Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-10-19 13:22:45 -0400 (Wed, 19 Oct 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
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 |
To the developers/maintainers of the cogena package: - Please 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 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 378/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cogena 1.30.0 (landing page) Zhilong Jia
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: cogena |
Version: 1.30.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cogena.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cogena_1.30.0.tar.gz |
StartedAt: 2022-10-19 00:49:31 -0400 (Wed, 19 Oct 2022) |
EndedAt: 2022-10-19 00:56:11 -0400 (Wed, 19 Oct 2022) |
EllapsedTime: 400.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: cogena.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cogena.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cogena_1.30.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/cogena.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘cogena/DESCRIPTION’ ... OK * this is package ‘cogena’ version ‘1.30.0’ * package encoding: UTF-8 * 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 ‘cogena’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘class::somgrid’ by ‘kohonen::somgrid’ when loading ‘cogena’ See ‘/Users/biocbuild/bbs-3.15-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 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed cogena_package 10.175 0.466 141.924 clEnrich_one 6.103 0.331 20.535 upDownGene 4.417 0.182 27.606 clEnrich 4.308 0.252 27.485 clusterMethods 2.450 0.018 17.092 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/Users/biocbuild/bbs-3.15-bioc/meat/cogena.Rcheck/00check.log’ for details.
cogena.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cogena ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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 | 1.184 | 0.124 | 1.311 | |
clEnrich | 4.308 | 0.252 | 27.485 | |
clEnrich_one | 6.103 | 0.331 | 20.535 | |
clusterMethods | 2.450 | 0.018 | 17.092 | |
coExp | 0.001 | 0.001 | 0.003 | |
cogena_package | 10.175 | 0.466 | 141.924 | |
corInCluster | 0.001 | 0.001 | 0.003 | |
enrichment | 0.002 | 0.001 | 0.004 | |
gene2set | 0.074 | 0.002 | 0.077 | |
geneExpInCluster | 0.003 | 0.002 | 0.004 | |
geneInCluster | 0.002 | 0.002 | 0.004 | |
geneclusters | 0 | 0 | 0 | |
gmt2list | 0.037 | 0.001 | 0.038 | |
gmtlist2file | 0.078 | 0.082 | 0.161 | |
heatmapCluster | 0.003 | 0.002 | 0.005 | |
heatmapCmap | 0.003 | 0.002 | 0.004 | |
heatmapPEI | 0.003 | 0.002 | 0.004 | |
mat | 0.000 | 0.000 | 0.001 | |
nClusters | 0 | 0 | 0 | |
show | 0 | 0 | 0 | |
sota | 2.935 | 0.253 | 3.191 | |
summary | 0 | 0 | 0 | |
upDownGene | 4.417 | 0.182 | 27.606 | |