Back to Build/check report for BioC 3.10 experimental data

CHECK report for pumadata on malbec1

This page was generated on 2020-04-14 17:46:16 -0400 (Tue, 14 Apr 2020).

Package 282/384HostnameOS / ArchINSTALLBUILDCHECK
pumadata 2.22.0
Xuejun liu
Snapshot Date: 2020-04-14 09:30:11 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/pumadata
Branch: RELEASE_3_10
Last Commit: ab944ec
Last Changed Date: 2019-10-29 13:29:34 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: pumadata
Version: 2.22.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:pumadata.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings pumadata_2.22.0.tar.gz
StartedAt: 2020-04-14 12:56:08 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 12:58:49 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 161.4 seconds
RetCode: 0
Status:  OK 
CheckDir: pumadata.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:pumadata.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings pumadata_2.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-data-experiment/meat/pumadata.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pumadata/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pumadata’ version ‘2.22.0’
* 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 ‘pumadata’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 105.0Mb
  sub-directories of 1Mb or more:
    data  104.9Mb
* 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 data for ASCII and uncompressed saves ... 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 NOTE
See
  ‘/home/biocbuild/bbs-3.10-data-experiment/meat/pumadata.Rcheck/00check.log’
for details.



Installation output

pumadata.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL pumadata
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘pumadata’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’
** testing if installed package can be loaded from final location
No methods found in package ‘RSQLite’ for request: ‘dbListFields’ when loading ‘oligo’
** testing if installed package keeps a record of temporary installation path
* DONE (pumadata)

Tests output


Example timings

pumadata.Rcheck/pumadata-Ex.timings

nameusersystemelapsed
eset_estrogen_comb0.0880.0040.089
eset_estrogen_mmgmos0.1720.0000.172
eset_estrogen_pmmmgmos0.0920.0000.093
eset_estrogen_rma0.0240.0000.024
pumapca_estrogen0.0080.0000.007