Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 406/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cogena 1.40.0 (landing page) Zhilong Jia
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the cogena package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cogena.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: cogena |
Version: 1.40.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:cogena.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings cogena_1.40.0.tar.gz |
StartedAt: 2024-12-19 21:47:41 -0500 (Thu, 19 Dec 2024) |
EndedAt: 2024-12-19 21:56:44 -0500 (Thu, 19 Dec 2024) |
EllapsedTime: 543.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: cogena.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:cogena.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings cogena_1.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/cogena.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘cogena/DESCRIPTION’ ... OK * this is package ‘cogena’ version ‘1.40.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 ‘cogena’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘class::somgrid’ by ‘kohonen::somgrid’ when loading ‘cogena’ See ‘/home/biocbuild/bbs-3.20-bioc/meat/cogena.Rcheck/00install.out’ for details. * 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 ... NOTE dist.fn: no visible global function definition for ‘cor’ heatmap.3: no visible binding for global variable ‘dist’ heatmap.3: no visible global function definition for ‘par’ heatmap.3: no visible global function definition for ‘median’ heatmap.3: no visible global function definition for ‘order.dendrogram’ heatmap.3: no visible global function definition for ‘reorder’ heatmap.3: no visible binding for global variable ‘sd’ heatmap.3: no visible global function definition for ‘layout’ heatmap.3: no visible global function definition for ‘image’ heatmap.3: no visible global function definition for ‘axis’ heatmap.3: no visible global function definition for ‘mtext’ heatmap.3: no visible global function definition for ‘rect’ heatmap.3: no visible global function definition for ‘abline’ heatmap.3: no visible global function definition for ‘lines’ heatmap.3: no visible global function definition for ‘text’ heatmap.3: no visible global function definition for ‘plot.new’ heatmap.3: no visible global function definition for ‘title’ heatmap.3: no visible global function definition for ‘density’ heatmap.3: no visible global function definition for ‘hist’ plot.sota: no visible global function definition for ‘par’ corInCluster,cogena: no visible global function definition for ‘cor’ heatmapCluster,cogena: no visible global function definition for ‘topo.colors’ heatmapCluster,cogena: no visible global function definition for ‘rainbow’ heatmapCluster,cogena: no visible global function definition for ‘par’ heatmapCluster,cogena: no visible global function definition for ‘legend’ heatmapPEI,cogena: no visible binding for global variable ‘clusterID’ heatmapPEI,cogena: no visible binding for global variable ‘TF’ heatmapPEI,cogena: no visible binding for global variable ‘clusterNumGene’ heatmapPEI,cogena: no visible binding for global variable ‘GS’ heatmapPEI,cogena: no visible binding for global variable ‘value’ heatmapPEI,cogena: no visible binding for global variable ‘GeneCount’ Undefined global functions or variables: GS GeneCount TF abline axis clusterID clusterNumGene cor density dist hist image layout legend lines median mtext order.dendrogram par plot.new rainbow rect reorder sd text title topo.colors value Consider adding importFrom("grDevices", "rainbow", "topo.colors") importFrom("graphics", "abline", "axis", "hist", "image", "layout", "legend", "lines", "mtext", "par", "plot.new", "rect", "text", "title") importFrom("stats", "cor", "density", "dist", "median", "order.dendrogram", "reorder", "sd") 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 LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed cogena_package 5.070 0.336 65.615 clEnrich_one 3.157 0.176 9.708 clEnrich 2.439 0.112 12.655 upDownGene 2.128 0.108 11.859 clusterMethods 1.085 0.005 7.632 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/cogena.Rcheck/00check.log’ for details.
cogena.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL cogena ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘cogena’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘class::somgrid’ by ‘kohonen::somgrid’ when loading ‘cogena’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘class::somgrid’ by ‘kohonen::somgrid’ when loading ‘cogena’ ** testing if installed package can be loaded from final location Warning: replacing previous import ‘class::somgrid’ by ‘kohonen::somgrid’ when loading ‘cogena’ ** testing if installed package keeps a record of temporary installation path * DONE (cogena)
cogena.Rcheck/cogena-Ex.timings
name | user | system | elapsed | |
PEI | 0.545 | 0.019 | 0.565 | |
clEnrich | 2.439 | 0.112 | 12.655 | |
clEnrich_one | 3.157 | 0.176 | 9.708 | |
clusterMethods | 1.085 | 0.005 | 7.632 | |
coExp | 0.001 | 0.000 | 0.001 | |
cogena_package | 5.070 | 0.336 | 65.615 | |
corInCluster | 0.000 | 0.001 | 0.002 | |
enrichment | 0.000 | 0.001 | 0.002 | |
gene2set | 0.032 | 0.001 | 0.033 | |
geneExpInCluster | 0.001 | 0.001 | 0.001 | |
geneInCluster | 0.001 | 0.000 | 0.001 | |
geneclusters | 0 | 0 | 0 | |
gmt2list | 0.014 | 0.000 | 0.013 | |
gmtlist2file | 0.022 | 0.017 | 0.038 | |
heatmapCluster | 0.002 | 0.000 | 0.001 | |
heatmapCmap | 0.002 | 0.000 | 0.001 | |
heatmapPEI | 0.001 | 0.000 | 0.001 | |
mat | 0 | 0 | 0 | |
nClusters | 0 | 0 | 0 | |
show | 0 | 0 | 0 | |
sota | 1.073 | 0.012 | 1.086 | |
summary | 0 | 0 | 0 | |
upDownGene | 2.128 | 0.108 | 11.859 | |