Hi,
I’ve installed all packages and their dependencies on R (version 4.2.1) needed for MelonnPan, aside from GenABEL package (version 1.8-0 as suggested in the installation tutorial), and when I try to install it I get the error:
fexact.c:1025:13: error: ‘PROBLEM’ undeclared (first use in this function)
1025 | PROBLEM “Bug in FEXACT: gave negative key” RECOVER(NULL_ENTRY);
| ^~~~~~~
fexact.c:1025:13: note: each undeclared identifier is reported only once for each function it appears in
fexact.c:1025:20: error: expected ‘;’ before string constant
1025 | PROBLEM “Bug in FEXACT: gave negative key” RECOVER(NULL_ENTRY);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| ;
fexact.c: In function ‘prterr’:
fexact.c:1806:5: error: ‘PROBLEM’ undeclared (first use in this function)
1806 | PROBLEM “FEXACT error %d.\n%s”, icode, mes RECOVER(NULL_ENTRY);
| ^~~~~~~
fexact.c:1806:12: error: expected ‘;’ before string constant
1806 | PROBLEM “FEXACT error %d.\n%s”, icode, mes RECOVER(NULL_ENTRY);
| ^~~~~~~~~~~~~~~~~~~~~~~
| ;
make: *** [/usr/lib/R/etc/Makeconf:168: fexact.o] Error 1
ERROR: compilation failed for package ‘GenABEL’
- removing ‘/home/studenti/R/x86_64-pc-linux-gnu-library/4.2/GenABEL’
Warning message:
In i.p(…) :
installation of package ‘/tmp/RtmpNT5RVJ/file3997a00da01/GenABEL_1.8-0.tar.gz’ had non-zero exit status
I also tried to install melonnpan from github to bypass the issue (because I thought the melonnpan package has a prepare script allowing to install the dependencies it needed)
devtools::install_github(“biobakery/melonnpan”)
but I got another error:
Error in utils::download.file(url, path, method = method, quiet = quiet, :
cannot open URL ‘https://api.github.com/repos/biobakery/melonnpan/tarball/HEAD’
What can I do to complete the installation? Is there something I should have checked for the previous steps? 
Hi @AndreaGatti - GenABEL is no longer a dependency for installing MelonnPan. Sorry that it was not updated in the tutorial although it’s updated in the GitHub README. Can you try to install the most updated version of MelonnPan from GitHub? If you have been able to install the other dependencies as listed here, you should be good to go.
Thanks a bunch,
Himel
Hi Himel,
thank you for the quick response!
I installed melonnpan using the git clone downloaded from the tutorial, and run in the command line:
Rscript melonnpan/train_metabolites.R -i “metabolites\ relab.txt” -g “training.data.tsv” -o melonnpan-train/
And the code starts loading the packages until:
Loading required package: fExtremes
Loading required package: optparse
Loading required package: tibble
Error in library(GenABEL) : there is no package called ‘GenABEL’
Execution halted
So it still looks for the GenABEL package, I don’t know why.
I also re-cloned the melonnpan directory but still gives me the same error 
Hi!
I have exactly the same problem…
Have you made any progress on this matter?
Thanks!
I just pushed an update to GitHub which should take care of this error. Please re-install the most updated version of MelonnPan from GitHub and let me know if that resolves the issue on your end.
Many thanks,
Himel
Now it works for me! Thanks @himel.mallick ! =)
Thank you so much for your work and I’m sorry I’m still bothering you, but, opening R and installing directly from github, it seems I can’t find the url:
devtools::install_github(“biobakery/melonnpan”)
Downloading GitHub repo biobakery/melonnpan@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet, :
cannot open URL ‘https://api.github.com/repos/biobakery/melonnpan/tarball/HEAD’
Then trying with
git clone GitHub - biobakery/melonnpan: Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
I downloaded the latest versione and run
R CMD INSTALL melonnpan
And it says it is installed correctly, but when I run the train_metabolites.R script, it still looks for the GenABEL package.
My question is why can’t I access the github url? I have the latest version of devtools package
EDIT:
I was able (tough I don’t know why) to overcome the issue, the script runs and set the default parameters for alpha, lambda, cutoff, etc., until:
…
$options$help
[1] FALSE
$args
character(0)
Error in FUN(newX[, i], …) : trait is binary
Calls: → apply → FUN
Execution halted
Hi @AndreaGatti - it looks like you have binary variables in your microbiome data (X) which is throwing the error. If you drop columns that take less than 3 values, this error should disappear. Can you give it a try and let me know? Thanks!
1 Like
That worked!
I’m so grateful for all your help, thank you again!