| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 2029/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SMITE 1.36.0 (landing page) Neil Ari Wijetunga
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
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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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: SMITE |
| Version: 1.36.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:SMITE.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SMITE_1.36.0.tar.gz |
| StartedAt: 2025-10-14 14:26:23 -0000 (Tue, 14 Oct 2025) |
| EndedAt: 2025-10-14 14:33:59 -0000 (Tue, 14 Oct 2025) |
| EllapsedTime: 455.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SMITE.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:SMITE.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings SMITE_1.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/SMITE.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SMITE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SMITE’ version ‘1.36.0’
* 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 loading without being on the library search path ... 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 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
SMITE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL SMITE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘SMITE’ ... ** this is package ‘SMITE’ version ‘1.36.0’ ** 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)
SMITE.Rcheck/SMITE-Ex.timings
| name | user | system | elapsed | |
| Reactome.Symbol.Igraph | 0.181 | 0.012 | 0.194 | |
| SMITE-package | 0.365 | 0.000 | 0.394 | |
| addShadowText | 0.002 | 0.000 | 0.002 | |
| annotateExpression | 0.406 | 0.000 | 0.626 | |
| annotateModification | 0 | 0 | 0 | |
| convertGeneIds | 3.599 | 0.224 | 4.438 | |
| curated_expression | 0.042 | 0.000 | 0.043 | |
| extractExpression | 0.225 | 0.008 | 0.233 | |
| extractGOseq | 0.064 | 0.012 | 0.076 | |
| extractModification | 2.468 | 0.072 | 2.604 | |
| extractModules | 0.075 | 0.000 | 0.075 | |
| extractScores | 0.075 | 0.000 | 0.075 | |
| genes_for_conversiontest | 1.358 | 0.004 | 1.374 | |
| hg19_gene_bed | 0.123 | 0.004 | 0.127 | |
| highScores | 0.067 | 0.008 | 0.075 | |
| histone_h3k4me1 | 0.065 | 0.000 | 0.065 | |
| makePvalueAnnotation | 0.904 | 0.000 | 0.958 | |
| makePvalueObject | 0.052 | 0.004 | 0.056 | |
| methylationdata | 0.051 | 0.000 | 0.051 | |
| normalizePval | 0.127 | 0.000 | 0.128 | |
| plotCompareScores | 0.579 | 0.000 | 0.629 | |
| plotDensityPval | 0.119 | 0.003 | 0.123 | |
| plotModule | 0.075 | 0.000 | 0.075 | |
| removeModification | 0.056 | 0.000 | 0.057 | |
| runBioNet | 0.066 | 0.007 | 0.074 | |
| runGOseq | 0.079 | 0.000 | 0.079 | |
| runSpinglass | 0.672 | 0.000 | 0.767 | |
| scorePval | 0.067 | 0.015 | 0.082 | |
| stoufferTest | 0.002 | 0.000 | 0.002 | |
| test_annotation_score_data | 0.156 | 0.024 | 0.181 | |