Back to Build/check report for BioC 3.15 experimental data
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This page was generated on 2022-10-18 14:50:12 -0400 (Tue, 18 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
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 GenomicDistributionsData on nebbiolo1


To the developers/maintainers of the GenomicDistributionsData package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 142/410HostnameOS / ArchINSTALLBUILDCHECK
GenomicDistributionsData 1.4.0  (landing page)
Kristyna Kupkova
Snapshot Date: 2022-10-18 07:30:03 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/GenomicDistributionsData
git_branch: RELEASE_3_15
git_last_commit: a1a67f8
git_last_commit_date: 2022-04-26 13:34:59 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

Summary

Package: GenomicDistributionsData
Version: 1.4.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GenomicDistributionsData.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GenomicDistributionsData_1.4.0.tar.gz
StartedAt: 2022-10-18 11:23:33 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 11:27:16 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 223.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GenomicDistributionsData.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:GenomicDistributionsData.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings GenomicDistributionsData_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-data-experiment/meat/GenomicDistributionsData.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicDistributionsData/DESCRIPTION’ ... OK
* this is package ‘GenomicDistributionsData’ version ‘1.4.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenomicDistributionsData’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'GenomicFeatures::proteinToGenome' by 'ensembldb::proteinToGenome' when loading 'GenomicDistributionsData'
See ‘/home/biocbuild/bbs-3.15-data-experiment/meat/GenomicDistributionsData.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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-data-experiment/meat/GenomicDistributionsData.Rcheck/00check.log’
for details.



Installation output

GenomicDistributionsData.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL GenomicDistributionsData
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘GenomicDistributionsData’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'GenomicFeatures::proteinToGenome' by 'ensembldb::proteinToGenome' when loading 'GenomicDistributionsData'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'GenomicFeatures::proteinToGenome' by 'ensembldb::proteinToGenome' when loading 'GenomicDistributionsData'
snapshotDate(): 2022-04-26
** testing if installed package can be loaded from final location
Warning: replacing previous import 'GenomicFeatures::proteinToGenome' by 'ensembldb::proteinToGenome' when loading 'GenomicDistributionsData'
snapshotDate(): 2022-04-26
** testing if installed package keeps a record of temporary installation path
* DONE (GenomicDistributionsData)

Tests output


Example timings

GenomicDistributionsData.Rcheck/GenomicDistributionsData-Ex.timings

nameusersystemelapsed
GenomicDistributionsData0.0000.0000.001
TSS_hg191.7330.2862.176
TSS_hg380.8230.0480.961
TSS_mm100.9160.0511.088
TSS_mm90.8130.0860.996
buildChromSizes0.0000.0000.001
buildGeneModels000
buildOpenSignalMatrix000
buildTSS0.0000.0010.000
chromSizes_hg190.6820.0630.861
chromSizes_hg380.6600.0480.797
chromSizes_mm100.6510.0640.821
chromSizes_mm90.6540.0640.806
geneModels_hg190.8340.1001.022
geneModels_hg380.8920.0921.110
geneModels_mm100.8150.0600.972
geneModels_mm91.7140.2232.037
loadBSgenome000
loadEnsDb0.0000.0000.001
loadTxDb000
openSignalMatrix_hg19000
openSignalMatrix_hg38000
openSignalMatrix_mm10000