Zhilong Jia
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/cogena |
| git_branch: RELEASE_3_17 |
| git_last_commit: 2e39593 |
| git_last_commit_date: 2023-04-25 10:39:00 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:00 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 396/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cogena 1.34.0 (landing page) Zhilong Jia
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the cogena package: - 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: 1.34.0 |
| 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_1.34.0.tar.gz |
| StartedAt: 2023-10-17 10:58:38 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 11:05:03 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 385.1 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_1.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/cogena.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cogena/DESCRIPTION’ ... OK
* this is package ‘cogena’ version ‘1.34.0’
* 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-3.17-bioc-mac-arm64/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 6.639 0.377 139.631
clEnrich_one 4.404 0.198 21.538
clEnrich 2.980 0.131 27.670
upDownGene 2.987 0.117 23.822
clusterMethods 1.689 0.027 15.239
* 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-3.17-bioc-mac-arm64/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/4.3-arm64/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 | 1.046 | 0.049 | 1.636 | |
| clEnrich | 2.980 | 0.131 | 27.670 | |
| clEnrich_one | 4.404 | 0.198 | 21.538 | |
| clusterMethods | 1.689 | 0.027 | 15.239 | |
| coExp | 0.001 | 0.002 | 0.004 | |
| cogena_package | 6.639 | 0.377 | 139.631 | |
| corInCluster | 0.002 | 0.002 | 0.005 | |
| enrichment | 0.002 | 0.001 | 0.005 | |
| gene2set | 0.044 | 0.004 | 0.066 | |
| geneExpInCluster | 0.002 | 0.002 | 0.004 | |
| geneInCluster | 0.002 | 0.001 | 0.003 | |
| geneclusters | 0.000 | 0.000 | 0.002 | |
| gmt2list | 0.022 | 0.001 | 0.033 | |
| gmtlist2file | 0.046 | 0.102 | 0.218 | |
| heatmapCluster | 0.002 | 0.002 | 0.006 | |
| heatmapCmap | 0.002 | 0.002 | 0.005 | |
| heatmapPEI | 0.002 | 0.002 | 0.007 | |
| mat | 0 | 0 | 0 | |
| nClusters | 0 | 0 | 0 | |
| show | 0 | 0 | 0 | |
| sota | 1.524 | 0.120 | 2.463 | |
| summary | 0.000 | 0.001 | 0.000 | |
| upDownGene | 2.987 | 0.117 | 23.822 | |