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This page was generated on 2024-03-29 11:36:25 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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 2034/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPLINTER 1.28.0  (landing page)
Diana Low
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/SPLINTER
git_branch: RELEASE_3_18
git_last_commit: 501b0f9
git_last_commit_date: 2023-10-24 10:53:00 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for SPLINTER on nebbiolo2


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: 1.28.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings SPLINTER_1.28.0.tar.gz
StartedAt: 2024-03-28 03:04:32 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 03:11:18 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 405.2 seconds
RetCode: 0
Status:   OK  
CheckDir: SPLINTER.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings SPLINTER_1.28.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SPLINTER.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* 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 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘SPLINTER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPLINTER’ version ‘1.28.0’
* 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 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 10.57  0.332  10.904
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

SPLINTER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL SPLINTER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-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)

Tests output


Example timings

SPLINTER.Rcheck/SPLINTER-Ex.timings

nameusersystemelapsed
acceptor.m0.0020.0000.002
addEnsemblAnnotation0.0060.0000.005
callPrimer30.0010.0000.000
checkPrimer0.0690.0000.069
compatible_cds0.0010.0000.001
compatible_tx0.0000.0000.001
donor.m0.0000.0000.001
eventOutcomeCompare1.2030.0601.264
eventOutcomeTranslate0.3610.0240.385
eventPlot10.570 0.33210.904
extendROI0.5860.0040.590
extractSpliceEvents0.0030.0000.003
extractSpliceSites0.0760.0000.075
findCompatibleEvents0.2910.0040.295
findCompatibleExon0.1980.0000.198
findTX0.0140.0000.014
getPCRsizes3.4620.2643.726
getRegionDNA0.2660.0000.266
insertRegion0.150.000.15
makeROI0.2570.0040.260
makeUniqueIDs0.0040.0000.004
pcr_result10.0010.0000.001
plot_seqlogo0.0360.0080.044
primers0.0010.0000.001
psiPlot0.2460.0040.251
region_minus_exon0.0010.0000.001
roi0.0010.0000.001
shapiroAcceptor0.4440.0080.452
shapiroDonor0.3630.0160.380
splice_data0.0000.0010.001
splice_fasta0.0000.0000.001
splitPCRhit0.0010.0010.002
thecds0.0010.0000.000
theexons0.0010.0000.000
valid_cds0.0010.0000.001
valid_tx0.0010.0000.001