Dada2 exit code -11 and .Rprofile

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!

From the issue tracker for context:

and then:

2 Likes

Dear Evan,

Please find attached a screenshot of the home directory after ls

Kind regards
George

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–[email protected] 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–[email protected] 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
[email protected] 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
[email protected] 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
[email protected] 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!

1 Like

That fixed it. Thanks!

2 Likes

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