Multiple platform build/check report for BioC 3.20 - CHECK results for interactiveDisplay on nebbiolo2

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"	4739
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4482
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4510
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4462
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*

CHECK results for interactiveDisplay on nebbiolo2

To the developers/maintainers of the interactiveDisplay package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/interactiveDisplay.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.

raw results

Summary

Package: interactiveDisplay

Version: 1.44.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:interactiveDisplay.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings interactiveDisplay_1.44.0.tar.gz

StartedAt: 2024-11-29 01:34:42 -0500 (Fri, 29 Nov 2024)

EndedAt: 2024-11-29 01:41:15 -0500 (Fri, 29 Nov 2024)

EllapsedTime: 393.3 seconds

RetCode: 0

Status: OK

CheckDir: interactiveDisplay.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:interactiveDisplay.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings interactiveDisplay_1.44.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/interactiveDisplay.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 ‘interactiveDisplay/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘interactiveDisplay’ version ‘1.44.0’
* 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'
 NOTE
Package which this enhances but not available for checking: ‘rstudio’
* 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 ‘interactiveDisplay’ 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 whether startup messages can be suppressed ... 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
.altgr : <anonymous>: no visible global function definition for
  ‘elementMetadata’
.altgr : <anonymous>: no visible global function definition for
  ‘seqlevels<-’
.bicgo : <anonymous>: no visible binding for global variable ‘GO.db’
.bicgo : <anonymous>: no visible global function definition for ‘exprs’
.bicgo : <anonymous>: no visible global function definition for
  ‘cutree’
.bicgo : <anonymous>: no visible global function definition for
  ‘hclust’
.bicgo : <anonymous>: no visible global function definition for ‘dist’
.bicgo : <anonymous>: no visible global function definition for ‘cim’
.choose_gen: no visible global function definition for ‘ucscGenomes’
.simplenet : <anonymous>: no visible global function definition for
  ‘cutree’
.simplenet : <anonymous>: no visible global function definition for
  ‘rainbow’
.simplenet : <anonymous> : hc: no visible global function definition
  for ‘hclust’
.simplenet : <anonymous> : hc: no visible global function definition
  for ‘dist’
.simplenet : <anonymous> : dm: no visible global function definition
  for ‘dist’
.usePackage: no visible global function definition for
  ‘installed.packages’
ggheat: no visible global function definition for ‘colorRampPalette’
ggheat: no visible binding for global variable ‘Var2’
ggheat: no visible binding for global variable ‘Var1’
ggheat: no visible binding for global variable ‘value’
ggheat: no visible global function definition for ‘coord_flip’
grid2jssvg: no visible global function definition for ‘png’
grid2jssvg: no visible global function definition for ‘dev.off’
subgr: no visible global function definition for ‘seqnames’
subgr: no visible global function definition for ‘seqlevels<-’
subgr: no visible global function definition for ‘ranges’
subgr2: no visible global function definition for ‘seqnames’
subgr2: no visible global function definition for ‘seqlevels<-’
subgr2: no visible global function definition for ‘ranges’
display,ExpressionSet : <anonymous>: no visible global function
  definition for ‘exprs’
display,ExpressionSet : <anonymous>: no visible global function
  definition for ‘experimentData’
display,ExpressionSet : <anonymous>: no visible binding for global
  variable ‘GO.db’
display,ExpressionSet : <anonymous>: no visible global function
  definition for ‘cutree’
display,ExpressionSet : <anonymous>: no visible global function
  definition for ‘rainbow’
display,ExpressionSet : <anonymous> : hc: no visible global function
  definition for ‘hclust’
display,ExpressionSet : <anonymous> : hc: no visible global function
  definition for ‘dist’
display,ExpressionSet : <anonymous> : dm: no visible global function
  definition for ‘dist’
display,ExpressionSet : <anonymous>: no visible global function
  definition for ‘as.dendrogram’
display,ExpressionSet : <anonymous> : <local> : <anonymous>: no visible
  global function definition for ‘is.leaf’
display,ExpressionSet : <anonymous>: no visible global function
  definition for ‘dendrapply’
display,GRanges: no visible global function definition for ‘mcols’
display,GRanges : <anonymous>: no visible global function definition
  for ‘AnnotationTrack’
display,GRanges : <anonymous>: no visible global function definition
  for ‘GenomeAxisTrack’
display,GRanges : <anonymous>: no visible global function definition
  for ‘IdeogramTrack’
display,GRanges : <anonymous>: no visible global function definition
  for ‘plotTracks’
display,GRanges : <anonymous>: no visible global function definition
  for ‘layout_circle’
display,GRanges : <anonymous>: no visible binding for global variable
  ‘seqnames’
