Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2022-11-30 11:06:39 -0500 (Wed, 30 Nov 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2022-10-25 r83175) -- "Unsuffered Consequences" 4462
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-10-11 r83083 ucrt) -- "Unsuffered Consequences" 4201
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-11-13 r83342) -- "Unsuffered Consequences" 4231
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 nebbiolo1


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 1881/2154HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SMITE 1.27.0  (landing page)
Neil Ari Wijetunga
Snapshot Date: 2022-11-29 14:00:14 -0500 (Tue, 29 Nov 2022)
git_url: https://git.bioconductor.org/packages/SMITE
git_branch: master
git_last_commit: 920bda8
git_last_commit_date: 2022-11-01 11:12:52 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SMITE
Version: 1.27.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SMITE.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SMITE_1.27.0.tar.gz
StartedAt: 2022-11-29 23:46:40 -0500 (Tue, 29 Nov 2022)
EndedAt: 2022-11-29 23:51:52 -0500 (Tue, 29 Nov 2022)
EllapsedTime: 312.5 seconds
RetCode: 0
Status:   OK  
CheckDir: SMITE.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SMITE.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SMITE_1.27.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SMITE.Rcheck’
* using R Under development (unstable) (2022-10-25 r83175)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘SMITE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SMITE’ version ‘1.27.0’
* 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 ...
  ‘SMITE.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

SMITE.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SMITE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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.Igraph0.8980.0120.910
SMITE-package0.3530.0240.377
addShadowText0.0030.0000.003
annotateExpression0.2090.0040.213
annotateModification0.0010.0000.000
convertGeneIds1.9090.1002.008
curated_expression0.0480.0000.047
extractExpression0.3460.0080.354
extractGOseq0.0880.0040.091
extractModification2.3360.0162.352
extractModules0.0820.0040.086
extractScores0.0860.0040.089
genes_for_conversiontest1.1780.0041.183
hg19_gene_bed0.1150.0000.115
highScores0.0860.0000.086
histone_h3k4me10.0650.0000.066
makePvalueAnnotation0.7150.0280.744
makePvalueObject0.0580.0040.063
methylationdata0.0550.0040.058
normalizePval0.090.000.09
plotCompareScores0.5220.0080.529
plotDensityPval0.1210.0040.125
plotModule0.0890.0000.090
removeModification0.0590.0040.063
runBioNet0.0850.0000.086
runGOseq0.0890.0000.089
runSpinglass0.6330.0080.641
scorePval0.0820.0070.090
stoufferTest0.0020.0000.002
test_annotation_score_data0.1220.0000.123