| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:52 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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 2063/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| trackViewer 1.35.4 (landing page) Jianhong Ou
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: trackViewer |
| Version: 1.35.4 |
| 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/library --timings trackViewer_1.35.4.tar.gz |
| StartedAt: 2023-02-28 17:44:37 -0000 (Tue, 28 Feb 2023) |
| EndedAt: 2023-02-28 18:10:08 -0000 (Tue, 28 Feb 2023) |
| EllapsedTime: 1530.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: trackViewer.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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/library --timings trackViewer_1.35.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/trackViewer.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* 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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘trackViewer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trackViewer’ version ‘1.35.4’
* 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
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
extdata 3.0Mb
libs 1.9Mb
* 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 30.637 0.056 30.693
browseTracks 21.722 0.660 25.258
parseWIG 21.674 0.064 21.738
viewTracks 21.260 0.180 21.440
geneModelFromTxdb 8.086 0.220 8.307
viewGene 7.777 0.020 7.798
GRoperator 3.514 0.167 5.610
* 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-3.17-bioc/meat/trackViewer.Rcheck/00check.log’
for details.
trackViewer.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL trackViewer
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘trackViewer’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-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);
| ^~~~~~~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o trackViewer.so RcppExports.o hic.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-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 Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
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 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 Feb 28 17:54:13 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
22.248 1.280 23.520
trackViewer.Rcheck/trackViewer-Ex.timings
| name | user | system | elapsed | |
| GRoperator | 3.514 | 0.167 | 5.610 | |
| addArrowMark | 0.010 | 0.000 | 0.011 | |
| addGuideLine | 0.006 | 0.000 | 0.006 | |
| browseTracks | 21.722 | 0.660 | 25.258 | |
| coverageGR | 0.285 | 0.000 | 0.285 | |
| dandelion.plot | 3.257 | 0.008 | 3.262 | |
| geneModelFromTxdb | 8.086 | 0.220 | 8.307 | |
| geneTrack | 4.029 | 0.128 | 4.157 | |
| getCurTrackViewport | 0.003 | 0.000 | 0.004 | |
| getGeneIDsFromTxDb | 1.177 | 0.004 | 1.181 | |
| getLocation | 1.728 | 0.040 | 1.768 | |
| gi2track | 0.062 | 0.004 | 0.066 | |
| gieStain | 0.007 | 0.000 | 0.008 | |
| ideogramPlot | 0 | 0 | 0 | |
| importBam | 0.425 | 0.000 | 0.425 | |
| importData | 3.354 | 0.000 | 3.354 | |
| importGInteractions | 2.345 | 0.008 | 2.363 | |
| importScSeqScore | 0 | 0 | 0 | |
| importScore | 0.895 | 0.000 | 0.896 | |
| listChromosomes | 0.751 | 0.032 | 0.783 | |
| listResolutions | 0.004 | 0.000 | 0.004 | |
| loadIdeogram | 0 | 0 | 0 | |
| lolliplot | 1.334 | 0.024 | 1.357 | |
| optimizeStyle | 0.803 | 0.008 | 0.812 | |
| parse2GRanges | 0.016 | 0.000 | 0.016 | |
| parseWIG | 21.674 | 0.064 | 21.738 | |
| plotGInteractions | 1.712 | 0.000 | 1.713 | |
| plotGRanges | 2.215 | 0.000 | 2.214 | |
| plotIdeo | 0 | 0 | 0 | |
| plotOneIdeo | 0 | 0 | 0 | |
| trackStyle-class | 0.064 | 0.004 | 0.068 | |
| trackViewer-package | 30.637 | 0.056 | 30.693 | |
| trackViewerStyle-class | 0 | 0 | 0 | |
| viewGene | 7.777 | 0.020 | 7.798 | |
| viewTracks | 21.26 | 0.18 | 21.44 | |