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This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 1952/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SMITE 1.33.0  (landing page)
Neil Ari Wijetunga
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/SMITE
git_branch: devel
git_last_commit: 68688bd
git_last_commit_date: 2024-04-30 10:48:07 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for SMITE on merida1

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: 1.33.0
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_1.33.0.tar.gz
StartedAt: 2024-06-10 10:18:05 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 10:28:50 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 645.8 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_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SMITE.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SMITE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SMITE’ version ‘1.33.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
convertGeneIds 6.573  0.781   8.393
* 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.Igraph0.1440.0160.193
SMITE-package0.6280.0240.802
addShadowText0.0040.0010.005
annotateExpression0.3760.0110.430
annotateModification0.0000.0010.002
convertGeneIds6.5730.7818.393
curated_expression0.0720.0040.084
extractExpression0.3720.0110.407
extractGOseq0.1290.0060.141
extractModification1.7580.0371.943
extractModules0.1250.0060.153
extractScores0.1250.0050.149
genes_for_conversiontest2.6270.0252.990
hg19_gene_bed0.2190.0070.271
highScores0.1240.0060.174
histone_h3k4me10.1160.0050.143
makePvalueAnnotation1.4360.0271.658
makePvalueObject0.0950.0060.123
methylationdata0.0910.0050.107
normalizePval0.1270.0070.161
plotCompareScores1.0460.0431.193
plotDensityPval0.1960.0100.222
plotModule0.1240.0060.142
removeModification0.1950.0090.221
runBioNet0.1250.0060.140
runGOseq0.1340.0080.164
runSpinglass1.0040.0371.139
scorePval0.1260.0050.144
stoufferTest0.0020.0010.004
test_annotation_score_data0.1780.0090.206