Thursday, May 17, 2018

Issues with installing ENMTools under newest versions of R

During the course I co-taught with Matt Fitzpatrick in Glasgow a few weeks ago, it came out that a number of people were having trouble installing ENMTools.  A lot of this seems to stem from the newest version of R, and in particular how it interacts with your Java installation.

Some Mac users (including me) were able to fix this just by going to the console and typing "R CMD javareconf" and restarting R.

Windows users seemed to have much more significant issues, however.  There seemed to be several issues, but here's a solution that helped several of the students, courtesy of Hirzi Luqman:

Error:
* installing *source* package ‘ENMTools’ ...
** R
** data
*** moving datasets to lazyload DB
** tests
** byte-compile and prepare package for lazy loading
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home/lib/server/libjvm.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/library/rJava/libs/rJava.so
  Reason: image not found
ERROR: lazy loading failed for package ‘ENMTools’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/ENMTools’
Installation failed: Command failed (1)


Problem:
ENMtools/rJava was looking for (and couldn't find) the library "libjvm.dylib" in the directory "/Library/Java/JavaVirtualMachines/jdk-9.jdk/Contents/Home/lib/server/", because no such directory existed (this refers to a Java 9 installation); I don't know why it looked for the file there...

Solution: I just copied the same file from the Java 8 directory (or whatever Java version is installed on the computer; in my case the directory was "/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/lib/server/") to the R library directory "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/", and it worked
Update: GitHub user Sandy had a different issue, detailed here.  The fix in that case was:

 I removed all PATH related to "java", then Add jvm.dll to PATH (adding "%JAVA_HOME%\jre\bin\server;" to PATH).
After that, I set up the JAVA_HOME in R:
Sys.setenv(JAVA_HOME="C:\\Program Files\\Java\\jdk1.8.0_171\\").
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6 comments:

  1. Daryl David Cruz FloresJanuary 18, 2019 at 1:19 PM

    Hello
    I tried to install ENMTools package on windows 10, but got this error:
    > install_github("danlwarren/ENMTools")
    Downloading GitHub repo danlwarren/ENMTools@master
    Error in read.dcf(path) :
    Found continuation line starting ' person("Olivier", " ...' at begin of record.

    Would you mind give me some suggestions?
    Best regards,
    Daryl

    ReplyDelete
  2. Dan WarrenJanuary 18, 2019 at 1:21 PM

    Hey there! This happens a lot. I think it's an issue with the DESCRIPTION file in ecospat. All you need to do is install ecospat first on its own (using install.packages("ecospat")), and then install ENMTools after that.

    ReplyDelete
    Replies
    1. UnknownFebruary 2, 2019 at 7:41 AM

      Hi Dan,

      I have been also facing some issues concerning ENMTools installation. I have updated R (v3.5.2) and Rstudio (v1.1.463) to the most recent versions. I was having the same error as reported above and I have installed the package "ecospat" as you recommended.

      However, R is now printing a different error while installing ENMTools. After listing if I want to update some packages, the following print messages are displayed:



      √ checking for file 'C:\Users\Andre\AppData\Local\Temp\RtmpovYBoN\remotes1ed4601d4e3e\danlwarren-ENMTools-e7c61ac/DESCRIPTION' ...
      - preparing 'ENMTools':
      √ checking DESCRIPTION meta-information ...
      - checking for LF line-endings in source and make files and shell scripts
      - checking for empty or unneeded directories
      - looking to see if a 'data/datalist' file should be added
      - building 'ENMTools_0.2.tar.gz'

      Installing package into ‘C:/Users/Andre/Documents/R/win-library/3.5’
      (as ‘lib’ is unspecified)
      * installing *source* package 'ENMTools' ...
      ** R
      ** data
      *** moving datasets to lazyload DB
      ** byte-compile and prepare package for lazy loading
      Error : object 'plotp' not found whilst loading namespace 'rms'
      ERROR: lazy loading failed for package 'ENMTools'
      * removing 'C:/Users/Andre/Documents/R/win-library/3.5/ENMTools'
      In R CMD INSTALL
      Error in i.p(...) :
      (converted from warning) installation of package ‘C:/Users/Andre/AppData/Local/Temp/RtmpovYBoN/file1ed4262c1f9f/ENMTools_0.2.tar.gz’ had non-zero exit status


      It looks like there is some issue with the package "rms". I checked online and it is possible that this is an issue with older R versions. Please, check for example this post: https://github.com/vegandevs/vegan/issues/274

      However, my R version and the rms package are updated to the most recent versions. Any ideas? Thank you for your help.

      Best,
      André

      Delete
    2. Dan WarrenFebruary 4, 2019 at 1:11 AM

      Try library(rms) and then type plotp and see what happens.

      Delete
  3. LayseJanuary 7, 2020 at 6:16 AM

    Hello Dan,

    I am getting the same error of installation ENMTools, and i've tried your recommendation but there is still an issue:

    * installing *source* package 'ENMTools' ...
    ** using staged installation
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** byte-compile and prepare package for lazy loading
    Error: (converted from warning) package 'raster' was built under R version 3.6.2
    Execution halted
    ERROR: lazy loading failed for package 'ENMTools'
    * removing 'C:/Users/layse/Documents/R/win-library/3.6/ENMTools'
    Error: Failed to install 'ENMTools' from GitHub:
    (converted from warning) installation of package ‘C:/Users/layse/AppData/Local/Temp/RtmpMBgsf8/file19482b8957a6/ENMTools_0.2.tar.gz’ had non-zero exit status

    its seems that i am having a problem with raster package, but i don't quite understand how to fix it..

    any ideias?

    Thanks in advance for you help

    ReplyDelete
    Replies
    1. Dan WarrenJanuary 7, 2020 at 3:43 PM

      What version of R are you running? It seems like the newest version of raster might not like your R version.

      Delete

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