Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 33/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
AGDEX 1.54.0 (landing page) Cuilan lani Gao
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the AGDEX package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AGDEX.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: AGDEX |
Version: 1.54.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:AGDEX.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings AGDEX_1.54.0.tar.gz |
StartedAt: 2024-11-20 05:01:24 -0000 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 05:02:48 -0000 (Wed, 20 Nov 2024) |
EllapsedTime: 84.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: AGDEX.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:AGDEX.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings AGDEX_1.54.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/AGDEX.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘AGDEX/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘AGDEX’ version ‘1.54.0’ * 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 ‘AGDEX’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Non-standard license specification: GPL Version 2 or later Standardizable: TRUE Standardized license specification: GPL (>= 2) * 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 ... NOTE Packages in Depends field not imported from: ‘Biobase’ ‘GSEABase’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE agdex: no visible global function definition for ‘exprs’ agdex: no visible global function definition for ‘qnorm’ agdex: no visible global function definition for ‘pnorm’ agdex: no visible global function definition for ‘sampleNames’ agdex: no visible global function definition for ‘pData’ agdex.scatterplot: no visible global function definition for ‘points’ agdex.scatterplot: no visible global function definition for ‘lines’ agdex.scatterplot: no visible global function definition for ‘prcomp’ agdex.scatterplot: no visible global function definition for ‘abline’ gsc.to.index.list: no visible global function definition for ‘geneIds’ prep.dex.set: no visible global function definition for ‘exprs’ prep.dex.set: no visible global function definition for ‘pData’ read.agdex.gset.details: no visible global function definition for ‘read.table’ read.agdex.gset.list: no visible global function definition for ‘read.table’ read.agdex.result: no visible global function definition for ‘read.table’ read.enrich.gset.list: no visible global function definition for ‘read.table’ read.gset.collection: no visible global function definition for ‘read.table’ read.gset.collection: no visible global function definition for ‘GeneSet’ read.gset.collection: no visible global function definition for ‘geneIds<-’ read.gset.collection: no visible global function definition for ‘GeneSetCollection’ write.agdex.gset.details: no visible global function definition for ‘write.table’ write.agdex.result: no visible global function definition for ‘write.table’ write.gset.list.result: no visible global function definition for ‘write.table’ Undefined global functions or variables: GeneSet GeneSetCollection abline exprs geneIds geneIds<- lines pData pnorm points prcomp qnorm read.table sampleNames write.table Consider adding importFrom("graphics", "abline", "lines", "points") importFrom("stats", "pnorm", "prcomp", "qnorm") importFrom("utils", "read.table", "write.table") to your NAMESPACE file. * 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: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/AGDEX.Rcheck/00check.log’ for details.
AGDEX.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL AGDEX ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘AGDEX’ ... ** using staged installation ** R ** data ** 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 (AGDEX)
AGDEX.Rcheck/AGDEX-Ex.timings
name | user | system | elapsed | |
agdex | 1.025 | 0.044 | 1.071 | |
agdex.scatterplot | 0.028 | 0.004 | 0.032 | |
get.gset.result.details | 0.036 | 0.000 | 0.037 | |
gset.data | 0.000 | 0.000 | 0.001 | |
human.data | 0.009 | 0.000 | 0.009 | |
make.dex.set.object | 0.027 | 0.000 | 0.026 | |
map.data | 0 | 0 | 0 | |
mouse.data | 0.016 | 0.000 | 0.016 | |
read.agdex.gset.details | 0.000 | 0.000 | 0.001 | |
read.agdex.result | 0 | 0 | 0 | |
write.agdex.gset.details | 0.031 | 0.000 | 0.031 | |
write.agdex.result | 0.000 | 0.004 | 0.005 | |