Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-08-12 11:08:22 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4375
palomino4Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4159
lconwaymacOS 12.2.1 Montereyx86_644.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" 4167
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 SMITE on lconway


To the developers/maintainers of the SMITE package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SMITE.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1867/2139HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SMITE 1.25.0  (landing page)
Neil Ari Wijetunga
Snapshot Date: 2022-08-11 14:00:04 -0400 (Thu, 11 Aug 2022)
git_url: https://git.bioconductor.org/packages/SMITE
git_branch: master
git_last_commit: b145409
git_last_commit_date: 2022-04-26 11:29:16 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SMITE
Version: 1.25.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SMITE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SMITE_1.25.0.tar.gz
StartedAt: 2022-08-11 22:38:04 -0400 (Thu, 11 Aug 2022)
EndedAt: 2022-08-11 22:42:26 -0400 (Thu, 11 Aug 2022)
EllapsedTime: 261.9 seconds
RetCode: 0
Status:   OK  
CheckDir: SMITE.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SMITE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SMITE_1.25.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/SMITE.Rcheck’
* using R version 4.2.1 Patched (2022-07-09 r82577)
* 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 ‘1.25.0’
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SMITE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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.Igraph0.0730.0060.079
SMITE-package0.3460.0100.358
addShadowText0.0020.0000.003
annotateExpression0.2380.0080.247
annotateModification0.0000.0010.000
convertGeneIds1.6260.1481.813
curated_expression0.0530.0040.061
extractExpression1.0160.0131.040
extractGOseq0.0780.0030.081
extractModification0.8010.0230.826
extractModules0.0800.0040.088
extractScores0.0810.0030.086
genes_for_conversiontest0.7660.0050.772
hg19_gene_bed0.1150.0020.117
highScores0.0820.0020.085
histone_h3k4me10.0690.0020.071
makePvalueAnnotation0.6410.0310.674
makePvalueObject0.0580.0020.060
methylationdata0.0580.0030.066
normalizePval0.0810.0030.083
plotCompareScores0.4210.0220.447
plotDensityPval0.1180.0050.126
plotModule0.1290.0070.136
removeModification0.0660.0030.070
runBioNet0.0810.0030.086
runGOseq0.0900.0030.093
runSpinglass0.5080.0450.557
scorePval0.0870.0020.089
stoufferTest0.0010.0000.002
test_annotation_score_data0.1140.0050.122