Weijun Luo
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/gage |
| git_branch: RELEASE_3_20 |
| git_last_commit: 04d50ac |
| git_last_commit_date: 2024-10-29 09:34:54 -0500 (Tue, 29 Oct 2024) |
| 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 764/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gage 2.56.0 (landing page) Weijun Luo
| 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 gage package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gage.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: gage |
| Version: 2.56.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gage.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gage_2.56.0.tar.gz |
| StartedAt: 2024-12-19 23:56:40 -0500 (Thu, 19 Dec 2024) |
| EndedAt: 2024-12-20 00:04:19 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 458.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: gage.Rcheck |
| Warnings: 2 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:gage.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings gage_2.56.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/gage.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 ‘gage/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gage’ version ‘2.56.0’
* 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 ‘gage’ 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 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 ... WARNING
'::' or ':::' import not declared from: ‘BiocManager’
'loadNamespace' or 'requireNamespace' call not declared from: ‘BiocManager’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
colorpanel: no visible global function definition for ‘col2rgb’
colorpanel: no visible global function definition for ‘rgb’
deComp: no visible global function definition for ‘annot.db’
deComp: no visible global function definition for ‘write.table’
eg2sym: no visible binding for global variable ‘egSymb’
essGene: no visible binding for global variable ‘sd’
essGene: no visible global function definition for ‘qchisq’
esset.grp: no visible global function definition for ‘sd’
esset.grp : <anonymous>: no visible global function definition for
‘phyper’
esset.grp: no visible global function definition for ‘as’
esset.grp: no visible global function definition for ‘write.table’
esset.grp: no visible global function definition for ‘nodes’
esset.grp: no visible global function definition for ‘edgeNames’
esset.grp: no visible global function definition for ‘pdf’
esset.grp: no visible global function definition for ‘make.graph’
esset.grp : <anonymous>: no visible global function definition for
‘nodes’
esset.grp: no visible global function definition for ‘points’
esset.grp: no visible global function definition for ‘dev.off’
gageComp: no visible global function definition for ‘pdf’
gageComp: no visible global function definition for ‘dev.off’
gagePipe: no visible global function definition for ‘write.table’
gagePipe: no visible global function definition for ‘pdf’
gagePipe: no visible global function definition for ‘dev.off’
gagePrep : <anonymous>: no visible global function definition for
‘t.test’
gageSum: no visible global function definition for ‘qnorm’
gageSum: no visible global function definition for ‘pnorm’
gageSum: no visible global function definition for ‘aggregate’
gageSum : <anonymous>: no visible global function definition for
‘pnorm’
gageSum: no visible global function definition for ‘pgamma’
gageSum: no visible global function definition for ‘p.adjust’
geneData: no visible global function definition for ‘write.table’
geneData: no visible global function definition for ‘pdf’
geneData: no visible global function definition for ‘dev.off’
geneData: no visible global function definition for ‘par’
geneData: no visible global function definition for ‘abline’
geneData: no visible global function definition for ‘points’
geneData: no visible global function definition for ‘legend’
go.gsets: no visible global function definition for ‘data’
go.gsets: no visible global function definition for ‘install.packages’
gs.KSTest : <anonymous>: no visible global function definition for
‘ks.test’
gs.tTest: no visible binding for global variable ‘sd’
gs.tTest: no visible global function definition for ‘pt’
gs.zTest: no visible binding for global variable ‘sd’
gs.zTest: no visible global function definition for ‘pnorm’
heatmap2: no visible binding for global variable ‘dist’
heatmap2: no visible binding for global variable ‘hclust’
heatmap2: no visible global function definition for ‘par’
