Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:53 -0400 (Fri, 15 Oct 2021).
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. |
Package 1794/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SMITE 1.20.0 (landing page) Neil Ari Wijetunga
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: SMITE |
Version: 1.20.0 |
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_1.20.0.tar.gz |
StartedAt: 2021-10-15 00:11:01 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 00:16:47 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 346.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SMITE.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running 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_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/SMITE.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘1.20.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * 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: 1 NOTE See ‘/Users/biocbuild/bbs-3.13-bioc/meat/SMITE.Rcheck/00check.log’ for details.
SMITE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL SMITE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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)
SMITE.Rcheck/SMITE-Ex.timings
name | user | system | elapsed | |
Reactome.Symbol.Igraph | 0.123 | 0.007 | 0.164 | |
SMITE-package | 0.456 | 0.013 | 0.505 | |
addShadowText | 0.004 | 0.000 | 0.006 | |
annotateExpression | 0.229 | 0.005 | 0.234 | |
annotateModification | 0.001 | 0.001 | 0.001 | |
convertGeneIds | 2.836 | 0.165 | 3.008 | |
curated_expression | 0.051 | 0.002 | 0.053 | |
extractExpression | 0.181 | 0.004 | 0.185 | |
extractGOseq | 0.049 | 0.003 | 0.052 | |
extractModification | 1.199 | 0.025 | 1.224 | |
extractModules | 0.042 | 0.002 | 0.044 | |
extractScores | 0.039 | 0.002 | 0.040 | |
genes_for_conversiontest | 0.993 | 0.009 | 1.002 | |
hg19_gene_bed | 0.122 | 0.002 | 0.125 | |
highScores | 0.036 | 0.001 | 0.037 | |
histone_h3k4me1 | 0.067 | 0.002 | 0.069 | |
makePvalueAnnotation | 1.039 | 0.021 | 1.060 | |
makePvalueObject | 0.072 | 0.003 | 0.074 | |
methylationdata | 0.072 | 0.002 | 0.074 | |
normalizePval | 0.045 | 0.002 | 0.047 | |
plotCompareScores | 1.136 | 0.016 | 1.152 | |
plotDensityPval | 0.079 | 0.003 | 0.083 | |
plotModule | 0.042 | 0.002 | 0.044 | |
removeModification | 0.074 | 0.004 | 0.078 | |
runBioNet | 0.042 | 0.003 | 0.045 | |
runGOseq | 0.046 | 0.003 | 0.050 | |
runSpinglass | 0.503 | 0.056 | 0.563 | |
scorePval | 0.044 | 0.003 | 0.046 | |
stoufferTest | 0.001 | 0.001 | 0.002 | |
test_annotation_score_data | 0.078 | 0.006 | 0.085 | |