Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-02-08 01:15:30 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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 |
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. |
Package 1936/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SPLINTER 1.25.0 (landing page) Diana Low
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
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/library --timings SPLINTER_1.25.0.tar.gz |
StartedAt: 2023-02-07 16:43:07 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 16:50:40 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 452.9 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: SPLINTER.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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/library --timings SPLINTER_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SPLINTER.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * 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 22.04.1 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 ... WARNING Killed A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... WARNING Killed * checking dependencies in R code ... OK * checking S3 generic/method consistency ... WARNING Killed See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * 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 ... ERROR Running examples in ‘SPLINTER-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: eventPlot > ### Title: eventPlot > ### Aliases: eventPlot > > ### ** Examples > > # define BAM files > data_path<-system.file("extdata",package="SPLINTER") > mt<-paste(data_path,"/mt_chr14.bam",sep="") > wt<-paste(data_path,"/wt_chr14.bam",sep="") > > # plot results > eventPlot(transcripts=valid_tx,roi_plot=roi,bams=c(wt,mt), + names=c('wt','mt'),rspan=1000) Killed * 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 ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘vignette.Rmd’ using rmarkdown Killed * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 3 WARNINGs See ‘/home/biocbuild/bbs-3.17-bioc/meat/SPLINTER.Rcheck/00check.log’ for details.
SPLINTER.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SPLINTER ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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)
SPLINTER.Rcheck/SPLINTER-Ex.timings
name | user | system | elapsed | |
acceptor.m | 0.003 | 0.000 | 0.007 | |
addEnsemblAnnotation | 0.007 | 0.000 | 0.020 | |
callPrimer3 | 0 | 0 | 0 | |
checkPrimer | 0.091 | 0.008 | 0.115 | |
compatible_cds | 0.001 | 0.000 | 0.002 | |
compatible_tx | 0.001 | 0.000 | 0.001 | |
donor.m | 0.001 | 0.000 | 0.001 | |
eventOutcomeCompare | 1.715 | 0.076 | 2.059 | |
eventOutcomeTranslate | 1.648 | 0.008 | 1.706 | |