No Package Called "misc3d"

[Rick]

Hi everyone!

I have used SAHM before and never had problems on installation. However, when I installed SAHM in a new PC, I got this error (see attached). I followed everything from the guide and checked the locations of R and maxent. What is this error on a missing package?

Thank you.

Rick

[Catherine Jarnevich]

Hi Rick,

I've encountered this error on a new PC. There hasn't been a fix rolled into the package yet, but it's not too hard to solve. 

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[Jarnevich, Catherine]

Sorry for the early sending.  How we've solved the issue:

1. Open the R instance installed with Vistrails_SAHM. You can find it where you installed SAHM in:

"...\VisTrails_SAHM\Central_R\R-3.2.0\bin\x64\Rgui.exe"

2.  Run the following lines of code in the Rgui:

libs<-list("adehabitatHR","ks","raster","rgdal","sp","spatstat")

      lib.mssg <- unlist(suppressMessages(suppressWarnings(lapply(libs,require,quietly = T, warn.conflicts=F,character.only=T))))

      if(any(!lib.mssg)){

            install.packages(unlist(libs[!lib.mssg]), repos = "http://cran.r-project.org")

            lib.mssg <- unlist(suppressMessages(suppressWarnings(lapply(libs,require,quietly = T, warn.conflicts=F,character.only=T))))

            }

Please let me know if this doesn't work for you or you have any further questions.

On Tue, May 22, 2018 at 8:25 AM, Catherine Jarnevich <cjarn...@gmail.com> wrote:

Hi Rick,

I've encountered this error on a new PC. There hasn't been a fix rolled into the package yet, but it's not too hard to solve. 

On Tue, May 22, 2018, 8:19 AM Rick <toprati...@gmail.com> wrote:

Hi everyone!

I have used SAHM before and never had problems on installation. However, when I installed SAHM in a new PC, I got this error (see attached). I followed everything from the guide and checked the locations of R and maxent. What is this error on a missing package?

Thank you.

Rick

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Catherine Jarnevich
Research Ecologist
U.S. Geological Survey
Fort Collins Science Center
2150 Center Ave Bldg C
Fort Collins, CO 80526
970-226-9439

[Rick]

Hello Catherine,

Thank you for the prompt response.

I run the code following the steps you mentioned.  It did install these packages:

package ‘filehash’ successfully unpacked and MD5 sums checked
package ‘CircStats’ successfully unpacked and MD5 sums checked
package ‘adehabitatMA’ successfully unpacked and MD5 sums checked
package ‘adehabitatLT’ successfully unpacked and MD5 sums checked
package ‘FNN’ successfully unpacked and MD5 sums checked
package ‘kernlab’ successfully unpacked and MD5 sums checked
package ‘mclust’ successfully unpacked and MD5 sums checked
package ‘multicool’ successfully unpacked and MD5 sums checked
package ‘mvtnorm’ successfully unpacked and MD5 sums checked
package ‘adehabitatHR’ successfully unpacked and MD5 sums checked
package ‘ks’ successfully unpacked and MD5 sums checked

However, the very end it said this: The downloaded binary packages are in
        C:\Users\.....\downloaded_packages
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
  there is no package called ‘misc3d’

I did try to run SAHM in case it would work.  Unfortunately, I got the same error as the last one I posted about the missing package ‘misc3d’.

Thank you,
Rick

[Rick]

Hello again Catherine,

I fixed the last issue and I just want to let you know. What I did, I downloaded ‘misc3d’ as a zip file directly from CRAN, then loaded it into the Rgui. 

Now, I have a new problem on correlation.  Please see attached screenshot.

Thanks for the help.

Rick

[Rick]

To those following the thread, this problem has been fixed.  Thanks to Catherine for the prompt help!

The first problem regarding a missing package "misc3d", you can follow Catherine's suggestions above.  If something is still missing, download the zip file directly from CRAN, then load it by running the Rgui that you can find here "...\VisTrails_SAHM\Central_R\R-3.2.0\bin\x64\Rgui.exe"

The second problem I posted was easy to fix.  In fact, had I been careful in checking the list of predictors (the csv file that contains the predictors), the problem would have been avoided.  I mistakenly categorized few predictors as categorical instead of continuous (the bad result of copying and pasting). I changed the category and everything worked perfect!

Best,
Rick