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problem with installation of metaXCMS on MAC

Hi,

every time I try to install metaXCMS from a local source package R crashes on my Mac. A metaXCMS lock directory is formed, but R crashes afterwards.

Koen

Re: problem with installation of metaXCMS on MAC

Reply #1
What R version are you using ?
Are you getting any error message from R before it crashes ?

Re: problem with installation of metaXCMS on MAC

Reply #2
R 2.15.0

I do not get an error message.

Re: problem with installation of metaXCMS on MAC

Reply #3
Are you installing it through he GUI or the command line ?

There should be something if you install it through the command line:
Code: [Select]
R CMD INSTALL metaXCMS_0.1.19.tar.gz

Re: problem with installation of metaXCMS on MAC

Reply #4
I tried to install it via the GUI: via the "Package Installer". This dis not work and made R to crash. I just tried to install metaXCMS via the console using the command line, but I got the error "Warning: invalid package 'metaXCMS_0.1.19.tar.gz'" and "Error: ERROR: no packages specified". Should I put these packages in a specific directory?

Re: problem with installation of metaXCMS on MAC

Reply #5
Hi Koen,

Please follow the following steps to install metaXCMS

1. Copy and Paste the following 3 lines in R console.
    install.packages(c("cairoDevice","RGtk2","gstat","RANN","xlsx"))
    source("http://bioconductor.org/biocLite.R")
    biocLite(c("Biobase","xcms"), dep=T)

2. Go to 'Packages & Data' and open 'Package Manager'
    if 'cairoDevice' is not loaded please check the status box to be loaded, which will take a few seconds to few minutes to load the package and ask you to install GTK+.
    Please install GTK+

3. Download metaXCMS source package (metaXCMS_0.1.19.tar.gz) at http://metlin.scripps.edu/metaxcms/download.php

4. Go to 'Packages & Data' and open 'Package Installer'
    Select 'Local Source Package'
    For Install Location, select 'At System Level (in R framework)'
    and click 'Install'
    then select the 'metaXCMS_0.1.19.tar.gz' from where your downloaded file is located

5. You may want to run the following line (If not working you may want to restart the R Gui)
    library(metaXCMS)

Please let me know if this doesn't work for you.

Kevin

Re: problem with installation of metaXCMS on MAC

Reply #6
Hi Kevin,
following your suggestions R crashes while loading the cairoDevice in the package manager. R does also not ask to install GTK+.
any idea why this is?
Koen

Re: problem with installation of metaXCMS on MAC

Reply #7
Hi Koen,

I have tried on 3 different Mac Computers here, and everything works fine if you follow the description.
I believe it might be your Mac Issues.  How much memory do you have on your computer? which version do you have? and have you tried to delete R from 'Applications' and reinstall it?

I tested R 64bit on iMac, MacBook Pro, and MacBook (all of them have version 10.6.8), and at least 4GB of RAM.

I am not sure why it keep crashes, but you may want to try it with a fresh installation, and may not run other softwares during installation(?)

I suggest you to try on different Mac if it's available, and if not you want to contact R-Project.

I found a couple of FAQ from their website... Please refer following.

Kevin
______________
4.8 R.app Bugs

On Unix systems a bug report can be generated using the function bug.report(). This automatically includes the version information and sends the bug to the correct address. Alternatively the bug report can be emailed to http://bugs.R-project.org/.

Before you fill a bug report, please try to reproduce it using both R.app and the console version of R (if applicable). If the bug if R.app-specific, please report the bug to http://r.research.att.com/tools/.

CRAN binaries of R versions 2.3.0 to 2.4.1 supplied their own complier (gcc 4.0.3 in /usr/local/gcc4.0), overriding the Apple-supplied compiler. The system compiler was kept in place, but R used the new compiler for compiling packages instead. The main reason for this was that the compiler supplied by Apple contained several fatal bugs that lead to crashes of R due to incorrectly generated code, especially for the Intel Macs. This has been fixed in Xcode 2.4.0 so we switched back to Apple's compilers for R 2.5.0 and later.

12.16 R.app GUI crashes on startup!

If your R.app GUI crashes on startup, there are usually two major causes for this: saved workspace or corrupted history

Saved workspaces can contain commands that implicitly load packages which in turn can trigger bugs in packages or feed R with incorrect starting values (especially if it was saved using another R). Try removing or renaming your workspace – it's called .RData. If you did not change your startup settings, you can e.g. use

    mv ~/.RData ~/workspace.RData
to move it aside and load later manually for inspection using load("~/workspace.RData").

Second most common cause of crashes on startup is a history file that was not created using the R.app GUI. Again, move it aside to see if that's the issue:

    mv ~/.Rhistory ~/history.txt
Although we are trying to recover from invalid history files, they can still crash R.app due to issues in the internal handling of strings in Mac OS X. We are currently working on preventing this issue.

If you did both of the above and R.app still crashes, please select `1' in the menu after the crash (if you get the crash menu in the console) and send us the resulting crash report (see see R.app Bugs above).

Re: problem with installation of metaXCMS on MAC

Reply #8
Hi Kevin,

I installed metaXCMS on another Mac without any problems. So I decided to completely remove R from my Mac and reinstall everything. Upon reinstalling R/xcms and metaXCMS, the same problem occured: R crashed during loading of the cairoDevice. Can it be that this has something to do with the fact that GTK+ is already installed on my Mac? If so, how can I remove this before reinstallation?

best,
Koen

 

Re: problem with installation of metaXCMS on MAC

Reply #9
Hi Koen,

I've been trying to find the right solution for your issues, but not successful.  Please try to update your OS X, and delete everything named gtk+ from your finder (But not sure whether this will help or not.)
I can't really reproduce this problem here, can't help you too much though.  I would recommend you to reinstall OS X from scratch, which is the optimal solution for this problem since you didn't find the same error on other Mac

Let me know if you still need help.
Kevin