| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-13 11:32:15 -0400 (Mon, 13 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
| 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 2117/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| trackViewer 1.41.0 (landing page) Jianhong Ou
| kjohnson1 | macOS 13.6.6 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: 1.41.0 |
| 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_1.41.0.tar.gz |
| StartedAt: 2024-05-13 05:41:36 -0400 (Mon, 13 May 2024) |
| EndedAt: 2024-05-13 05:51:07 -0400 (Mon, 13 May 2024) |
| EllapsedTime: 571.1 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_1.41.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/trackViewer.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-apple-darwin20
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘trackViewer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trackViewer’ version ‘1.41.0’
* 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 ... 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 code 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 23.948 0.189 24.297
viewTracks 17.460 0.105 17.604
browseTracks 16.754 0.081 16.896
parseWIG 15.806 0.115 15.944
geneModelFromTxdb 7.763 0.199 8.009
viewGene 6.694 0.102 6.847
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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/4.4-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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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, 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 -- Mon May 13 05:50:56 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
21.428 0.824 22.379
trackViewer.Rcheck/trackViewer-Ex.timings
| name | user | system | elapsed | |
| ARA | 1.805 | 0.089 | 1.910 | |
| GIoperator | 0.431 | 0.012 | 0.444 | |
| GRoperator | 2.268 | 0.015 | 2.312 | |
| addArrowMark | 0.014 | 0.001 | 0.016 | |
| addGuideLine | 0.004 | 0.000 | 0.005 | |
| addInteractionAnnotation | 0.738 | 0.013 | 0.754 | |
| browseTracks | 16.754 | 0.081 | 16.896 | |
| coverageGR | 0.263 | 0.010 | 0.275 | |
| dandelion.plot | 2.018 | 0.018 | 2.131 | |
| geneModelFromTxdb | 7.763 | 0.199 | 8.009 | |
| geneTrack | 4.104 | 0.127 | 4.264 | |
| getCurTrackViewport | 0.003 | 0.001 | 0.004 | |
| getGeneIDsFromTxDb | 1.021 | 0.042 | 1.065 | |
| getLocation | 1.983 | 0.079 | 2.068 | |
| gi2track | 0.048 | 0.001 | 0.050 | |
| gieStain | 0.005 | 0.001 | 0.007 | |
| ideogramPlot | 0.000 | 0.001 | 0.000 | |
| importBam | 0.342 | 0.002 | 0.345 | |
| importData | 3.691 | 0.025 | 3.729 | |
| importGInteractions | 0.535 | 0.015 | 0.554 | |
| importScSeqScore | 0.000 | 0.000 | 0.001 | |
| importScore | 0.652 | 0.019 | 0.673 | |
| listChromosomes | 0.465 | 0.029 | 0.495 | |
| listResolutions | 0.004 | 0.002 | 0.006 | |
| loadIdeogram | 0 | 0 | 0 | |
| lolliplot | 1.017 | 0.009 | 1.028 | |
| loopBouquetPlot | 2.025 | 0.058 | 2.100 | |
| optimizeStyle | 0.566 | 0.018 | 0.586 | |
| parse2GRanges | 0.012 | 0.001 | 0.012 | |
| parseWIG | 15.806 | 0.115 | 15.944 | |
| plotGRanges | 1.649 | 0.009 | 1.674 | |
| plotIdeo | 0.000 | 0.001 | 0.000 | |
| plotOneIdeo | 0 | 0 | 0 | |
| reduce-GInteractions-method | 0 | 0 | 0 | |
| trackStyle-class | 0.093 | 0.002 | 0.096 | |
| trackViewer-package | 23.948 | 0.189 | 24.297 | |
| trackViewerStyle-class | 0.001 | 0.000 | 0.000 | |
| viewGene | 6.694 | 0.102 | 6.847 | |
| viewTracks | 17.460 | 0.105 | 17.604 | |