Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-08-11 11:06:01 -0400 (Thu, 11 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" 4165
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 nebbiolo2


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: 2022-08-10 14:00:02 -0400 (Wed, 10 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: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:SMITE.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings SMITE_1.25.0.tar.gz
StartedAt: 2022-08-10 22:04:21 -0400 (Wed, 10 Aug 2022)
EndedAt: 2022-08-10 22:08:55 -0400 (Wed, 10 Aug 2022)
EllapsedTime: 274.5 seconds
RetCode: 0
Status:   OK  
CheckDir: SMITE.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:SMITE.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --no-vignettes --timings SMITE_1.25.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/SMITE.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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 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:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL SMITE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/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.Igraph0.0860.0080.094
SMITE-package0.3850.0000.385
addShadowText0.0040.0000.004
annotateExpression0.2300.0230.254
annotateModification000
convertGeneIds1.3760.0881.464
curated_expression0.1740.0080.182
extractExpression0.1890.0080.197
extractGOseq0.080.000.08
extractModification1.8460.1161.962
extractModules0.0750.0080.083
extractScores0.1020.0000.102
genes_for_conversiontest0.8140.0000.814
hg19_gene_bed0.1230.0120.135
highScores0.1200.0040.124
histone_h3k4me10.0640.0000.064
makePvalueAnnotation0.6040.0080.613
makePvalueObject0.0560.0040.060
methylationdata0.0530.0030.057
normalizePval0.0770.0040.081
plotCompareScores0.4470.0000.447
plotDensityPval0.120.000.12
plotModule0.0810.0030.084
removeModification0.0700.0010.070
runBioNet0.0780.0080.086
runGOseq0.0890.0080.098
runSpinglass0.5490.0160.565
scorePval0.0830.0000.084
stoufferTest0.0020.0000.002
test_annotation_score_data0.1160.0000.116