Diana Low
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/SPLINTER |
| git_branch: RELEASE_3_17 |
| git_last_commit: 5116d5b |
| git_last_commit_date: 2023-04-25 10:49:52 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:37:35 -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 1997/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SPLINTER 1.26.0 (landing page) Diana Low
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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: 1.26.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SPLINTER_1.26.0.tar.gz |
| StartedAt: 2023-10-16 07:32:49 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 07:45:24 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 755.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SPLINTER.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SPLINTER_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/SPLINTER.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPLINTER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPLINTER’ version ‘1.26.0’
* 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 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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
eventPlot 20.157 0.349 25.590
getPCRsizes 5.225 0.269 6.789
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
SPLINTER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SPLINTER ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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 | 0.004 | 0.003 | 0.011 | |
| addEnsemblAnnotation | 0.011 | 0.003 | 0.018 | |
| callPrimer3 | 0.000 | 0.000 | 0.001 | |
| checkPrimer | 0.163 | 0.024 | 0.239 | |
| compatible_cds | 0.001 | 0.002 | 0.004 | |
| compatible_tx | 0.002 | 0.003 | 0.005 | |
| donor.m | 0.001 | 0.002 | 0.005 | |
| eventOutcomeCompare | 2.737 | 0.216 | 3.720 | |
| eventOutcomeTranslate | 0.812 | 0.108 | 1.138 | |
| eventPlot | 20.157 | 0.349 | 25.590 | |
| extendROI | 1.436 | 0.047 | 1.925 | |
| extractSpliceEvents | 0.007 | 0.001 | 0.010 | |
| extractSpliceSites | 0.185 | 0.002 | 0.232 | |
| findCompatibleEvents | 0.749 | 0.003 | 0.932 | |
| findCompatibleExon | 0.471 | 0.004 | 0.592 | |
| findTX | 0.033 | 0.001 | 0.043 | |
| getPCRsizes | 5.225 | 0.269 | 6.789 | |
| getRegionDNA | 0.524 | 0.026 | 0.690 | |
| insertRegion | 0.329 | 0.003 | 0.415 | |
| makeROI | 0.582 | 0.004 | 0.743 | |
| makeUniqueIDs | 0.007 | 0.001 | 0.013 | |
| pcr_result1 | 0.002 | 0.002 | 0.004 | |
| plot_seqlogo | 0.075 | 0.005 | 0.098 | |
| primers | 0.002 | 0.002 | 0.004 | |
| psiPlot | 0.567 | 0.026 | 0.768 | |
| region_minus_exon | 0.002 | 0.002 | 0.004 | |
| roi | 0.001 | 0.003 | 0.006 | |
| shapiroAcceptor | 0.878 | 0.046 | 1.101 | |
| shapiroDonor | 0.917 | 0.035 | 1.136 | |
| splice_data | 0.002 | 0.002 | 0.005 | |
| splice_fasta | 0.001 | 0.002 | 0.006 | |
| splitPCRhit | 0.004 | 0.000 | 0.005 | |
| thecds | 0.002 | 0.003 | 0.004 | |
| theexons | 0.001 | 0.002 | 0.004 | |
| valid_cds | 0.002 | 0.003 | 0.004 | |
| valid_tx | 0.002 | 0.003 | 0.005 | |