Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:10 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
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 1568/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pigengene 1.35.0 (landing page) Habil Zare
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
To the developers/maintainers of the Pigengene package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Pigengene.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. |
Package: Pigengene |
Version: 1.35.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Pigengene_1.35.0.tar.gz |
StartedAt: 2025-08-08 20:54:14 -0400 (Fri, 08 Aug 2025) |
EndedAt: 2025-08-08 20:56:31 -0400 (Fri, 08 Aug 2025) |
EllapsedTime: 137.6 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: Pigengene.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Pigengene_1.35.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Pigengene.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Pigengene/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Pigengene’ version ‘1.35.0’ * 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 ‘Pigengene’ 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 ... NOTE 'library' or 'require' calls in package code: ‘AnnotationDbi’ ‘biomaRt’ ‘energy’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE Found the following possibly unsafe calls: File ‘Pigengene/R/bn.calculation.R’: assignInNamespace("supported.clusters", fixArgs, "bnlearn") one.step.pigengene: no visible binding for global variable ‘org.Hs.eg.db’ Undefined global functions or variables: org.Hs.eg.db * checking Rd files ... NOTE checkRd: (-1) draw.bn.Rd:47: Lost braces 47 | rename the nodes name. See code{rename.node}.} | ^ checkRd: (-1) eigengenes33.Rd:21-22: Lost braces 21 | {A 202 by 34 matrix. | ^ checkRd: (-1) eigengenes33.Rd:25: Lost braces; missing escapes or markup? 25 | {A 164 by 34 matrix for MDS cases with columns similar to aml.} | ^ checkRd: (-1) eigengenes33.Rd:28: Lost braces; missing escapes or markup? 28 | {A numeric vector of length 9166 labeling members of each module. Named by Entrez ID.} | ^ checkRd: (-1) pigengene-class.Rd:25-26: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:27-29: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:30-39: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:40-41: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:42-44: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:45-47: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:48-49: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:50-52: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:53-55: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:56-57: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:58-59: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:60-63: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:64-68: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:73-76: Lost braces in \itemize; meant \describe ? checkRd: (-1) pigengene-class.Rd:77-79: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Non-topic package-anchored link(s) in Rd file 'draw.bn.Rd': ‘[bnlearn:bn.class]{bn-class}’ Non-topic package-anchored link(s) in Rd file 'gene.mapping.Rd': ‘[org.Hs.eg.db:org.Hs.egBASE]{org.Hs.eg.db}’ ‘[org.Mm.eg.db:org.Mm.egBASE]{org.Mm.eg.db}’ Non-topic package-anchored link(s) in Rd file 'learn.bn.Rd': ‘[bnlearn:preprocessing]{discretize}’ ‘[bnlearn:bn.class]{bn-class}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 ... ERROR Running examples in ‘Pigengene-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: gene.mapping > ### Title: Maps gene IDs > ### Aliases: gene.mapping > ### Keywords: misc > > ### ** Examples > > library(org.Hs.eg.db) Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: IRanges Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following object is masked from ‘package:utils’: findMatches The following objects are masked from ‘package:base’: I, expand.grid, unname > g1 <- gene.mapping(ids="NM_001159995") Loading required package: org.Mm.eg.db 'select()' returned 1:1 mapping between keys and columns > print(g1) input output1 output2 NM_001159995 "NM_001159995" "NRG1" "NRG1" > > ## Mapping to multiple convention > library(org.Mm.eg.db) > g2 <- gene.mapping(ids=c("NM_170730", "NM_001013580"), + inputType="REFSEQ", inputDb=org.Mm.eg.db, + outputType=c("SYMBOL","ENTREZID"), + outputDb=list(org.Hs.eg.db,org.Mm.eg.db), verbose=1) Mapping to: org.Hs.eg.db-SYMBOL 'select()' returned 1:1 mapping between keys and columns Loading required package: biomaRt Warning: Ensembl will soon enforce the use of https. Ensure the 'host' argument includes "https://" Error: Your query has been redirected to http://status.ensembl.org indicating this Ensembl service is currently unavailable. Look at ?useEnsembl for details on how to try a mirror site. Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed Pigengene-package 32.658 1.075 33.769 apply.filter 6.094 0.123 6.218 combine.networks 5.875 0.025 5.901 compute.pigengene 5.283 0.390 5.699 determine.modules 5.536 0.024 5.562 * 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: 1 ERROR, 4 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/Pigengene.Rcheck/00check.log’ for details.
Pigengene.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Pigengene ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘Pigengene’ ... ** this is package ‘Pigengene’ version ‘1.35.0’ ** 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 (Pigengene)
Pigengene.Rcheck/Pigengene-Ex.timings
name | user | system | elapsed | |
Pigengene-package | 32.658 | 1.075 | 33.769 | |
aml | 0.051 | 0.003 | 0.054 | |
apply.filter | 6.094 | 0.123 | 6.218 | |
balance | 0.094 | 0.022 | 0.116 | |
calculate.beta | 0.312 | 0.008 | 0.320 | |
check.nas | 0.021 | 0.002 | 0.022 | |
check.pigengene.input | 0.021 | 0.002 | 0.022 | |
combine.networks | 5.875 | 0.025 | 5.901 | |
compact.tree | 4.038 | 0.578 | 4.620 | |
compute.pigengene | 5.283 | 0.390 | 5.699 | |
dcor.matrix | 0.060 | 0.012 | 0.072 | |
determine.modules | 5.536 | 0.024 | 5.562 | |
draw.bn | 0 | 0 | 0 | |
eigengenes33 | 0.037 | 0.004 | 0.041 | |