heatmap2: no visible global function definition for ‘median’
heatmap2: no visible binding for global variable ‘sd’
heatmap2: no visible global function definition for ‘order.dendrogram’
heatmap2: no visible global function definition for ‘as.dendrogram’
heatmap2: no visible global function definition for ‘reorder’
heatmap2: no visible global function definition for ‘layout’
heatmap2: no visible global function definition for ‘image’
heatmap2: no visible global function definition for ‘axis’
heatmap2: no visible global function definition for ‘mtext’
heatmap2: no visible global function definition for ‘rect’
heatmap2: no visible global function definition for ‘abline’
heatmap2: no visible global function definition for ‘lines’
heatmap2: no visible global function definition for ‘text’
heatmap2: no visible global function definition for ‘plot.new’
heatmap2: no visible global function definition for ‘title’
heatmap2: no visible global function definition for ‘density’
heatmap2: no visible global function definition for ‘hist’
kegg.gsets: no visible global function definition for ‘data’
kegg.gsets: no visible binding for global variable ‘khier’
kegg.species.code: no visible global function definition for ‘data’
kegg.species.code: no visible binding for global variable ‘korg.1’
readExpData: no visible global function definition for ‘read.delim’
rownorm : <anonymous>: no visible global function definition for ‘sd’
sigGeneSet: no visible global function definition for ‘pdf’
sigGeneSet: no visible global function definition for ‘dev.off’
sym2eg: no visible binding for global variable ‘egSymb’
vennDiagram2: no visible global function definition for ‘is’
vennDiagram2: no visible global function definition for ‘par’
vennDiagram2: no visible global function definition for ‘lines’
vennDiagram2: no visible global function definition for ‘text’
vennDiagram2: no visible global function definition for ‘rect’
vennDiagram2 : printing: no visible global function definition for
‘text’
Undefined global functions or variables:
abline aggregate annot.db as as.dendrogram axis col2rgb data density
dev.off dist edgeNames egSymb hclust hist image install.packages is
khier korg.1 ks.test layout legend lines make.graph median mtext
nodes order.dendrogram p.adjust par pdf pgamma phyper plot.new pnorm
points pt qchisq qnorm read.delim rect reorder rgb sd t.test text
title write.table
Consider adding
importFrom("grDevices", "col2rgb", "dev.off", "pdf", "rgb")
importFrom("graphics", "abline", "axis", "hist", "image", "layout",
"legend", "lines", "mtext", "par", "plot.new", "points",
"rect", "text", "title")
importFrom("methods", "as", "is")
importFrom("stats", "aggregate", "as.dendrogram", "density", "dist",
"hclust", "ks.test", "median", "order.dendrogram",
"p.adjust", "pgamma", "phyper", "pnorm", "pt", "qchisq",
"qnorm", "reorder", "sd", "t.test")
importFrom("utils", "data", "install.packages", "read.delim",
"write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) go.gsets.Rd:17: Lost braces; missing escapes or markup?
17 | species names, type in: {data(bods); bods}
| ^
checkRd: (-1) go.gsets.Rd:33: Lost braces; missing escapes or markup?
33 | gene IDs, please type in: {data(bods); bods} to check the details.
| ^
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
kegg.gsets 0.682 0.008 7.952
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... WARNING
Warning in re-building vignettes:
Warning: file stem ‘gage-heter.gage’ is not portable
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.20-bioc/meat/gage.Rcheck/00check.log’
for details.
gage.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL gage ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘gage’ ... ** 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 (gage)
gage.Rcheck/gage-Ex.timings
| name | user | system | elapsed | |
| eg2sym | 0.652 | 0.015 | 0.668 | |
| egSymb | 0.763 | 0.008 | 0.771 | |
| essGene | 0.210 | 0.002 | 0.212 | |
| esset.grp | 0.899 | 0.013 | 0.911 | |
| gage | 1.152 | 0.014 | 1.166 | |
| gageComp | 0.649 | 0.022 | 0.673 | |
| gagePipe | 0.884 | 0.059 | 0.943 | |
| geneData | 0.174 | 0.002 | 0.175 | |
| go.gsets | 0.001 | 0.000 | 0.001 | |
| gs.tTest | 0.142 | 0.004 | 0.146 | |
| gse16873 | 0.227 | 0.002 | 0.228 | |
| heter.gage | 0.334 | 0.001 | 0.334 | |
| kegg.gs | 0.582 | 0.001 | 0.584 | |
| kegg.gsets | 0.682 | 0.008 | 7.952 | |
| readExpData | 0.007 | 0.000 | 0.007 | |
| readList | 0.133 | 0.002 | 0.135 | |
| sigGeneSet | 0.370 | 0.029 | 0.400 | |