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This page was generated on 2025-09-26 12:06 -0400 (Fri, 26 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4831
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4619
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4563
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4563
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 2025/2334HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SMITE 1.37.0  (landing page)
Neil Ari Wijetunga
Snapshot Date: 2025-09-25 13:45 -0400 (Thu, 25 Sep 2025)
git_url: https://git.bioconductor.org/packages/SMITE
git_branch: devel
git_last_commit: daef10f
git_last_commit_date: 2025-04-15 10:58:12 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for SMITE on kjohnson3

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: 1.37.0
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_1.37.0.tar.gz
StartedAt: 2025-09-25 21:45:04 -0400 (Thu, 25 Sep 2025)
EndedAt: 2025-09-25 21:47:04 -0400 (Thu, 25 Sep 2025)
EllapsedTime: 120.3 seconds
RetCode: 0
Status:   OK  
CheckDir: SMITE.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SMITE.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SMITE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SMITE’ version ‘1.37.0’
* 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/4.5-arm64/Resources/library’
* installing *source* package ‘SMITE’ ...
** this is package ‘SMITE’ version ‘1.37.0’
** 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.Igraph0.1200.0050.124
SMITE-package0.1660.0060.171
addShadowText0.0010.0000.001
annotateExpression0.5140.0040.518
annotateModification000
convertGeneIds0.9870.0891.104
curated_expression0.0210.0010.031
extractExpression0.1090.0040.113
extractGOseq0.0400.0010.041
extractModification0.7280.0120.742
extractModules0.0390.0010.040
extractScores0.0390.0020.039
genes_for_conversiontest0.5290.0030.532
hg19_gene_bed0.0550.0020.056
highScores0.0400.0010.042
histone_h3k4me10.0290.0010.029
makePvalueAnnotation0.2290.0100.239
makePvalueObject0.0280.0010.029
methylationdata0.0270.0010.028
normalizePval0.0420.0020.043
plotCompareScores0.2050.0080.213
plotDensityPval0.0530.0030.056
plotModule0.0420.0010.043
removeModification0.0280.0010.030
runBioNet0.0420.0020.043
runGOseq0.0450.0020.046
runSpinglass0.2120.0150.228
scorePval0.0420.0010.043
stoufferTest0.0000.0010.000
test_annotation_score_data0.0570.0020.059