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CHECK report for signatureSearchData on malbec1

This page was generated on 2021-05-06 14:10:14 -0400 (Thu, 06 May 2021).

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 343/398HostnameOS / ArchINSTALLBUILDCHECK
signatureSearchData 1.4.0  (landing page)
Yuzhu Duan
Snapshot Date: 2021-05-06 09:00:13 -0400 (Thu, 06 May 2021)
URL: https://git.bioconductor.org/packages/signatureSearchData
Branch: RELEASE_3_12
Last Commit: 6e452bf
Last Changed Date: 2020-10-27 10:31:00 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: signatureSearchData
Version: 1.4.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:signatureSearchData.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings signatureSearchData_1.4.0.tar.gz
StartedAt: 2021-05-06 12:45:55 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 12:49:34 -0400 (Thu, 06 May 2021)
EllapsedTime: 219.2 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-3.12-bioc/R/bin/R CMD check --install=check:signatureSearchData.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings signatureSearchData_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-data-experiment/meat/signatureSearchData.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.4.0’
* 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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
ES_NULL 5.352  0.176   6.499
* 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-3.12-bioc/R/bin/R CMD INSTALL signatureSearchData
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* installing to library ‘/home/biocbuild/bbs-3.12-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_NULL5.3520.1766.499
GO_DATA1.6560.0401.985
GO_DATA_drug1.6320.0361.939
cmap0.0640.0000.062
cmap_expr0.0760.0000.075
cmap_rank0.0600.0000.058
combineNormRes0.0040.0000.001
combineResults000
dtlink_db_clue_sti1.8480.0362.159
getCmapCEL000
goAnno1.4040.0321.707
goAnno_drug1.5360.0161.834
inst_filter0.0040.0000.007
lincs0.0600.0000.062
lincs_expr0.0760.0000.079
meanExpr0.0480.0040.148
meanExpr2h50.4160.0560.550
normalizeCel0.0000.0000.001
probe2gene0.0000.0000.002
runLimma2.1280.0003.032
sampleList1.7880.0001.789
sig_filter0.0080.0000.008
signatureSearchData1.7600.0242.237
taurefList1.3840.0281.725