##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:geneplotter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings geneplotter_1.85.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/geneplotter.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geneplotter/DESCRIPTION’ ... OK
* this is package ‘geneplotter’ version ‘1.85.0’
* 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 ‘geneplotter’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘annotate’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘Rgraphviz’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotExpressionGraph: no visible global function definition for
  ‘selectMethod’
Undefined global functions or variables:
  selectMethod
Consider adding
  importFrom("methods", "selectMethod")
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 ... NOTE
Unknown package ‘prada’ in Rd xrefs
* 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 ... ERROR
Running examples in ‘geneplotter-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotExpressionGraph
> ### Title: A function to plot a graph colored by expression data
> ### Aliases: plotExpressionGraph getPlotExpressionColors IMCAEntrezLink
> ###   defMapFun
> ### Keywords: utilities graphs hplot
> 
> ### ** Examples
> 
>    if (require("Rgraphviz") && require("hgu95av2.db") &&
+        require("fibroEset")) {
+        data(integrinMediatedCellAdhesion)
+ 	   data(IMCAEntrezLink)
+        data(fibroEset)
+        attrs <- getDefaultAttrs()
+        attrs$graph$rankdir <- "LR"
+        plotExpressionGraph(IMCAGraph, IMCAEntrezLink,
+                            exprs(fibroEset)[,1],
+                            hgu95av2ENTREZID, attrs = attrs)
+    }
Loading required package: Rgraphviz
Loading required package: graph

Attaching package: ‘graph’

The following object is masked from ‘package:XML’:

    addNode

Loading required package: grid

Attaching package: ‘Rgraphviz’

The following object is masked from ‘package:annotate’:

    toFile

The following objects are masked from ‘package:IRanges’:

    from, to

The following objects are masked from ‘package:S4Vectors’:

    from, to

Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
Loading required package: fibroEset
Warning in contents(ENTREZIDenvir) :
    The contents() method for Bimap objects is deprecated. Please use as.list()
  instead.
Error in buildEdgeList(graph, recipEdges, edgeAttrs, subGList, attrs$edge) : 
  attempt to set index 65/65 in SET_STRING_ELT
Calls: plotExpressionGraph -> .plot.graph -> .local -> agopen -> buildEdgeList
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/geneplotter.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘geneplotter’ ...
** this is package ‘geneplotter’ version ‘1.85.0’
** 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 (geneplotter)