I am having the same issue but when I introduced the .Rprofile file in my home directory the problem remains.
I am still getting the same error
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code -11),
please inspect stdout and stderr to learn more.
Any suggestions
George
Hi @George_Tsiamis,
Thanks for following up on the forum!
Could you provide an ls of your home directory? The screenshot of your editor seems to show that file as just ~/Rprofile which isn't right.
I wonder if you have two files on your system right now: ~/Rprofile and ~/.Rprofile (the latter being empty?)
Could you run:
cat ~/.Rprofile
Thanks!
and then:
Sorry @George_Tsiamis,
I should have asked you to run:
ls -al
in your home directory. I always forget dotfiles don't show up with a normal "ls".
Also could you run the following?:
cat ~/.Rprofile
Thanks!
Hi @ebolyen,
I think I am having the same problem as @George_Tsiamis,
I also am on OSX and have R and RStudio already installed.
I ran
ls -al and cat ~/.Rprofile
in my home directory, as seen below:
LSB4139A-4DM:~ msullivan$ ls -al
total 43816
drwxr-xr-x+ 46 msullivan staff 1564 Oct 10 16:56 .
drwxr-xr-x 8 root admin 272 Apr 7 2017 ..
-r-------- 1 msullivan staff 7 Apr 10 2017 .CFUserTextEncoding
-rw-r--r--@ 1 msullivan staff 22532 Oct 10 12:34 .DS_Store
-rw-r--r-- 1 msullivan staff 0 Jul 24 15:01 .Rapp.history
-rw-r--r-- 1 msullivan staff 293 Sep 11 11:30 .Rhistory
-rw-r--r--@ 1 msullivan staff 25 Oct 10 16:56 .Rprofile
drwx------ 42 msullivan staff 1428 Oct 10 16:28 .Trash
-rw------- 1 msullivan staff 67718 Oct 10 16:52 .bash_history
-rw-r--r-- 1 msullivan staff 196 May 15 19:05 .bash_profile
drwx------ 49 msullivan staff 1666 Oct 10 16:56 .bash_sessions
drwxr-xr-x 4 msullivan staff 136 Aug 31 14:23 .conda
drwxr-xr-x 2 msullivan staff 68 Apr 10 2017 .continuum
drwx------ 3 msullivan staff 102 Jun 5 21:18 .cups
drwxr-xr-x 3 msullivan staff 102 Oct 6 13:58 .idlerc
drwxr-xr-x 6 msullivan staff 204 Oct 10 17:02 .matplotlib
-rw-r--r-- 1 msullivan staff 40 Aug 10 11:08 .ncbirc
drwxr-xr-x 6 msullivan staff 204 Aug 9 11:38 .oracle_jre_usage
-rw-r--r-- 1 msullivan staff 57 May 15 18:35 .profile
-rw------- 1 msullivan staff 125 Aug 31 15:57 .python_history
drwxr-xr-x 25 msullivan staff 850 Sep 27 16:50 .rstudio-desktop
drwx------ 3 msullivan staff 102 Aug 3 15:45 .ssh
drwxr-xr-x 6 msullivan staff 204 Apr 25 15:43 .subversion
-rw------- 1 msullivan staff 1797 Sep 1 17:17 .viminfo
drwx------@ 3 msullivan staff 102 Apr 11 2017 Applications
drwx------+ 31 msullivan staff 1054 Oct 5 12:18 Desktop
drwx------+ 23 msullivan staff 782 Oct 10 13:25 Documents
drwx------+ 71 msullivan staff 2414 Oct 10 16:28 Downloads
drwxr-xr-x 23 msullivan staff 782 Apr 10 2017 Geneious 10.1 Data
drwxr-xr-x 19 msullivan staff 646 Aug 9 12:24 Geneious_9.1_Data
drwxr-xr-x 25 msullivan staff 850 Sep 6 14:11 Geneious_Data_Restored
drwx------@ 67 msullivan staff 2278 Sep 6 22:25 Library
drwx------+ 3 msullivan staff 102 Apr 7 2017 Movies
drwx------+ 4 msullivan staff 136 Jun 21 14:25 Music
drwx------+ 3 msullivan staff 102 Apr 7 2017 Pictures
drwxr-xr-x+ 6 msullivan staff 204 Oct 9 12:00 Public
drwxr-xr-x 11 msullivan staff 374 Aug 9 22:43 Round2_Claire_Again_Blast
-rw-r--r-- 1 msullivan staff 22305708 Jul 14 17:29 its_12_11_otus.tgz
drwxr-xr-x 14 msullivan staff 476 Oct 10 13:17 miniconda3
drwxr-xr-x@ 8 msullivan staff 272 Dec 7 2016 ncbi-blast-2.6.0+
drwxr-xr-x 6 msullivan staff 204 Oct 3 15:51 plots_at_level
drwxr-xr-x 6 msullivan staff 204 Oct 3 15:49 plots_at_level12
drwxr-xr-x 6 msullivan staff 204 Oct 3 16:00 plots_at_level_2
drwxr-xr-x 6 msullivan staff 204 Oct 3 16:05 plots_at_level_3
drwxr-xr-x 6 msullivan staff 204 Oct 3 16:07 plots_at_level_4
-rw-r--r-- 1 msullivan staff 0 Sep 1 15:28 silva_fungi_only
LSB4139A-4DM:~ msullivan$ cat ~/.Rprofile
Let me know if I need to open a new support forum or what would be best to do for help.
Thank you very much,
Madsen
Hey @MSullivan,
Thanks for the detailed output! Based on your cat command, it looks like your .Rprofile is empty.
You should add this line to it (while using QIIME 2):
.libPaths(.libPaths()[2])
This will make a regular R Studio act weird, so you'll want to remove it if you plan on using R externally to QIIME 2. This isn't a great solution, it's just something that happens to work ok for the moment.
If adding that line doesn't fix your issue, could you follow up by creating a new topic with the --verbose output (or attached debug file) so we can take a closer look? Thanks!
It also occurred to me I haven't looked at what conda puts in .libPaths recently. If anyone is still having troubles, could you provide the output from:
R -e ".libPaths()"
For example, I see:
> .libPaths()
[1] "/home/evan/.conda/envs/qiime2-2017.9/lib/R/library"
>
>
(Which is why I can't reproduce the problem myself)
I'm having the same problem even after adding ./Rprofile. Here is my output from cat ~/.Rprofile and R -e "./libPaths()"
.libPaths()
[1] "/Users/Jed/Library/R/3.3/library"
[2] "/Users/Jed/miniconda3/envs/qiime2-2017.10/lib/R/library"(qiime2-2017.10) MacBook-Pro-3:~ Jed$ cat ~/.Rprofile
.libPaths(.libPaths()[2])(qiime2-2017.10) MacBook-Pro-3:~ Jed$
Thanks for the output @bioengineer!
It looks like there's no newline in your .Rprofile file. Could you try running this:
echo ".libPaths(.libPaths()[2])" > $HOME/.Rprofile
(it will add the newline and replace what is in there)
Alternatively, you could just add a couple lines to the end of the file in your favorite text editor.
I am pretty sure that will fix the issue, but please let me know if it doesn't!
That fixed it. Thanks!
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.