Warning: unable to load shared object R_X11.so

[gtollefson]

I receive the following warning when running the heatmaply() plotting function using heatmaply version 0.15.3 on R version 3.4.3 (2017-11-30) on MacOS High Sierra. The code works and the plot is produced without error. However, I am implementing heatmaply in a command line tool we're developing and as a result the printed output is messy.

Does this warning need to be displayed? If so, is there a way for me to include code to suppress this warning from being printed?

Warning message: In doTryCatch(return(expr), name, parentenv, handler) : unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so': dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Library not loaded: /opt/X11/lib/libSM.6.dylib Referenced from: /Library/Frameworks/R.framework/Resources/modules//R_X11.so Reason: image not found

I believe the warning is triggered because heatmaply looks for XQuartz to be installed but it is not installed on current Mac OSX. Manually installing XQuartz has been reported to solve the issue here [https://github.com/RevolutionAnalytics/RRO/issues/312] . However as heatmaply will be installed as a dependency of our command line tool, ideally heatmaply would install onto Mac OS without additional manual installation.

[alanocallaghan]

You can use suppressWarnings to not print warnings, though unfortunately it catches all warnings. I don't have access to a Mac so this might be hard to test but I can have a look later. This isn't something I'm aware of so would prefer to prevent it outright

[gtollefson]

Thanks for your reply @Alanocallaghan. I will plan to use suppressWarnings if necessary, but preventing it outright would be great! Please let me know how I can help test.

[talgalili]

I just installed a fresh copy of heatmaply from CRAN on my mac at work, and couldn't reproduce the issue. For reference:

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

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

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

other attached packages:
[1] heatmaply_0.15.2  viridis_0.4.1     viridisLite_0.2.0 plotly_4.7.1      ggplot2_2.2.1    

loaded via a namespace (and not attached):
 [1] httr_1.3.1          tidyr_0.8.0         jsonlite_1.5        foreach_1.4.4       gtools_3.5.0        shiny_1.0.5         assertthat_0.2.0   
 [8] stats4_3.4.3        yaml_2.1.16         robustbase_0.92-8   pillar_1.1.0        lattice_0.20-35     glue_1.2.0          digest_0.6.13      
[15] RColorBrewer_1.1-2  colorspace_1.3-2    htmltools_0.3.6     httpuv_1.3.5        plyr_1.8.4          pkgconfig_2.0.1     purrr_0.2.4        
[22] xtable_1.8-2        mvtnorm_1.0-6       scales_0.5.0        webshot_0.5.1       gdata_2.18.0        whisker_0.3-2       tibble_1.4.2       
[29] nnet_7.3-12         lazyeval_0.2.1      magrittr_1.5        mime_0.5            mclust_5.4          MASS_7.3-47         gplots_3.0.1       
[36] class_7.3-14        Cairo_1.5-9         tools_3.4.3         registry_0.5        data.table_1.10.4-3 trimcluster_0.1-2   stringr_1.3.0      
[43] kernlab_0.9-25      munsell_0.4.3       cluster_2.0.6       fpc_2.1-10          bindrcpp_0.2        compiler_3.4.3      caTools_1.17.1     
[50] rlang_0.2.0         grid_3.4.3          iterators_1.0.9     htmlwidgets_1.0     crosstalk_1.0.0     bitops_1.0-6        labeling_0.3       
[57] gtable_0.2.0        codetools_0.2-15    flexmix_2.3-14      TSP_1.1-6           reshape2_1.4.3      R6_2.2.2            seriation_1.2-3    
[64] gridExtra_2.3       prabclus_2.2-6      dplyr_0.7.4         bindr_0.1           KernSmooth_2.23-15  dendextend_1.6.0    modeltools_0.2-21  
[71] stringi_1.1.7       Rcpp_0.12.16        gclus_1.3.1         DEoptimR_1.0-8      diptest_0.75-7     

[talgalili]

mmm, update: I see I already have XQuartz installed on my system. So is it required to have it installed for heatmaply to work properly on Mac, or does it run properly without it? @gtollefson - can you see which command is triggering the warning?

[alanocallaghan]

can you see which command is triggering the warning?

You can test this easily by setting options(warn=2) (this converts warnings to errors - reset using options(warn=0)).

Also, are you using Microsoft R Open (given the related issue was specific to RRO)?

