| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:20 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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 | ||||
| Package 2157/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| trackViewer 1.38.2 (landing page) Jianhong Ou
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | NA | ||||||||
|
To the developers/maintainers of the trackViewer package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: trackViewer |
| Version: 1.38.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings trackViewer_1.38.2.tar.gz |
| StartedAt: 2024-04-18 06:34:03 -0400 (Thu, 18 Apr 2024) |
| EndedAt: 2024-04-18 06:43:16 -0400 (Thu, 18 Apr 2024) |
| EllapsedTime: 552.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: trackViewer.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:trackViewer.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings trackViewer_1.38.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/trackViewer.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘trackViewer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trackViewer’ version ‘1.38.2’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
trackViewer-package 24.512 0.201 25.231
viewTracks 18.138 0.088 18.466
browseTracks 17.569 0.135 18.369
parseWIG 16.841 0.091 17.335
geneModelFromTxdb 7.916 0.223 8.297
viewGene 6.906 0.186 7.430
* 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: OK
trackViewer.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL trackViewer ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 -- Thu Apr 18 06:43:04 2024
***********************************************
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
23.871 1.154 25.530
trackViewer.Rcheck/trackViewer-Ex.timings
| name | user | system | elapsed | |
| ARA | 3.200 | 0.112 | 3.349 | |
| GIoperator | 0.431 | 0.008 | 0.441 | |
| GRoperator | 2.266 | 0.084 | 2.379 | |
| addArrowMark | 0.014 | 0.002 | 0.015 | |
| addGuideLine | 0.004 | 0.000 | 0.004 | |
| addInteractionAnnotation | 0.735 | 0.013 | 0.753 | |
| browseTracks | 17.569 | 0.135 | 18.369 | |
| coverageGR | 0.243 | 0.002 | 0.252 | |
| dandelion.plot | 2.494 | 0.032 | 2.569 | |
| geneModelFromTxdb | 7.916 | 0.223 | 8.297 | |
| geneTrack | 2.488 | 0.046 | 2.638 | |
| getCurTrackViewport | 0.003 | 0.001 | 0.003 | |
| getGeneIDsFromTxDb | 1.207 | 0.036 | 1.270 | |
| getLocation | 1.962 | 0.093 | 2.111 | |
| gi2track | 0.051 | 0.002 | 0.052 | |
| gieStain | 0.006 | 0.001 | 0.008 | |
| ideogramPlot | 0.000 | 0.001 | 0.000 | |
| importBam | 0.348 | 0.005 | 0.357 | |
| importData | 3.877 | 0.037 | 3.995 | |
| importGInteractions | 0.577 | 0.015 | 0.604 | |
| importScSeqScore | 0.001 | 0.000 | 0.000 | |
| importScore | 0.694 | 0.027 | 0.733 | |
| listChromosomes | 0.439 | 0.007 | 0.491 | |
| listResolutions | 0.005 | 0.001 | 0.007 | |
| loadIdeogram | 0.000 | 0.001 | 0.000 | |
| lolliplot | 1.104 | 0.014 | 1.174 | |
| optimizeStyle | 0.584 | 0.018 | 0.644 | |
| parse2GRanges | 0.014 | 0.000 | 0.016 | |
| parseWIG | 16.841 | 0.091 | 17.335 | |
| plotGInteractions | 1.520 | 0.069 | 1.673 | |
| plotGRanges | 1.769 | 0.020 | 1.911 | |
| plotIdeo | 0 | 0 | 0 | |
| plotOneIdeo | 0 | 0 | 0 | |
| trackStyle-class | 0.059 | 0.001 | 0.064 | |
| trackViewer-package | 24.512 | 0.201 | 25.231 | |
| trackViewerStyle-class | 0.000 | 0.000 | 0.001 | |
| viewGene | 6.906 | 0.186 | 7.430 | |
| viewTracks | 18.138 | 0.088 | 18.466 | |