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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:NCIgraphData.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings NCIgraphData_1.43.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/NCIgraphData.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘NCIgraphData/DESCRIPTION’ ... OK
* this is package ‘NCIgraphData’ version ‘1.43.0’
* 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 ‘NCIgraphData’ can be installed ... OK
* checking installed package size ... INFO
installed size is 5.4Mb
sub-directories of 1Mb or more:
data 5.3Mb
* checking package 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 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 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 LazyData ... WARNING
LazyData DB of 5.3 MB without LazyDataCompression set
See §1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... WARNING
Note: significantly better compression could be obtained
by using R CMD build --resave-data
old_size new_size compress
NCI-cyList.RData 4.3Mb 2.0Mb xz
reactome-cyList.RData 1.1Mb 558Kb xz
* checking examples ... ERROR
Running examples in ‘NCIgraphData-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NCI.cyList
> ### Title: Raw NCI networks from Nature curated pathways and BioCarta
> ### imported as graphNEL objects
> ### Aliases: NCI.cyList
> ### Keywords: datasets
>
> ### ** Examples
>
> data("NCI-cyList")
> length(NCI.cyList)
[1] 460
>
> library(Rgraphviz)
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: grid
> plot(NCI.cyList[[1]])
Error in buildEdgeList(graph, recipEdges, edgeAttrs, subGList, attrs$edge) :
attempt to set index 36/36 in SET_STRING_ELT
Calls: plot -> plot -> .local -> agopen -> buildEdgeList
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
‘/home/biocbuild/bbs-3.21-data-experiment/meat/NCIgraphData.Rcheck/00check.log’
for details.