Michael Stadler
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/monaLisa |
| git_branch: RELEASE_3_19 |
| git_last_commit: fb2fed9 |
| git_last_commit_date: 2024-07-10 03:28:06 -0400 (Wed, 10 Jul 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:38 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 1318/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| monaLisa 1.10.1 (landing page) Michael Stadler
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. - 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: monaLisa |
| Version: 1.10.1 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:monaLisa.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings monaLisa_1.10.1.tar.gz |
| StartedAt: 2024-10-17 02:39:43 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 02:49:30 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 587.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: monaLisa.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:monaLisa.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings monaLisa_1.10.1.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/monaLisa.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.5 LTS
* using session charset: UTF-8
* checking for file ‘monaLisa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘monaLisa’ version ‘1.10.1’
* 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 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 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 ... NOTE
checkRd: (-1) calcBinnedKmerEnr.Rd:137-138: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedKmerEnr.Rd:139: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedKmerEnr.Rd:140-144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedKmerEnr.Rd:145-154: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedKmerEnr.Rd:155-162: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedKmerEnr.Rd:181-184: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedKmerEnr.Rd:185-188: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedKmerEnr.Rd:105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedKmerEnr.Rd:106: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedKmerEnr.Rd:107: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedKmerEnr.Rd:108-109: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedKmerEnr.Rd:110: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedKmerEnr.Rd:111-112: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedKmerEnr.Rd:113-114: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrHomer.Rd:62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrHomer.Rd:63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrHomer.Rd:64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrHomer.Rd:65-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrHomer.Rd:67: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrHomer.Rd:68-69: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrHomer.Rd:70-71: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrR.Rd:130-131: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedMotifEnrR.Rd:132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedMotifEnrR.Rd:133-137: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedMotifEnrR.Rd:138-147: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedMotifEnrR.Rd:166-169: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedMotifEnrR.Rd:170-173: Lost braces in \itemize; meant \describe ?
checkRd: (-1) calcBinnedMotifEnrR.Rd:96: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrR.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrR.Rd:98: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrR.Rd:99-100: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrR.Rd:101: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrR.Rd:102-103: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) calcBinnedMotifEnrR.Rd:104-105: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcKmerEnrichment.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcKmerEnrichment.Rd:23-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcKmerEnrichment.Rd:26-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcKmerEnrichment.Rd:28-29: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcKmerEnrichment.Rd:30-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcKmerEnrichment.Rd:32-33: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcMotifEnrichment.Rd:28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcMotifEnrichment.Rd:29-31: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcMotifEnrichment.Rd:32-34: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcMotifEnrichment.Rd:35-37: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcMotifEnrichment.Rd:38-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-calcMotifEnrichment.Rd:40-41: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-checkDfValidity.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-checkDfValidity.Rd:14-15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-checkDfValidity.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-checkDfValidity.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-checkDfValidity.Rd:18-19: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-checkDfValidity.Rd:20-21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) dot-iterativeNormForKmers.Rd:35-39: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) dot-iterativeNormForKmers.Rd:39-40: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) findMotifHits-methods.Rd:142-144: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findMotifHits-methods.Rd:145: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findMotifHits-methods.Rd:146: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findMotifHits-methods.Rd:151-152: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findMotifHits-methods.Rd:153: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findMotifHits-methods.Rd:154: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findMotifHits-methods.Rd:155-156: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findMotifHits-methods.Rd:165: Lost braces in \itemize; meant \describe ?
checkRd: (-1) findMotifHits-methods.Rd:166: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotBinDiagnostics.Rd:37-38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotBinDiagnostics.Rd:39-40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotBinDiagnostics.Rd:41-45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) randLassoStabSel.Rd:48-51: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:52-55: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:53: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:56-66: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:57-58: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:59-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:61-62: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:63-64: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:67-94: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:69-70: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:71-73: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:74-75: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:76-77: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:78-79: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:80-81: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:82-83: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:84-85: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:86-87: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:88-89: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:90: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) randLassoStabSel.Rd:91-92: Lost braces in \itemize; \value handles \item{}{} directly
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.19-bioc/meat/monaLisa.Rcheck/00check.log’
for details.
monaLisa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL monaLisa ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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 539 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_Homer.R:134:1'
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 539 ]
>
> proc.time()
user system elapsed
47.047 5.631 50.644
monaLisa.Rcheck/monaLisa-Ex.timings
| name | user | system | elapsed | |
| annoSeqlogo | 0.116 | 0.024 | 0.148 | |
| bin | 0.005 | 0.004 | 0.010 | |
| calcBinnedKmerEnr | 0.666 | 0.028 | 0.694 | |
| calcBinnedMotifEnrHomer | 0.006 | 0.000 | 0.006 | |
| calcBinnedMotifEnrR | 0.676 | 0.100 | 0.776 | |
| dumpJaspar | 0.023 | 0.004 | 0.027 | |
| findHomer | 0.004 | 0.000 | 0.004 | |
| findMotifHits-methods | 0.255 | 0.016 | 0.271 | |
| getColsByBin | 0.004 | 0.000 | 0.004 | |
| getKmerFreq | 0.034 | 0.000 | 0.034 | |
| getSetZeroBin | 0.002 | 0.000 | 0.002 | |
| homerToPFMatrixList | 0.06 | 0.00 | 0.06 | |
| motifKmerSimilarity | 0.017 | 0.004 | 0.021 | |
| motifSimilarity | 0.009 | 0.000 | 0.010 | |
| parseHomerOutput | 0.01 | 0.00 | 0.01 | |
| plotBinDensity | 0.013 | 0.000 | 0.013 | |
| plotBinDiagnostics | 0.617 | 0.004 | 0.622 | |
| plotBinHist | 0.009 | 0.000 | 0.009 | |
| plotBinScatter | 0.007 | 0.000 | 0.008 | |
| plotMotifHeatmaps | 4.236 | 0.036 | 4.273 | |
| plotSelectionProb | 2.041 | 0.136 | 2.177 | |
| plotStabilityPaths | 0.589 | 0.028 | 0.617 | |
| prepareHomer | 0.046 | 0.004 | 0.049 | |
| randLassoStabSel | 0.868 | 0.259 | 1.087 | |
| sampleRandomRegions | 0.37 | 0.12 | 0.05 | |
| seqLogoGrob | 0.182 | 0.024 | 0.207 | |