[gtollefson]

Thanks for looking into this @Alanocallaghan and @talgalili. I am not using MRO - I'm using the following version:

R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

@talgalili the function runs fine without XQuartz and produces the plot I would expect. Also, it only produces the warning on the first time running the function in a session.

Interestingly, I do not get the error/warning message when I set options(warn=2) but does trigger the warning I run without setting this. Since setting warn=2 isn't working, I ran line by line to find the command and it looks like the error message comes from heatmaply(x).

I've pasted the output from loading heatmaply (which produces two warnings) and the warning when I run the heatmaply() function.

library(heatmaply)
Loading required package: plotly
Loading required package: ggplot2

Attaching package: ‘plotly’

The following object is masked from ‘package:ggplot2’:

    last_plot

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

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 0.15.3

Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.

The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>
======================

Warning messages:
1: package ‘ggplot2’ was built under R version 3.4.4 
2: package ‘viridis’ was built under R version 3.4.4 

heatmaply(gt_num_array_1)
Warning message:
In doTryCatch(return(expr), name, parentenv, handler) :
  unable to load shared object '/Library/Frameworks/R.framework/Resources/modules//R_X11.so':
  dlopen(/Library/Frameworks/R.framework/Resources/modules//R_X11.so, 6): Library not loaded: /opt/X11/lib/libSM.6.dylib
  Referenced from: /Library/Frameworks/R.framework/Resources/modules//R_X11.so
  Reason: image not found

[alanocallaghan]

Can you post what this returns in your R shell? .Platform$GUI

[alanocallaghan]

Also, could you try adding the argument plot_method="plotly" to your call to heatmaply, and then check if the warning still occurs?

[gtollefson]

Can you post what this returns in your R shell? .Platform$GUI Returns:

[1] "X11"

[gtollefson]

Also, could you try adding the argument plot_method="plotly" to your call to heatmaply, and then check if the warning still occurs?

The warning does not occur when I add this argument to the heatmaply() function.

[alanocallaghan]

Okay I think I know the issue! Great.

[alanocallaghan]

If you run this line, does it reproduce the warning?

grDevices::png()

[gtollefson]

If you run this line, does it reproduce the warning?

grDevices::png()

When I run this line alone in the R shell it does not reproduce the warning.

[gtollefson]

When I run this line alone in the R shell it does not reproduce the warning.

On Wed, Dec 19, 2018 at 11:56 AM Alanocallaghan notifications@github.com wrote:

If you run this line, does it reproduce the warning?

grDevices::png()

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/talgalili/heatmaply/issues/196#issuecomment-448667529, or mute the thread https://github.com/notifications/unsubscribe-auth/AfcN7NmNaZUU9bXP4wxzUpS5ev2WHuocks5u6m_TgaJpZM4ZYyqY .

[alanocallaghan]

Hmm, curious. How about grDevices::jpeg()?

[alanocallaghan]

Or grDevices::dev.list()

[gtollefson]

@Alanocallaghan grDevices::jpeg() produces nothing but grDevices::dev.list()returns NULL.

[alanocallaghan]

No warnings? Hmm, I really thought the problem might be with ggplotly. How about the following:

library(plotly)
p <- ggplot(iris, aes(x=Sepal.Length, y=Sepal.Width, color=Species, shape=Species)) + 
    geom_point(size=6, alpha=0.6)
ggplotly(p)

[gtollefson]

@Alanocallaghan this returns the following output (including several warnings) and plots correctly.

> library(plotly)
Loading required package: ggplot2
p <- ggplot(iris, aes(x=Sepal.Length, y=Sepal.Width, color=Species, shape=Species)) + 
    geom_point(size=6, alpha=0.6)
ggplotly(p)

Attaching package: ‘plotly’

The following object is masked from ‘package:ggplot2’:

    last_plot

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

    filter

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

    layout

Warning message:
package ‘ggplot2’ was built under R version 3.4.4 
> p <- ggplot(iris, aes(x=Sepal.Length, y=Sepal.Width, color=Species, shape=Species)) + 
+     geom_point(size=6, alpha=0.6)
> ggplotly(p)

[alanocallaghan]

I only see one warning there, and not the relevant one! Quite confusing.

btw, the "package ‘X’ was built under R version 3.4.4" warnings can be fixed by re-installing package X.

[talgalili]

This bug seems not updated (not reproducible?!). Can we close this issue?

[alanocallaghan]

Couldn't get to the bottom of this, and it didn't affect output, so yep