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This page was generated on 2025-04-02 19:33 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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 2043/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPLINTER 1.32.0  (landing page)
Diana Low
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/SPLINTER
git_branch: RELEASE_3_20
git_last_commit: 547f458
git_last_commit_date: 2024-10-29 10:14:24 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for SPLINTER on merida1

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: 1.32.0
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: 2025-04-01 09:41:21 -0400 (Tue, 01 Apr 2025)
EndedAt: 2025-04-01 09:52:22 -0400 (Tue, 01 Apr 2025)
EllapsedTime: 660.9 seconds
RetCode: 0
Status:   OK  
CheckDir: SPLINTER.Rcheck
Warnings: 0

Command output

##############################################################################
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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 4.4.3 (2025-02-28)
* 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 ... 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   20.299  0.237  21.195
getPCRsizes  5.379  0.260   5.740
* 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/4.4-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)

Tests output


Example timings

SPLINTER.Rcheck/SPLINTER-Ex.timings

nameusersystemelapsed
acceptor.m0.0030.0030.005
addEnsemblAnnotation0.0110.0020.034
callPrimer30.0000.0010.001
checkPrimer0.1620.0050.198
compatible_cds0.0020.0020.003
compatible_tx0.0010.0020.003
donor.m0.0020.0020.004
eventOutcomeCompare2.8800.1493.070
eventOutcomeTranslate0.8310.0270.882
eventPlot20.299 0.23721.195
extendROI1.4780.0101.502
extractSpliceEvents0.0070.0010.008
extractSpliceSites0.2030.0020.208
findCompatibleEvents0.8060.0030.820
findCompatibleExon0.5340.0030.539
findTX0.0310.0010.033
getPCRsizes5.3790.2605.740
getRegionDNA0.6020.0250.631
insertRegion0.3720.0030.377
makeROI0.6560.0030.673
makeUniqueIDs0.0060.0010.007
pcr_result10.0020.0020.004
plot_seqlogo0.0800.0050.086
primers0.0010.0030.004
psiPlot0.5630.0170.584
region_minus_exon0.0020.0020.004
roi0.0010.0020.003
shapiroAcceptor0.9190.0300.974
shapiroDonor0.9190.0310.954
splice_data0.0010.0020.004
splice_fasta0.0020.0020.004
splitPCRhit0.0040.0010.005
thecds0.0020.0020.004
theexons0.0010.0020.004
valid_cds0.0020.0020.003
valid_tx0.0010.0020.004