Back to Multiple platform build/check report for BioC 3.22:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2025-10-30 12:36 -0400 (Thu, 30 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4901
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4691
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
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 2110/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPLINTER 1.36.0  (landing page)
Diana Low
Snapshot Date: 2025-10-29 19:52 -0400 (Wed, 29 Oct 2025)
git_url: https://git.bioconductor.org/packages/SPLINTER
git_branch: RELEASE_3_22
git_last_commit: 00c62ac
git_last_commit_date: 2025-10-29 10:34:37 -0400 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped


CHECK results for SPLINTER on lconway

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.

raw results


Summary

Package: SPLINTER
Version: 1.36.0
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_1.36.0.tar.gz
StartedAt: 2025-10-30 07:10:08 -0400 (Thu, 30 Oct 2025)
EndedAt: 2025-10-30 07:16:28 -0400 (Thu, 30 Oct 2025)
EllapsedTime: 379.8 seconds
RetCode: 0
Status:   OK  
CheckDir: SPLINTER.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SPLINTER.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘1.36.0’
* 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 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 12.753   0.22  13.017
* 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


Installation output

SPLINTER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SPLINTER
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SPLINTER’ ...
** this is package ‘SPLINTER’ version ‘1.36.0’
** 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)

Tests output


Example timings

SPLINTER.Rcheck/SPLINTER-Ex.timings

nameusersystemelapsed
acceptor.m0.0020.0010.003
addEnsemblAnnotation0.0070.0020.008
callPrimer3000
checkPrimer0.0780.0090.087
compatible_cds0.0010.0020.002
compatible_tx0.0010.0010.002
donor.m0.0010.0010.002
eventOutcomeCompare1.5380.0971.652
eventOutcomeTranslate0.4550.0480.505
eventPlot12.753 0.22013.017
extendROI0.6150.0180.635
extractSpliceEvents0.0030.0010.003
extractSpliceSites0.0900.0010.090
findCompatibleEvents0.3520.0010.354
findCompatibleExon0.2330.0010.234
findTX0.0190.0010.019
getPCRsizes2.4730.1772.666
getRegionDNA0.3670.0190.388
insertRegion0.2370.0020.241
makeROI0.3100.0010.312
makeUniqueIDs0.0030.0000.004
pcr_result10.0010.0010.002
plot_seqlogo0.0470.0030.051
primers0.0010.0010.002
psiPlot0.3530.0070.361
region_minus_exon0.0010.0010.002
roi0.0010.0010.002
shapiroAcceptor0.5530.0470.608
shapiroDonor0.5600.0260.593
splice_data0.0000.0010.002
splice_fasta0.0000.0010.002
splitPCRhit0.0010.0010.002
thecds0.0010.0010.002
theexons0.0010.0010.002
valid_cds0.0000.0010.002
valid_tx0.0010.0010.003