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This page was generated on 2022-06-27 11:10:09 -0400 (Mon, 27 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
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

CHECK results for SPLINTER on nebbiolo1


To the developers/maintainers of the SPLINTER package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1913/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPLINTER 1.22.0  (landing page)
Diana Low
Snapshot Date: 2022-06-26 13:55:11 -0400 (Sun, 26 Jun 2022)
git_url: https://git.bioconductor.org/packages/SPLINTER
git_branch: RELEASE_3_15
git_last_commit: b0553c0
git_last_commit_date: 2022-04-26 11:35:57 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SPLINTER
Version: 1.22.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings SPLINTER_1.22.0.tar.gz
StartedAt: 2022-06-26 22:05:33 -0400 (Sun, 26 Jun 2022)
EndedAt: 2022-06-26 22:10:34 -0400 (Sun, 26 Jun 2022)
EllapsedTime: 300.0 seconds
RetCode: 0
Status:   OK  
CheckDir: SPLINTER.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings SPLINTER_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/SPLINTER.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPLINTER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPLINTER’ version ‘1.22.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
eventPlot 11.457  0.395  11.856
* 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


Installation output

SPLINTER.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL SPLINTER
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘SPLINTER’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
** testing if installed package can be loaded from final location
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
** testing if installed package keeps a record of temporary installation path
* DONE (SPLINTER)

Tests output


Example timings

SPLINTER.Rcheck/SPLINTER-Ex.timings

nameusersystemelapsed
acceptor.m0.0000.0020.002
addEnsemblAnnotation0.0060.0000.007
callPrimer3000
checkPrimer0.0630.0030.066
compatible_cds0.0000.0000.001
compatible_tx000
donor.m0.0000.0010.001
eventOutcomeCompare1.1660.0891.256
eventOutcomeTranslate0.3610.0030.366
eventPlot11.457 0.39511.856
extendROI0.6380.0160.654
extractSpliceEvents0.0020.0000.003
extractSpliceSites0.0760.0000.075
findCompatibleEvents0.2890.0000.289
findCompatibleExon0.2010.0120.213
findTX0.0140.0000.014
getPCRsizes3.3900.3243.714
getRegionDNA0.3010.0040.305
insertRegion0.1480.0080.155
makeROI0.2360.0160.252
makeUniqueIDs0.0000.0040.004
pcr_result10.0000.0010.001
plot_seqlogo0.0390.0060.045
primers0.0010.0000.001
psiPlot0.2130.0240.237
region_minus_exon0.0010.0000.001
roi0.0010.0000.001
shapiroAcceptor0.4070.0120.421
shapiroDonor0.3470.0040.351
splice_data0.0000.0020.001
splice_fasta0.0000.0010.001
splitPCRhit0.0000.0030.003
thecds0.0000.0000.001
theexons0.0010.0000.001
valid_cds0.0010.0000.001
valid_tx0.0000.0010.001