| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:23 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 818/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenVisR 1.32.0 (landing page) Zachary Skidmore
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the GenVisR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenVisR.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: GenVisR |
| Version: 1.32.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GenVisR_1.32.0.tar.gz |
| StartedAt: 2023-10-15 21:37:30 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 21:48:32 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 661.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: GenVisR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:GenVisR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings GenVisR_1.32.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/GenVisR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GenVisR/DESCRIPTION’ ... OK
* this is package ‘GenVisR’ version ‘1.32.0’
* 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 ‘GenVisR’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘reshape2’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
setTierTwo,data.table : a: no visible binding for global variable ‘tmp’
toLolliplot,GMS: no visible binding for global variable ‘missingINdex’
Undefined global functions or variables:
missingINdex tmp
* 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 LazyData ... 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
Lolliplot-class 18.867 1.639 31.612
genCov 7.026 0.288 7.315
geneViz 6.933 0.196 7.130
cnFreq 5.188 0.352 5.540
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
• MutSpectra-class/mutspectra-frequency-plot-custom-pallette.svg
• MutSpectra-class/mutspectra-frequency-plot.svg
• MutSpectra-class/mutspectra-proportion-plot-add-layer.svg
• MutSpectra-class/mutspectra-proportion-plot-custom-pallette.svg
• MutSpectra-class/mutspectra-proportion-plot.svg
• Rainfall-class/density-main-plot.svg
• Rainfall-class/density-plot-add-layer.svg
• Rainfall-class/drawplot-rainfall.svg
• Rainfall-class/final-rainfall-alter-section-hieghts.svg
• Rainfall-class/final-rainfall-base.svg
• Rainfall-class/rainfall-main-plot.svg
• Rainfall-class/rainfall-plot-add-layer.svg
• Rainfall-class/rainfall-plot-aesthetic-options.svg
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘Intro.Rmd’ using ‘UTF-8’... OK
‘waterfall_introduction.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/GenVisR.Rcheck/00check.log’
for details.
GenVisR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL GenVisR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘GenVisR’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (GenVisR)
GenVisR.Rcheck/tests/testthat.Rout.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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.
> library(testthat)
> library(GenVisR)
>
> test_check("GenVisR")
[ FAIL 1 | WARN 17 | SKIP 54 | PASS 601 ]
══ Skipped tests (54) ══════════════════════════════════════════════════════════
• On Bioconductor (54): 'test-Lolliplot-class.R:581:5',
'test-Lolliplot-class.R:591:6', 'test-Lolliplot-class.R:619:5',
'test-Lolliplot-class.R:631:5', 'test-Lolliplot-class.R:645:5',
'test-Lolliplot-class.R:657:5', 'test-Lolliplot-class.R:673:5',
'test-Lolliplot-class.R:756:5', 'test-Lolliplot-class.R:766:5',
'test-Lolliplot-class.R:808:5', 'test-MutSpectra-class.R:284:5',
'test-MutSpectra-class.R:294:5', 'test-MutSpectra-class.R:305:5',
'test-MutSpectra-class.R:341:5', 'test-MutSpectra-class.R:351:5',
'test-MutSpectra-class.R:362:5', 'test-MutSpectra-class.R:416:5',
'test-MutSpectra-class.R:426:5', 'test-MutSpectra-class.R:456:5',
'test-MutSpectra-class.R:464:5', 'test-Rainfall-class.R:246:5',
'test-Rainfall-class.R:255:5', 'test-Rainfall-class.R:265:5',
'test-Rainfall-class.R:302:5', 'test-Rainfall-class.R:311:5',
'test-Rainfall-class.R:357:5', 'test-Rainfall-class.R:366:5',
'test-Rainfall-class.R:403:5', 'test-Waterfall-class.R:661:5',
'test-Waterfall-class.R:671:5', 'test-Waterfall-class.R:681:5',
'test-Waterfall-class.R:691:5', 'test-Waterfall-class.R:728:5',
'test-Waterfall-class.R:742:5', 'test-Waterfall-class.R:752:5',
'test-Waterfall-class.R:762:5', 'test-Waterfall-class.R:772:5',
'test-Waterfall-class.R:809:5', 'test-Waterfall-class.R:823:5',
'test-Waterfall-class.R:836:5', 'test-Waterfall-class.R:849:5',
'test-Waterfall-class.R:862:5', 'test-Waterfall-class.R:875:5',
'test-Waterfall-class.R:888:5', 'test-Waterfall-class.R:932:5',
'test-Waterfall-class.R:1023:5', 'test-Waterfall-class.R:1033:5',
'test-Waterfall-class.R:1049:5', 'test-Waterfall-class.R:1065:5',
'test-Waterfall-class.R:1081:5', 'test-Waterfall-class.R:1098:5',
'test-Waterfall-class.R:1114:5', 'test-Waterfall-class.R:1152:5',
'test-Waterfall-class.R:1159:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-Lolliplot-class.R:526:5'): setDomainHeights domains are nested correctly ──
`expected` not equivalent to `actual`.
