Neil Ari Wijetunga
| Snapshot Date: 2023-03-24 14:00:04 -0400 (Fri, 24 Mar 2023) |
| git_url: https://git.bioconductor.org/packages/SMITE |
| git_branch: RELEASE_3_16 |
| git_last_commit: 1293d18 |
| git_last_commit_date: 2022-11-01 11:12:52 -0400 (Tue, 01 Nov 2022) |
| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-03-27 11:06:20 -0400 (Mon, 27 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4480 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4276 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4304 |
| 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 | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1903/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SMITE 1.26.0 (landing page) Neil Ari Wijetunga
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SMITE |
| Version: 1.26.0 |
| 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_1.26.0.tar.gz |
| StartedAt: 2023-03-24 22:41:19 -0400 (Fri, 24 Mar 2023) |
| EndedAt: 2023-03-24 22:45:34 -0400 (Fri, 24 Mar 2023) |
| EllapsedTime: 255.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SMITE.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/SMITE.Rcheck’ * using R version 4.2.3 (2023-03-15) * 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 ‘1.26.0’ * 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 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
SMITE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SMITE ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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 | 0.102 | 0.006 | 0.107 | |
| SMITE-package | 0.313 | 0.008 | 0.322 | |
| addShadowText | 0.004 | 0.000 | 0.004 | |
| annotateExpression | 0.285 | 0.007 | 0.293 | |
| annotateModification | 0 | 0 | 0 | |
| convertGeneIds | 2.602 | 0.111 | 2.720 | |
| curated_expression | 0.042 | 0.001 | 0.043 | |
| extractExpression | 0.163 | 0.004 | 0.168 | |
| extractGOseq | 0.066 | 0.002 | 0.070 | |
| extractModification | 0.810 | 0.028 | 0.843 | |
| extractModules | 0.077 | 0.002 | 0.079 | |
| extractScores | 0.069 | 0.002 | 0.071 | |
| genes_for_conversiontest | 1.042 | 0.016 | 1.058 | |
| hg19_gene_bed | 0.133 | 0.002 | 0.134 | |
| highScores | 0.077 | 0.002 | 0.080 | |
| histone_h3k4me1 | 0.058 | 0.002 | 0.060 | |
| makePvalueAnnotation | 0.554 | 0.017 | 0.572 | |
| makePvalueObject | 0.082 | 0.006 | 0.089 | |
| methylationdata | 0.046 | 0.001 | 0.047 | |
| normalizePval | 0.072 | 0.002 | 0.074 | |
| plotCompareScores | 0.478 | 0.025 | 0.506 | |
| plotDensityPval | 0.106 | 0.003 | 0.109 | |
| plotModule | 0.075 | 0.002 | 0.076 | |
| removeModification | 0.055 | 0.002 | 0.057 | |
| runBioNet | 0.079 | 0.002 | 0.081 | |
| runGOseq | 0.079 | 0.002 | 0.083 | |
| runSpinglass | 1.415 | 0.039 | 1.458 | |
| scorePval | 0.075 | 0.002 | 0.078 | |
| stoufferTest | 0.002 | 0.000 | 0.002 | |
| test_annotation_score_data | 0.105 | 0.003 | 0.109 | |