| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:39 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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 | ||||
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To the developers/maintainers of the monaLisa package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/monaLisa.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1264/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| monaLisa 1.5.0 (landing page) Michael Stadler
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: monaLisa |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:monaLisa.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings monaLisa_1.5.0.tar.gz |
| StartedAt: 2023-04-12 07:36:45 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 07:48:05 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 680.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: monaLisa.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:monaLisa.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings monaLisa_1.5.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/monaLisa.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘monaLisa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘monaLisa’ version ‘1.5.0’
* 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 ‘monaLisa’ 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 ... 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘monaLisa.Rmd’ using ‘UTF-8’... OK
‘selecting_motifs_with_randLassoStabSel.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
monaLisa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL monaLisa ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘monaLisa’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (monaLisa)
monaLisa.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
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(monaLisa)
>
> test_check("monaLisa")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 537 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (1)
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 537 ]
>
> proc.time()
user system elapsed
51.427 4.218 53.428
monaLisa.Rcheck/monaLisa-Ex.timings
| name | user | system | elapsed | |
| annoSeqlogo | 0.149 | 0.016 | 0.172 | |
| bin | 0.008 | 0.000 | 0.007 | |
| calcBinnedKmerEnr | 0.809 | 0.079 | 0.888 | |
| calcBinnedMotifEnrHomer | 0.001 | 0.004 | 0.005 | |
| calcBinnedMotifEnrR | 0.623 | 0.092 | 0.715 | |
| dumpJaspar | 0.022 | 0.008 | 0.032 | |
| findHomer | 0.003 | 0.000 | 0.003 | |
| findMotifHits-methods | 1.244 | 0.120 | 1.364 | |
| getColsByBin | 0.003 | 0.000 | 0.003 | |
| getKmerFreq | 0.026 | 0.000 | 0.026 | |
| getSetZeroBin | 0.000 | 0.001 | 0.002 | |
| homerToPFMatrixList | 0.048 | 0.002 | 0.050 | |
| motifKmerSimilarity | 0.017 | 0.000 | 0.017 | |
| motifSimilarity | 0.008 | 0.000 | 0.008 | |
| parseHomerOutput | 0.009 | 0.000 | 0.008 | |
| plotBinDensity | 0.012 | 0.000 | 0.013 | |
| plotBinDiagnostics | 0.536 | 0.000 | 0.538 | |
| plotBinHist | 0.007 | 0.000 | 0.008 | |
| plotBinScatter | 0.006 | 0.000 | 0.007 | |
| plotMotifHeatmaps | 4.627 | 0.072 | 4.700 | |
| plotSelectionProb | 0.889 | 0.028 | 0.916 | |
| plotStabilityPaths | 0.637 | 0.020 | 0.657 | |
| prepareHomer | 0.054 | 0.004 | 0.058 | |
| randLassoStabSel | 0.976 | 0.350 | 1.259 | |
| sampleRandomRegions | 0.396 | 0.264 | 0.076 | |
| seqLogoGrob | 0.188 | 0.024 | 0.214 | |