display,GRanges : <anonymous>: no visible global function definition
  for ‘seqnames’
display,GRanges : <anonymous>: no visible global function definition
  for ‘ranges’
display,GRanges : <anonymous>: no visible global function definition
  for ‘ucscGenomes’
display,GRanges : <anonymous>: no visible global function definition
  for ‘GRanges’
display,GRanges : <anonymous>: no visible global function definition
  for ‘IRanges’
display,GRanges : <anonymous>: no visible global function definition
  for ‘seqlengths<-’
display,GRanges : <anonymous>: no visible global function definition
  for ‘seqlengths’
display,GRangesList : <anonymous>: no visible global function
  definition for ‘mcols’
display,GRangesList : <anonymous>: no visible global function
  definition for ‘AnnotationTrack’
display,GRangesList : <anonymous>: no visible global function
  definition for ‘GenomeAxisTrack’
display,GRangesList : <anonymous>: no visible global function
  definition for ‘IdeogramTrack’
display,GRangesList : <anonymous>: no visible global function
  definition for ‘plotTracks’
display,GRangesList : <anonymous>: no visible global function
  definition for ‘layout_circle’
display,GRangesList : <anonymous>: no visible binding for global
  variable ‘seqnames’
display,GRangesList : <anonymous>: no visible global function
  definition for ‘seqnames’
display,GRangesList : <anonymous>: no visible global function
  definition for ‘ranges’
display,GRangesList : <anonymous>: no visible global function
  definition for ‘ucscGenomes’
display,GRangesList : <anonymous>: no visible global function
  definition for ‘GRanges’
display,GRangesList : <anonymous>: no visible global function
  definition for ‘IRanges’
display,GRangesList : <anonymous>: no visible global function
  definition for ‘seqlengths<-’
display,GRangesList : <anonymous>: no visible global function
  definition for ‘seqlengths’
display,GRangesList : <anonymous>: no visible global function
  definition for ‘GRangesList’
display,MRexperiment : <anonymous>: no visible global function
  definition for ‘MRcounts’
display,MRexperiment : <anonymous>: no visible global function
  definition for ‘pData’
display,MRexperiment : <anonymous>: no visible global function
  definition for ‘colorRampPalette’
display,MRexperiment : <anonymous>: no visible global function
  definition for ‘legend’
display,MRexperiment : <anonymous>: no visible global function
  definition for ‘plotFeature’
display,MRexperiment : <anonymous>: no visible global function
  definition for ‘plotOrd’
display,MRexperiment : <anonymous>: no visible global function
  definition for ‘libSize’
display,MRexperiment : <anonymous>: no visible global function
  definition for ‘fData’
display,RangedSummarizedExperiment : <anonymous>: no visible global
  function definition for ‘seqnames’
display,RangedSummarizedExperiment : <anonymous>: no visible global
  function definition for ‘rowRanges’
display,RangedSummarizedExperiment : <anonymous>: no visible global
  function definition for ‘assays’
display,RangedSummarizedExperiment : <anonymous>: no visible global
  function definition for ‘colorRampPalette’
display,RangedSummarizedExperiment : <anonymous>: no visible binding
  for global variable ‘Var1’
display,RangedSummarizedExperiment : <anonymous>: no visible binding
  for global variable ‘Var2’
display,RangedSummarizedExperiment : <anonymous>: no visible binding
  for global variable ‘value’
Undefined global functions or variables:
  AnnotationTrack GO.db GRanges GRangesList GenomeAxisTrack IRanges
  IdeogramTrack MRcounts Var1 Var2 as.dendrogram assays cim
  colorRampPalette coord_flip cutree dendrapply dev.off dist
  elementMetadata experimentData exprs fData hclust installed.packages
  is.leaf layout_circle legend libSize mcols pData plotFeature plotOrd
  plotTracks png rainbow ranges rowRanges seqlengths seqlengths<-
  seqlevels<- seqnames ucscGenomes value
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "png",
             "rainbow")
  importFrom("graphics", "legend")
  importFrom("stats", "as.dendrogram", "cutree", "dendrapply", "dist",
             "hclust", "is.leaf")
  importFrom("utils", "installed.packages")
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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/interactiveDisplay.Rcheck/00check.log’
for details.

Installation output

interactiveDisplay.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL interactiveDisplay
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘interactiveDisplay’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘display’ with signature ‘object="GRanges"’: no definition for class “GRanges”
in method for ‘display’ with signature ‘object="GRangesList"’: no definition for class “GRangesList”
in method for ‘display’ with signature ‘object="RangedSummarizedExperiment"’: no definition for class “RangedSummarizedExperiment”
in method for ‘display’ with signature ‘object="MRexperiment"’: no definition for class “MRexperiment”
** 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 (interactiveDisplay)

Tests output

Example timings

interactiveDisplay.Rcheck/interactiveDisplay-Ex.timings

name	user	system	elapsed
altgr	0	0	0
bicgo	0	0	0
expr	0.014	0.000	0.014
gridsvgjs	0	0	0
gridtweak	0	0	0
interactiveDisplay-methods	0.000	0.000	0.001
mmgr	0.004	0.000	0.003
mmgrl	0.002	0.000	0.002
se	0.071	0.001	0.072
simplenet	0.000	0.000	0.001