| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:42 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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: - 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 2098/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| trackViewer 1.35.5 (landing page) Jianhong Ou
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: trackViewer |
| Version: 1.35.5 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings trackViewer_1.35.5.tar.gz |
| StartedAt: 2023-04-12 09:58:23 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 10:19:02 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 1238.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: trackViewer.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings trackViewer_1.35.5.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/trackViewer.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘trackViewer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trackViewer’ version ‘1.35.5’
* 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
* used C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 7.5Mb
sub-directories of 1Mb or more:
extdata 3.0Mb
libs 3.0Mb
* 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 22.729 0.356 23.085
browseTracks 16.623 0.531 17.157
parseWIG 15.983 0.332 16.316
viewTracks 15.975 0.192 16.167
geneModelFromTxdb 6.090 0.336 6.426
viewGene 5.520 0.048 5.567
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/trackViewer.Rcheck/00check.log’
for details.
trackViewer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL trackViewer ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘trackViewer’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -c straw.cpp -o straw.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o trackViewer.so RcppExports.o straw.o -lcurl -lz -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-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 Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
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 -- Wed Apr 12 10:06:54 2023
***********************************************
Number of test functions: 3
Number of errors: 0
Number of failures: 0
1 Test Suite :
trackViewer RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
17.704 1.345 19.041
trackViewer.Rcheck/trackViewer-Ex.timings
| name | user | system | elapsed | |
| GRoperator | 2.375 | 0.148 | 2.524 | |
| addArrowMark | 0.007 | 0.000 | 0.008 | |
| addGuideLine | 0.005 | 0.000 | 0.004 | |
| browseTracks | 16.623 | 0.531 | 17.157 | |
| coverageGR | 0.197 | 0.000 | 0.197 | |
| dandelion.plot | 2.352 | 0.012 | 2.363 | |
| geneModelFromTxdb | 6.090 | 0.336 | 6.426 | |
| geneTrack | 2.039 | 0.056 | 2.095 | |
| getCurTrackViewport | 0.002 | 0.000 | 0.003 | |
| getGeneIDsFromTxDb | 0.804 | 0.016 | 0.820 | |
| getLocation | 1.497 | 0.028 | 1.527 | |
| gi2track | 0.045 | 0.000 | 0.045 | |
| gieStain | 0.005 | 0.000 | 0.005 | |
| ideogramPlot | 0 | 0 | 0 | |
| importBam | 0.300 | 0.000 | 0.299 | |
| importData | 3.265 | 0.020 | 3.285 | |
| importGInteractions | 0.639 | 0.003 | 0.646 | |
| importScSeqScore | 0 | 0 | 0 | |
| importScore | 0.642 | 0.016 | 0.657 | |
| listChromosomes | 0.471 | 0.004 | 0.475 | |
| listResolutions | 0.003 | 0.000 | 0.003 | |
| loadIdeogram | 0 | 0 | 0 | |
| lolliplot | 0.956 | 0.000 | 0.957 | |
| optimizeStyle | 0.521 | 0.008 | 0.530 | |
| parse2GRanges | 0.011 | 0.000 | 0.011 | |
| parseWIG | 15.983 | 0.332 | 16.316 | |
| plotGInteractions | 1.214 | 0.012 | 1.226 | |
| plotGRanges | 1.499 | 0.000 | 1.499 | |
| plotIdeo | 0 | 0 | 0 | |
| plotOneIdeo | 0 | 0 | 0 | |
| readHicBpResolutions | 0.001 | 0.000 | 0.001 | |
| readHicChroms | 0.002 | 0.000 | 0.002 | |
| readHicNormTypes | 0.003 | 0.000 | 0.004 | |
| straw | 0.003 | 0.000 | 0.003 | |
| trackStyle-class | 0.046 | 0.000 | 0.045 | |
| trackViewer-package | 22.729 | 0.356 | 23.085 | |
| trackViewerStyle-class | 0 | 0 | 0 | |
| viewGene | 5.520 | 0.048 | 5.567 | |
| viewTracks | 15.975 | 0.192 | 16.167 | |