| Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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 2043/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SPLINTER 1.32.0 (landing page) Diana Low
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
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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: 1.32.0 |
| 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_1.32.0.tar.gz |
| StartedAt: 2024-11-20 03:02:27 -0500 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 03:11:01 -0500 (Wed, 20 Nov 2024) |
| EllapsedTime: 513.4 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_1.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SPLINTER.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPLINTER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPLINTER’ version ‘1.32.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 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 9.333 0.146 9.537
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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/4.4-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 | 0.002 | 0.001 | 0.002 | |
| addEnsemblAnnotation | 0.004 | 0.001 | 0.005 | |
| callPrimer3 | 0 | 0 | 0 | |
| checkPrimer | 0.056 | 0.002 | 0.058 | |
| compatible_cds | 0.001 | 0.001 | 0.001 | |
| compatible_tx | 0.001 | 0.000 | 0.001 | |
| donor.m | 0.001 | 0.000 | 0.001 | |
| eventOutcomeCompare | 1.079 | 0.059 | 1.145 | |
| eventOutcomeTranslate | 0.333 | 0.016 | 0.350 | |
| eventPlot | 9.333 | 0.146 | 9.537 | |
| extendROI | 0.536 | 0.004 | 0.542 | |
| extractSpliceEvents | 0.003 | 0.001 | 0.003 | |
| extractSpliceSites | 0.071 | 0.001 | 0.072 | |
| findCompatibleEvents | 0.260 | 0.001 | 0.263 | |
| findCompatibleExon | 0.189 | 0.001 | 0.193 | |
| findTX | 0.011 | 0.000 | 0.011 | |
| getPCRsizes | 2.993 | 0.143 | 3.158 | |
| getRegionDNA | 0.211 | 0.015 | 0.227 | |
| insertRegion | 0.127 | 0.001 | 0.130 | |
| makeROI | 0.215 | 0.002 | 0.219 | |
| makeUniqueIDs | 0.003 | 0.000 | 0.003 | |
| pcr_result1 | 0.001 | 0.001 | 0.001 | |
| plot_seqlogo | 0.032 | 0.003 | 0.036 | |
| primers | 0.001 | 0.001 | 0.001 | |
| psiPlot | 0.223 | 0.012 | 0.236 | |
| region_minus_exon | 0.001 | 0.001 | 0.002 | |
| roi | 0.001 | 0.001 | 0.002 | |
| shapiroAcceptor | 0.361 | 0.021 | 0.386 | |
| shapiroDonor | 0.340 | 0.018 | 0.359 | |
| splice_data | 0.001 | 0.001 | 0.001 | |
| splice_fasta | 0.001 | 0.001 | 0.001 | |
| splitPCRhit | 0.002 | 0.000 | 0.002 | |
| thecds | 0.001 | 0.001 | 0.002 | |
| theexons | 0.000 | 0.001 | 0.002 | |
| valid_cds | 0.000 | 0.001 | 0.002 | |
| valid_tx | 0.000 | 0.000 | 0.002 | |