackViewer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘trackViewer’ ... ** using staged installation ** 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 ** 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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: grid
[1] TRUE
> require("RUnit") || stop("unable to load Package:RUnit")
Loading required package: RUnit
[1] TRUE
> BiocGenerics:::testPackage("trackViewer")
RUNIT TEST PROTOCOL -- Tue May 30 21:45:51 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
23.804 1.070 24.865
trackViewer.Rcheck/trackViewer-Ex.timings
| name | user | system | elapsed | |
| GRoperator | 4.315 | 0.232 | 4.548 | |
| addArrowMark | 0.01 | 0.00 | 0.01 | |
| addGuideLine | 0.006 | 0.000 | 0.005 | |
| browseTracks | 20.830 | 0.435 | 21.274 | |
| coverageGR | 0.286 | 0.008 | 0.294 | |
| dandelion.plot | 3.165 | 0.008 | 3.173 | |
| geneModelFromTxdb | 8.296 | 0.287 | 8.585 | |
| geneTrack | 2.884 | 0.060 | 2.944 | |
| getCurTrackViewport | 0.004 | 0.000 | 0.004 | |
| getGeneIDsFromTxDb | 1.278 | 0.028 | 1.306 | |
| getLocation | 1.964 | 0.056 | 2.020 | |
| gi2track | 0.058 | 0.008 | 0.067 | |
| gieStain | 0.008 | 0.000 | 0.008 | |
| ideogramPlot | 0.001 | 0.000 | 0.000 | |
| importBam | 0.444 | 0.000 | 0.443 | |
| importData | 3.648 | 0.047 | 3.696 | |
| importGInteractions | 0.896 | 0.004 | 0.910 | |
| importScSeqScore | 0.001 | 0.000 | 0.001 | |
| importScore | 0.916 | 0.000 | 0.917 | |
| listChromosomes | 0.739 | 0.008 | 0.747 | |
| listResolutions | 0.001 | 0.004 | 0.005 | |
| loadIdeogram | 0 | 0 | 0 | |
| lolliplot | 1.438 | 0.012 | 1.451 | |
| optimizeStyle | 0.838 | 0.000 | 0.840 | |
| parse2GRanges | 0.013 | 0.003 | 0.016 | |
| parseWIG | 22.579 | 0.208 | 22.789 | |
| plotGInteractions | 1.761 | 0.016 | 1.778 | |
| plotGRanges | 2.333 | 0.008 | 2.340 | |
| plotIdeo | 0 | 0 | 0 | |
| plotOneIdeo | 0 | 0 | 0 | |
| trackStyle-class | 0.069 | 0.000 | 0.069 | |
| trackViewer-package | 31.254 | 0.284 | 31.540 | |
| trackViewerStyle-class | 0.001 | 0.000 | 0.000 | |
| viewGene | 7.984 | 0.100 | 8.084 | |
| viewTracks | 22.059 | 0.248 | 22.308 | |