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This page was generated on 2023-03-27 05:50:44 -0000 (Mon, 27 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" 6083
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CHECK results for SPLINTER on kunpeng1


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 1966/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPLINTER 1.25.0  (landing page)
Diana Low
Snapshot Date: 2023-03-24 01:40:07 -0000 (Fri, 24 Mar 2023)
git_url: https://git.bioconductor.org/packages/SPLINTER
git_branch: devel
git_last_commit: a01a9bb
git_last_commit_date: 2022-11-01 15:14:31 -0000 (Tue, 01 Nov 2022)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: SPLINTER
Version: 1.25.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SPLINTER_1.25.0.tar.gz
StartedAt: 2023-03-25 13:19:59 -0000 (Sat, 25 Mar 2023)
EndedAt: 2023-03-25 13:27:40 -0000 (Sat, 25 Mar 2023)
EllapsedTime: 461.6 seconds
RetCode: 0
Status:   OK  
CheckDir: SPLINTER.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SPLINTER.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SPLINTER_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SPLINTER.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘SPLINTER/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SPLINTER’ version ‘1.25.0’
* 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 13.666  0.724  14.395
* 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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SPLINTER
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/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
addEnsemblAnnotation0.0020.0040.007
callPrimer3000
checkPrimer0.0920.0000.092
compatible_cds0.0010.0000.001
compatible_tx0.0010.0000.001
donor.m0.0010.0000.000
eventOutcomeCompare1.5780.0881.667
eventOutcomeTranslate0.4220.0520.474
eventPlot13.666 0.72414.395
extendROI0.7780.0440.822
extractSpliceEvents0.0040.0000.004
extractSpliceSites0.1080.0000.107
findCompatibleEvents0.4130.0040.416
findCompatibleExon0.2560.0000.256
findTX0.0140.0040.018
getPCRsizes4.3690.2724.666
getRegionDNA0.2990.0240.323
insertRegion0.1960.0200.215
makeROI0.3420.0040.346
makeUniqueIDs0.0040.0000.005
pcr_result10.0010.0000.001
plot_seqlogo0.0510.0000.050
primers0.0010.0000.001
psiPlot0.3050.0200.324
region_minus_exon0.0010.0000.002
roi0.0010.0000.001
shapiroAcceptor0.5090.0150.527
shapiroDonor0.4530.0210.474
splice_data0.0010.0000.001
splice_fasta0.0010.0000.001
splitPCRhit0.0020.0000.002
thecds0.0010.0000.001
theexons0.0010.0000.001
valid_cds0.0000.0000.001
valid_tx0.0010.0000.001