Weijun Luo
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/gage |
| git_branch: master |
| git_last_commit: f320555 |
| git_last_commit_date: 2021-10-26 11:57:14 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:33 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 gage package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 696/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gage 2.45.0 (landing page) Weijun Luo
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: gage |
| Version: 2.45.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gage.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings gage_2.45.0.tar.gz |
| StartedAt: 2022-03-17 19:08:33 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:10:19 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 106.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: gage.Rcheck |
| Warnings: 1 |
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### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gage.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings gage_2.45.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/gage.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gage/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gage' version '2.45.0'
* 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 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 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 ... 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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
kegg.gsets 0.88 0.02 5.61
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/gage.Rcheck/00check.log'
for details.
gage.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL gage
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'gage' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'gage'
finding HTML links ... done
eg2sym html
egSymb html
essGene html
esset.grp html
gage-internal html
gage html
gageComp html
gagePipe html
geneData html
go.gsets html
gs.tTest html
gse16873 html
heter.gage html
kegg.gs html
kegg.gsets html
readExpData html
readList html
sigGeneSet html
** 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)
Making 'packages.html' ... done
gage.Rcheck/gage-Ex.timings
| name | user | system | elapsed | |
| eg2sym | 0.81 | 0.18 | 1.00 | |
| egSymb | 0.47 | 0.16 | 0.63 | |
| essGene | 0.25 | 0.03 | 0.28 | |
| esset.grp | 0.82 | 0.10 | 0.91 | |
| gage | 1.20 | 0.15 | 1.35 | |
| gageComp | 0.48 | 0.22 | 0.72 | |
| gagePipe | 0.51 | 0.05 | 0.56 | |
| geneData | 0.18 | 0.04 | 0.22 | |
| go.gsets | 0 | 0 | 0 | |
| gs.tTest | 0.15 | 0.02 | 0.17 | |
| gse16873 | 0.19 | 0.03 | 0.22 | |
| heter.gage | 0.31 | 0.04 | 0.36 | |
| kegg.gs | 0.64 | 0.02 | 0.65 | |
| kegg.gsets | 0.88 | 0.02 | 5.61 | |
| readExpData | 0.01 | 0.00 | 0.02 | |
| readList | 0.11 | 0.00 | 0.11 | |
| sigGeneSet | 0.41 | 0.01 | 0.42 | |