Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:47 -0000 (Wed, 01 Mar 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
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To the developers/maintainers of the Pigengene package: - Please 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 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 1477/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pigengene 1.25.10 (landing page) Habil Zare
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: Pigengene |
Version: 1.25.10 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Pigengene_1.25.10.tar.gz |
StartedAt: 2023-02-28 11:15:47 -0000 (Tue, 28 Feb 2023) |
EndedAt: 2023-02-28 11:35:05 -0000 (Tue, 28 Feb 2023) |
EllapsedTime: 1157.5 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: Pigengene.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:Pigengene.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings Pigengene_1.25.10.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/Pigengene.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘Pigengene/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘Pigengene’ version ‘1.25.10’ * 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 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 ... 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") compute.pigengene: no visible global function definition for ‘prcomp’ one.step.pigengene: no visible binding for global variable ‘org.Hs.eg.db’ Undefined global functions or variables: org.Hs.eg.db prcomp Consider adding importFrom("stats", "prcomp") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) get.enriched.pw.Rd:71: Escaped LaTeX specials: \_ * 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 ... 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 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://" Warning in hu.mouse(verbose = verbose) : Some genes with multiple homologs are selected arbitrarily. 'select()' returned 1:1 mapping between keys and columns Mapping to: org.Hs.eg.db-ENTREZID 'select()' returned 1:1 mapping between keys and columns Warning: Ensembl will soon enforce the use of https. Ensure the 'host' argument includes "https://" Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [www.ensembl.org:80] Operation timed out after 10001 milliseconds with 0 bytes received Calls: gene.mapping ... request_fetch -> request_fetch.write_memory -> <Anonymous> Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘Pigengene_inference.Rnw’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/Pigengene.Rcheck/00check.log’ for details.
Pigengene.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Pigengene ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘Pigengene’ ... ** 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 | 313.960 | 1.064 | 314.945 | |
aml | 0.200 | 0.000 | 0.186 | |
apply.filter | 24.418 | 0.104 | 24.524 | |
balance | 1.047 | 0.000 | 1.048 | |
calculate.beta | 0.856 | 0.004 | 0.860 | |
check.nas | 0.045 | 0.004 | 0.049 | |
check.pigengene.input | 0.047 | 0.000 | 0.048 | |
combine.networks | 15.393 | 0.064 | 15.434 | |
compact.tree | 15.244 | 0.052 | 15.296 | |
compute.pigengene | 22.527 | 0.184 | 22.712 | |
dcor.matrix | 0.158 | 0.000 | 0.159 | |
determine.modules | 14.792 | 0.057 | 14.851 | |
draw.bn | 0 | 0 | 0 | |
eigengenes33 | 0.095 | 0.008 | 0.102 | |