# Warning message: 'is.R' is deprecated

**URL:** <https://igraph.discourse.group/t/warning-message-is-r-is-deprecated/1837>\
**Category:** Usage\
**Tags:** R\
**Created:** [2 August 2024 10:03 UTC](https://igraph.discourse.group/t/warning-message-is-r-is-deprecated/1837 "2024-08-02T10:03:56Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![striatum](https://yyz2.discourse-cdn.com/free1/user_avatar/igraph.discourse.group/striatum/32/1090_2.png) [@striatum](https://igraph.discourse.group/u/striatum)\
**Post date:** [2 August 2024 10:03 UTC](https://igraph.discourse.group/t/warning-message-is-r-is-deprecated/1837/1 "2024-08-02T10:03:56Z")

</div>

I am running a `pc()` model, implemented in the `pcalg` package. Then, I am getting a graph from the saved `pc.object`, and plot it using `igraph`:

```auto
gr = graph_from_graphnel(pc.object@graph)
plot.igraph(gr)

```

The `plot.igraph()` function returns the warning message: `'is.R' is deprecated`. Can you help me understand how can I fix this? Thanks!

---

<div class="post-metadata">

**Author:** ![szhorvat](https://yyz2.discourse-cdn.com/free1/user_avatar/igraph.discourse.group/szhorvat/32/3_2.png) [@szhorvat](https://igraph.discourse.group/u/szhorvat)\
**Post date:** [2 August 2024 13:56 UTC](https://igraph.discourse.group/t/warning-message-is-r-is-deprecated/1837/2 "2024-08-02T13:56:32Z")

</div>

Please test this with the latest version of igraph. If it still happens, provide a [minimal reproducible example](https://stackoverflow.com/help/minimal-reproducible-example), along with the output of `sessionInfo()`.

---

<div class="post-metadata">

**Author:** ![striatum](https://yyz2.discourse-cdn.com/free1/user_avatar/igraph.discourse.group/striatum/32/1090_2.png) [@striatum](https://igraph.discourse.group/u/striatum)\
**Post date:** [2 August 2024 14:49 UTC](https://igraph.discourse.group/t/warning-message-is-r-is-deprecated/1837/3 "2024-08-02T14:49:21Z")

</div>

The warning message does not occur once I’ve upgraded `R` and all the packages. Thanks.

For completeness, here is the minimal code example:

```auto

library(MASS)
library(pcalg)
library(igraph)

# Some variance-covariance
Corrs <- matrix(c(1.0,0.6,0.7,0.5,0.6,1.0,0.5,0.6,0.7,0.5,1.0,0.7,0.5,0.6,0.7,1.0), 4, 4)
SDs <- c(1.0,0.5,2.0,1.0)
Covs <- SDs %*% t(SDs) * Corrs

dat = as.data.frame(mvrnorm(100, mu=c(0,0,0,0), Sigma=Covs))

n = nrow(dat)
V = colnames(dat) # node names
pc1 = pc(suffStat=list(C=cor(dat), n=n),
             indepTest=gaussCItest, # indep.test: partial correlations
             alpha=0.05, labels=V, u2pd='retry')

gr = graph_from_graphnel(pc1@graph)

plot.igraph(gr, layout=layout_in_circle,
    vertex.label=V, vertex.shape='circle', vertex.size=30,
    vertex.label.cex=0.55, vertex.label.color='black',
    edge.arrow.size=0.6)

```

Output from `sessionInfo()` is:

```auto
R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS Sonoma 14.5

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

time zone: Europe/London
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base     

other attached packages:
[1] igraph_2.0.3 pcalg_2.7-11 MASS_7.3-61 

loaded via a namespace (and not attached):
 [1] graph_1.82.0 DEoptimR_1.1-3 clue_0.3-65        
 [4] magrittr_2.0.3 fastICA_1.2-4 abind_1.4-5        
 [7] BiocGenerics_0.50.0 pkgconfig_2.0.3 stats4_4.4.1       
[10] lifecycle_1.0.4 cli_3.6.3 sfsmisc_1.1-18     
[13] ggm_2.5.1 corpcor_1.6.10 robustbase_0.99-3  
[16] compiler_4.4.1 RBGL_1.80.0 tools_4.4.1        
[19] cluster_2.1.6 bdsmatrix_1.3-7 Rcpp_1.0.13        
[22] BiocManager_1.30.23 rlang_1.1.4        

```