Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:06:51 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 palomino3


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: 2022-06-23 13:55:15 -0400 (Thu, 23 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
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: SPLINTER
Version: 1.22.0
Command: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SPLINTER.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings SPLINTER_1.22.0.tar.gz
StartedAt: 2022-06-24 05:14:26 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 05:19:56 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 329.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: SPLINTER.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SPLINTER.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings SPLINTER_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/SPLINTER.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (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 whether package 'SPLINTER' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'SPLINTER'
See 'F:/biocbuild/bbs-3.15-bioc/meat/SPLINTER.Rcheck/00install.out' for details.
* 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 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   12.56   0.04   12.61
getPCRsizes  9.50   0.03    9.75
* 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: 1 WARNING
See
  'F:/biocbuild/bbs-3.15-bioc/meat/SPLINTER.Rcheck/00check.log'
for details.



Installation output

SPLINTER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL SPLINTER
###
##############################################################################
##############################################################################


* installing to library 'F:/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'
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'SPLINTER'
** 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'
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'SPLINTER'
** testing if installed package can be loaded from final location
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'SPLINTER'
** testing if installed package keeps a record of temporary installation path
* DONE (SPLINTER)

Tests output


Example timings

SPLINTER.Rcheck/SPLINTER-Ex.timings

nameusersystemelapsed
acceptor.m000
addEnsemblAnnotation0.020.000.02
callPrimer3000
checkPrimer0.110.000.11
compatible_cds000
compatible_tx0.000.010.02
donor.m000
eventOutcomeCompare1.220.111.32
eventOutcomeTranslate0.400.020.42
eventPlot12.56 0.0412.61
extendROI0.670.020.68
extractSpliceEvents000
extractSpliceSites0.130.000.13
findCompatibleEvents0.440.000.44
findCompatibleExon0.280.000.28
findTX0.010.000.01
getPCRsizes9.500.039.75
getRegionDNA0.420.030.45
insertRegion0.180.000.19
makeROI0.250.000.25
makeUniqueIDs000
pcr_result1000
plot_seqlogo0.050.010.06
primers000
psiPlot0.220.000.22
region_minus_exon000
roi000
shapiroAcceptor0.450.060.56
shapiroDonor0.440.000.43
splice_data0.000.020.02
splice_fasta000
splitPCRhit000
thecds000
theexons0.000.020.02
valid_cds000
valid_tx000