Back to Mac ARM64 build report for BioC 3.17
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-10-20 09:38:02 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (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 751/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gage 2.50.0  (landing page)
Weijun Luo
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/gage
git_branch: RELEASE_3_17
git_last_commit: a6d1e96
git_last_commit_date: 2023-04-25 10:18:08 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for gage on kjohnson2


To the developers/maintainers of the gage 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.

raw results


Summary

Package: gage
Version: 2.50.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gage.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gage_2.50.0.tar.gz
StartedAt: 2023-10-17 20:38:53 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 20:42:13 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 199.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: gage.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gage.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gage_2.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/gage.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 ‘gage/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gage’ version ‘2.50.0’
* 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 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 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 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
kegg.gsets 0.845  0.101  10.116
* 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/gage.Rcheck/00check.log’
for details.



Installation output

gage.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gage
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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)

Tests output


Example timings

gage.Rcheck/gage-Ex.timings

nameusersystemelapsed
eg2sym1.1640.0451.822
egSymb0.9170.0341.462
essGene0.2870.0260.467
esset.grp1.1730.0471.846
gage1.6690.0492.610
gageComp0.9150.0531.477
gagePipe1.1010.0581.754
geneData0.2330.0230.393
go.gsets0.0010.0010.005
gs.tTest0.1920.0110.309
gse168730.2640.0180.443
heter.gage0.4930.0210.783
kegg.gs0.7690.0361.240
kegg.gsets 0.845 0.10110.116
readExpData0.0070.0010.009
readList0.1110.0050.185
sigGeneSet0.4470.0180.726