1/1 mismatches
[1] 2 - 10 == -8
[ FAIL 1 | WARN 17 | SKIP 54 | PASS 601 ]
Deleting unused snapshots:
• Lolliplot-class/drawplot-lolliplot.svg
• Lolliplot-class/final-lolliplot-alter-section-height.svg
• Lolliplot-class/final-lolliplot-base.svg
• Lolliplot-class/lolliplot-density-plot-layer.svg
• Lolliplot-class/lolliplot-density-plot.svg
• Lolliplot-class/lolliplot-plot-base-add-domain-palette.svg
• Lolliplot-class/lolliplot-plot-base-add-labels.svg
• Lolliplot-class/lolliplot-plot-base-add-layer.svg
• Lolliplot-class/lolliplot-plot-base-add-mutation-palette.svg
• Lolliplot-class/lolliplot-plot-base.svg
• MutSpectra-class/drawplot-mutspectra.svg
• MutSpectra-class/final-mutspectra-alter-section-heights.svg
• MutSpectra-class/final-mutspectra-base.svg
• MutSpectra-class/mutspectra-clinical.svg
• MutSpectra-class/mutspectra-frequency-plot-add-layer.svg
• MutSpectra-class/mutspectra-frequency-plot-custom-pallette.svg
• MutSpectra-class/mutspectra-frequency-plot.svg
• MutSpectra-class/mutspectra-proportion-plot-add-layer.svg
• MutSpectra-class/mutspectra-proportion-plot-custom-pallette.svg
• MutSpectra-class/mutspectra-proportion-plot.svg
• Rainfall-class/density-main-plot.svg
• Rainfall-class/density-plot-add-layer.svg
• Rainfall-class/drawplot-rainfall.svg
• Rainfall-class/final-rainfall-alter-section-hieghts.svg
• Rainfall-class/final-rainfall-base.svg
• Rainfall-class/rainfall-main-plot.svg
• Rainfall-class/rainfall-plot-add-layer.svg
• Rainfall-class/rainfall-plot-aesthetic-options.svg
Error: Test failures
Execution halted
GenVisR.Rcheck/GenVisR-Ex.timings
| name | user | system | elapsed | |
| Lolliplot-class | 18.867 | 1.639 | 31.612 | |
| TvTi | 1.624 | 0.172 | 1.795 | |
| Waterfall-class | 0.506 | 0.036 | 0.541 | |
| cnFreq | 5.188 | 0.352 | 5.540 | |
| cnSpec | 3.794 | 0.132 | 3.926 | |
| cnView | 0.631 | 0.020 | 0.652 | |
| compIdent | 1.656 | 0.232 | 1.888 | |
| covBars | 0.850 | 0.064 | 0.914 | |
| genCov | 7.026 | 0.288 | 7.315 | |
| geneViz | 6.933 | 0.196 | 7.130 | |
| ideoView | 0.409 | 0.028 | 0.437 | |
| lohSpec | 3.640 | 0.172 | 3.820 | |
| lohView | 0.553 | 0.003 | 0.557 | |
| waterfall | 0.969 | 0.004 | 0.972 | |