| 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 2058/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SPLINTER 1.30.0 (landing page) Diana Low
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the SPLINTER package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SPLINTER.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: SPLINTER |
| Version: 1.30.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SPLINTER_1.30.0.tar.gz |
| StartedAt: 2024-10-17 05:29:51 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 05:36:30 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 398.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SPLINTER.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings SPLINTER_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/SPLINTER.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 ‘SPLINTER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPLINTER’ version ‘1.30.0’
* 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 ‘SPLINTER’ 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 ... 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
eventPlot 11.815 0.848 12.665
* 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: OK
SPLINTER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL SPLINTER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘SPLINTER’ ... ** 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 (SPLINTER)
SPLINTER.Rcheck/SPLINTER-Ex.timings
| name | user | system | elapsed | |
| acceptor.m | 0.002 | 0.000 | 0.002 | |
| addEnsemblAnnotation | 0.006 | 0.000 | 0.005 | |
| callPrimer3 | 0.000 | 0.000 | 0.001 | |
| checkPrimer | 0.07 | 0.00 | 0.07 | |
| compatible_cds | 0.001 | 0.000 | 0.001 | |
| compatible_tx | 0.001 | 0.000 | 0.001 | |
| donor.m | 0.000 | 0.000 | 0.001 | |
| eventOutcomeCompare | 1.184 | 0.051 | 1.235 | |
| eventOutcomeTranslate | 0.391 | 0.028 | 0.419 | |
| eventPlot | 11.815 | 0.848 | 12.665 | |
| extendROI | 0.613 | 0.083 | 0.696 | |
| extractSpliceEvents | 0.004 | 0.000 | 0.003 | |
| extractSpliceSites | 0.083 | 0.012 | 0.095 | |
| findCompatibleEvents | 0.341 | 0.008 | 0.349 | |
| findCompatibleExon | 0.189 | 0.004 | 0.193 | |
| findTX | 0.014 | 0.000 | 0.013 | |
| getPCRsizes | 2.298 | 0.184 | 2.481 | |
| getRegionDNA | 0.285 | 0.020 | 0.305 | |
| insertRegion | 0.227 | 0.016 | 0.243 | |
| makeROI | 0.256 | 0.008 | 0.264 | |
| makeUniqueIDs | 0.004 | 0.000 | 0.003 | |
| pcr_result1 | 0.001 | 0.000 | 0.001 | |
| plot_seqlogo | 0.045 | 0.000 | 0.045 | |
| primers | 0.001 | 0.000 | 0.001 | |
| psiPlot | 0.246 | 0.016 | 0.261 | |
| region_minus_exon | 0.001 | 0.000 | 0.001 | |
| roi | 0.001 | 0.000 | 0.001 | |
| shapiroAcceptor | 0.480 | 0.028 | 0.508 | |
| shapiroDonor | 0.398 | 0.004 | 0.403 | |
| splice_data | 0.000 | 0.001 | 0.001 | |
| splice_fasta | 0.000 | 0.001 | 0.001 | |
| splitPCRhit | 0.001 | 0.001 | 0.003 | |
| thecds | 0.001 | 0.000 | 0.001 | |
| theexons | 0.001 | 0.000 | 0.001 | |
| valid_cds | 0.001 | 0.000 | 0.001 | |
| valid_tx | 0.000 | 0.000 | 0.001 | |