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CHECK report for SMITE on merida1

This page was generated on 2021-05-06 12:36:52 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the SMITE package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1739/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SMITE 1.18.0  (landing page)
Neil Ari Wijetunga
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/SMITE
Branch: RELEASE_3_12
Last Commit: 7c95087
Last Changed Date: 2020-10-27 11:11:05 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: SMITE
Version: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SMITE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SMITE_1.18.0.tar.gz
StartedAt: 2021-05-06 06:24:14 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:30:27 -0400 (Thu, 06 May 2021)
EllapsedTime: 374.0 seconds
RetCode: 0
Status:   OK  
CheckDir: SMITE.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SMITE.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SMITE_1.18.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/SMITE.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SMITE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SMITE’ version ‘1.18.0’
* 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 ‘SMITE’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... 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

SMITE.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SMITE
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘SMITE’ ...
** using staged installation
** R
** data
** 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 (SMITE)

Tests output


Example timings

SMITE.Rcheck/SMITE-Ex.timings

nameusersystemelapsed
Reactome.Symbol.Igraph0.1510.0090.160
SMITE-package0.4260.0130.440
addShadowText0.0050.0010.005
annotateExpression0.3000.0060.306
annotateModification0.0010.0000.000
convertGeneIds2.8270.1562.986
curated_expression0.0530.0030.056
extractExpression0.1980.0060.204
extractGOseq0.0480.0030.050
extractModification1.0560.0281.084
extractModules0.0430.0020.045
extractScores0.0690.0030.073
genes_for_conversiontest0.9900.0080.999
hg19_gene_bed0.1610.0020.164
highScores0.0470.0020.049
histone_h3k4me10.0750.0020.076
makePvalueAnnotation0.9400.0150.956
makePvalueObject0.0680.0020.070
methylationdata0.0670.0020.069
normalizePval0.0430.0030.046
plotCompareScores0.5030.0140.518
plotDensityPval0.0960.0040.101
plotModule0.0500.0020.052
removeModification0.0920.0040.097
runBioNet0.0360.0020.038
runGOseq0.0410.0020.043
runSpinglass0.5530.0320.586
scorePval0.0500.0020.052
stoufferTest0.0020.0000.001
test_annotation_score_data0.0860.0040.091