Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-13 11:32:05 -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 904/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Gviz 1.49.0 (landing page) Robert Ivanek
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the Gviz 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: Gviz |
Version: 1.49.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Gviz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Gviz_1.49.0.tar.gz |
StartedAt: 2024-05-12 15:51:33 -0400 (Sun, 12 May 2024) |
EndedAt: 2024-05-12 16:01:40 -0400 (Sun, 12 May 2024) |
EllapsedTime: 606.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Gviz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Gviz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Gviz_1.49.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/Gviz.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 ‘Gviz/DESCRIPTION’ ... OK * this is package ‘Gviz’ version ‘1.49.0’ * 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 ‘Gviz’ can be installed ... OK * checking installed package size ... NOTE installed size is 5.1Mb sub-directories of 1Mb or more: R 1.7Mb extdata 2.5Mb * 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 whether startup messages can be suppressed ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed AlignmentsTrack-class 18.545 0.566 19.214 AnnotationTrack-class 9.628 0.117 9.796 GeneRegionTrack-class 7.472 0.088 7.644 SequenceTrack-class 6.457 0.352 6.938 plotTracks 5.638 0.033 5.692 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: 1 NOTE See ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/Gviz.Rcheck/00check.log’ for details.
Gviz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Gviz ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘Gviz’ ... ** using staged installation ** R ** data ** 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 (Gviz)
Gviz.Rcheck/tests/testthat.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. > library(testthat) > library(Gviz) Loading required package: S4Vectors 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 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: GenomicRanges Loading required package: GenomeInfoDb Loading required package: grid > > test_check("Gviz") Loading required package: BSgenome Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:grid': pattern The following object is masked from 'package:base': strsplit Loading required package: BiocIO Loading required package: rtracklayer Attaching package: 'rtracklayer' The following object is masked from 'package:BiocIO': FileForFormat [ FAIL 0 | WARN 0 | SKIP 1 | PASS 293 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • Biomart not available (1): 'test_AllClasses.R:174:5' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 293 ] > > proc.time() user system elapsed 76.494 4.673 81.670
Gviz.Rcheck/Gviz-Ex.timings
name | user | system | elapsed | |
AlignmentsTrack-class | 18.545 | 0.566 | 19.214 | |
AnnotationTrack-class | 9.628 | 0.117 | 9.796 | |
BiomartGeneRegionTrack-class | 4.048 | 0.043 | 4.109 | |
CustomTrack-class | 0.010 | 0.001 | 0.010 | |
DataTrack-class | 2.939 | 0.034 | 2.982 | |
DisplayPars-class | 0.017 | 0.002 | 0.019 | |
GdObject-class | 0.518 | 0.004 | 0.523 | |
GeneRegionTrack-class | 7.472 | 0.088 | 7.644 | |
GenomeAxisTrack-class | 4.836 | 0.028 | 4.909 | |
HighlightTrack-class | 0.230 | 0.006 | 0.238 | |
IdeogramTrack-class | 1.847 | 0.016 | 1.870 | |
ImageMap-class | 0 | 0 | 0 | |
OverlayTrack-class | 0.049 | 0.001 | 0.050 | |
RangeTrack-class | 0.506 | 0.004 | 0.513 | |
ReferenceTrack-class | 2.499 | 0.096 | 2.602 | |
SequenceTrack-class | 6.457 | 0.352 | 6.938 | |
StackedTrack-class | 0.959 | 0.009 | 0.973 | |
UcscTrack | 0.919 | 0.013 | 0.934 | |
exportTracks | 0.090 | 0.002 | 0.092 | |
plotTracks | 5.638 | 0.033 | 5.692 | |
settings | 0.814 | 0.007 | 0.826 | |