Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-06-07 11:06:32 -0400 (Wed, 07 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.0 RC (2023-04-13 r84269) -- "Already Tomorrow" 4628
palomino3Windows Server 2022 Datacenterx644.3.0 RC (2023-04-13 r84269 ucrt) -- "Already Tomorrow" 4379
merida1macOS 12.6.4 Montereyx86_644.3.0 RC (2023-04-13 r84257) -- "Already Tomorrow" 4385
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 palomino3


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

Package 1948/2229HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SMITE 1.28.0  (landing page)
Neil Ari Wijetunga
Snapshot Date: 2023-06-06 14:00:07 -0400 (Tue, 06 Jun 2023)
git_url: https://git.bioconductor.org/packages/SMITE
git_branch: RELEASE_3_17
git_last_commit: 876db9d
git_last_commit_date: 2023-04-25 10:44:07 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: SMITE
Version: 1.28.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SMITE.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings SMITE_1.28.0.tar.gz
StartedAt: 2023-06-07 07:21:40 -0400 (Wed, 07 Jun 2023)
EndedAt: 2023-06-07 07:26:25 -0400 (Wed, 07 Jun 2023)
EllapsedTime: 285.1 seconds
RetCode: 0
Status:   OK  
CheckDir: SMITE.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SMITE.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings SMITE_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/SMITE.Rcheck'
* using R version 4.3.0 RC (2023-04-13 r84269 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SMITE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SMITE' version '1.28.0'
* 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 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: OK


Installation output

SMITE.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL SMITE
###
##############################################################################
##############################################################################


* installing to library 'F:/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.Igraph0.060.010.08
SMITE-package0.260.080.34
addShadowText000
annotateExpression0.250.030.29
annotateModification000
convertGeneIds2.310.202.51
curated_expression0.050.000.05
extractExpression0.180.000.19
extractGOseq0.060.000.06
extractModification1.640.051.69
extractModules0.080.000.08
extractScores0.060.000.06
genes_for_conversiontest1.420.001.42
hg19_gene_bed0.150.000.14
highScores0.070.000.08
histone_h3k4me10.050.000.05
makePvalueAnnotation0.560.020.58
makePvalueObject0.050.000.05
methylationdata0.050.000.05
normalizePval0.060.020.08
plotCompareScores0.50.00.5
plotDensityPval0.090.010.11
plotModule0.070.000.06
removeModification0.100.020.13
runBioNet0.080.000.08
runGOseq0.080.000.07
runSpinglass0.450.010.47
scorePval0.080.000.08
stoufferTest000
test_annotation_score_data0.100.000.09