Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-04-12 10:55:42 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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 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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1976/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPLINTER 1.25.0  (landing page)
Diana Low
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/SPLINTER
git_branch: devel
git_last_commit: a01a9bb
git_last_commit_date: 2022-11-01 11:14:31 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  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: 2023-04-12 09:39:10 -0400 (Wed, 12 Apr 2023)
EndedAt: 2023-04-12 09:46:15 -0400 (Wed, 12 Apr 2023)
EllapsedTime: 425.1 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) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 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 12.782  0.683  13.467
* 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/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.m0.0030.0000.002
addEnsemblAnnotation0.0050.0000.006
callPrimer30.0000.0000.001
checkPrimer0.0850.0000.085
compatible_cds0.0010.0000.001
compatible_tx0.0010.0000.001
donor.m0.0000.0000.001
eventOutcomeCompare3.0080.0833.093
eventOutcomeTranslate0.5080.0120.520
eventPlot12.782 0.68313.467
extendROI0.6640.0000.663
extractSpliceEvents0.0030.0000.003
extractSpliceSites0.0810.0000.082
findCompatibleEvents0.340.000.34
findCompatibleExon0.2120.0000.213
findTX0.0140.0000.014
getPCRsizes3.7280.3174.075
getRegionDNA0.3030.0000.303
insertRegion0.1620.0000.162
makeROI0.2650.0000.264
makeUniqueIDs0.0040.0000.004
pcr_result10.0010.0000.000
plot_seqlogo0.0480.0000.048
primers0.0010.0000.001
psiPlot0.2960.0160.311
region_minus_exon0.0010.0000.001
roi0.0000.0000.001
shapiroAcceptor0.5110.0400.552
shapiroDonor0.4700.0520.522
splice_data0.0010.0000.001
splice_fasta0.0000.0010.001
splitPCRhit0.0000.0030.003
thecds0.0010.0000.001
theexons0.0000.0000.001
valid_cds0.0010.0000.001
valid_tx0.0000.0010.001