Back to Build/check report for BioC 3.11 experimental data

CHECK report for signatureSearchData on malbec2

This page was generated on 2020-10-15 20:46:01 -0400 (Thu, 15 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE signatureSearchData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 338/391HostnameOS / ArchINSTALLBUILDCHECK
signatureSearchData 1.2.2
Yuzhu Duan
Snapshot Date: 2020-10-15 07:30:17 -0400 (Thu, 15 Oct 2020)
URL: https://git.bioconductor.org/packages/signatureSearchData
Branch: RELEASE_3_11
Last Commit: 8bf572a
Last Changed Date: 2020-08-19 02:32:19 -0400 (Wed, 19 Aug 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: signatureSearchData
Version: 1.2.2
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:signatureSearchData.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings signatureSearchData_1.2.2.tar.gz
StartedAt: 2020-10-15 14:10:20 -0400 (Thu, 15 Oct 2020)
EndedAt: 2020-10-15 14:13:53 -0400 (Thu, 15 Oct 2020)
EllapsedTime: 213.6 seconds
RetCode: 0
Status:  OK 
CheckDir: signatureSearchData.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:signatureSearchData.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings signatureSearchData_1.2.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-data-experiment/meat/signatureSearchData.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘signatureSearchData/DESCRIPTION’ ... OK
* this is package ‘signatureSearchData’ version ‘1.2.2’
* 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 ‘signatureSearchData’ 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 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: OK


Installation output

signatureSearchData.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL signatureSearchData
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘signatureSearchData’ ...
** using staged installation
** R
** 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 (signatureSearchData)

Tests output


Example timings

signatureSearchData.Rcheck/signatureSearchData-Ex.timings

nameusersystemelapsed
ES_NULL4.3070.2124.982
GO_DATA1.2080.0161.295
GO_DATA_drug1.3320.0161.416
cmap0.0680.0000.068
cmap_expr0.0640.0000.064
cmap_rank0.0620.0000.062
combineNormRes000
combineResults000
dtlink_db_clue_sti1.2790.0041.363
getCmapCEL0.0000.0000.001
goAnno0.9530.0001.011
goAnno_drug0.9250.0161.021
inst_filter0.0070.0000.007
lincs0.0710.0040.075
lincs_expr0.0770.0000.077
meanExpr0.0470.0000.065
meanExpr2h50.4260.0590.511
normalizeCel0.0000.0000.001
probe2gene0.0160.0000.016
runLimma1.9540.0001.967
sampleList2.1820.0002.182
sig_filter0.0060.0000.006
signatureSearchData1.5110.0161.915
taurefList1.0290.0041.095