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This page was generated on 2021-11-29 15:05:09 -0500 (Mon, 29 Nov 2021).

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? here 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 1823/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SMITE 1.22.0  (landing page)
Neil Ari Wijetunga
Snapshot Date: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 2021)
git_url: https://git.bioconductor.org/packages/SMITE
git_branch: RELEASE_3_14
git_last_commit: 6979357
git_last_commit_date: 2021-10-26 12:25:15 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SMITE
Version: 1.22.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:SMITE.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings SMITE_1.22.0.tar.gz
StartedAt: 2021-11-28 11:02:26 -0500 (Sun, 28 Nov 2021)
EndedAt: 2021-11-28 11:06:25 -0500 (Sun, 28 Nov 2021)
EllapsedTime: 238.9 seconds
RetCode: 0
Status:   OK  
CheckDir: SMITE.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:SMITE.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings SMITE_1.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/SMITE.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.22.0’
* 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-3.14-bioc/R/bin/R CMD INSTALL SMITE
###
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* installing to library ‘/home/biocbuild/bbs-3.14-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.Igraph0.1380.0040.143
SMITE-package0.3190.0120.330
addShadowText0.0030.0000.004
annotateExpression0.1560.0120.169
annotateModification000
convertGeneIds1.3720.1041.476
curated_expression0.0480.0040.052
extractExpression0.2900.0000.289
extractGOseq0.0370.0000.036
extractModification1.8720.0201.891
extractModules0.0350.0000.035
extractScores0.0390.0000.038
genes_for_conversiontest0.8120.0160.829
hg19_gene_bed0.1170.0000.118
highScores0.0350.0000.035
histone_h3k4me10.0580.0040.062
makePvalueAnnotation0.7450.0120.758
makePvalueObject0.0590.0000.060
methylationdata0.0560.0000.056
normalizePval0.0360.0000.036
plotCompareScores0.3940.0040.399
plotDensityPval0.0700.0000.071
plotModule0.0350.0000.035
removeModification0.0590.0040.064
runBioNet0.0360.0000.037
runGOseq0.0390.0000.040
runSpinglass0.4450.0160.461
scorePval0.0370.0000.037
stoufferTest0.0010.0000.001
test_annotation_score_data0.0670.0000.066