Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQR[S]TUVWXYZ

This page was generated on 2024-05-27 11:36:09 -0400 (Mon, 27 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4752
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4517
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

Package 2008/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SMITE 1.32.0  (landing page)
Neil Ari Wijetunga
Snapshot Date: 2024-05-26 14:00:09 -0400 (Sun, 26 May 2024)
git_url: https://git.bioconductor.org/packages/SMITE
git_branch: RELEASE_3_19
git_last_commit: 1dab5bd
git_last_commit_date: 2024-04-30 10:48:07 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  NO, package depends on 'goseq' which is not available
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'goseq' which is not available
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for SMITE on lconway


To the developers/maintainers of the SMITE package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SMITE
Version: 1.32.0
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_1.32.0.tar.gz
StartedAt: 2024-05-27 00:23:34 -0400 (Mon, 27 May 2024)
EndedAt: 2024-05-27 00:29:18 -0400 (Mon, 27 May 2024)
EllapsedTime: 344.8 seconds
RetCode: 0
Status:   OK  
CheckDir: SMITE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SMITE.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SMITE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SMITE’ version ‘1.32.0’
* 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 code 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 ... 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SMITE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/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.Igraph0.0890.0080.098
SMITE-package0.4070.0160.426
addShadowText0.0010.0000.002
annotateExpression0.2230.0060.229
annotateModification0.0000.0000.001
convertGeneIds4.3230.3594.768
curated_expression0.0470.0030.049
extractExpression0.2080.0070.216
extractGOseq0.0900.0030.093
extractModification1.0250.0331.066
extractModules0.0860.0040.092
extractScores0.0720.0020.075
genes_for_conversiontest1.7620.0231.800
hg19_gene_bed0.1340.0040.139
highScores0.0760.0030.080
histone_h3k4me10.0670.0020.070
makePvalueAnnotation0.8500.0360.896
makePvalueObject0.0660.0030.069
methylationdata0.0580.0020.061
normalizePval0.0760.0020.078
plotCompareScores0.5590.0340.597
plotDensityPval0.1180.0060.126
plotModule0.0860.0030.090
removeModification0.1340.0060.140
runBioNet0.0820.0030.083
runGOseq0.0890.0040.094
runSpinglass0.6410.0370.686
scorePval0.0880.0050.094
stoufferTest0.0020.0010.003
test_annotation_score_data0.1260.0060.134