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Problems trying to use the igraph package
Posted: Fri Dec 07, 2018 9:39 pm
by Fhas
Hi!
I am trying to use the igraph package, my functions run just fine under R, but when I add igraph to Jamovi, after many lines of successful build commands, is see this error:
Code: Select all
ld: warning: directory not found for option '-L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.5'
ld: warning: directory not found for option '-L/opt/local/lib/gcc48'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [igraph.so] Error 1
ERROR: compilation failed for package ‘igraph’
* removing '.../casnet-jmvMAC/build/R/igraph’
Any ideas on how to resolve this?
Re: Problems trying to use the igraph package
Posted: Fri Dec 07, 2018 10:55 pm
by jonathon
remind me where your repo is. i'll take a look.
Re: Problems trying to use the igraph package
Posted: Fri Dec 07, 2018 11:44 pm
by Fhas
Re: Problems trying to use the igraph package
Posted: Sat Dec 08, 2018 2:13 am
by jonathon
in the mean time, you can just unzip this into your casnet-jmvMAC/build/R folder
are you able to build igraph from source in an R session? i.e.
install.packages('igraph', type='source')
cheers
jonathon
Re: Problems trying to use the igraph package
Posted: Sat Dec 08, 2018 2:33 am
by Fhas
Thanks!
It appears to install from source, with these warnings:
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ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation are out of sync.
Falling back to library file for linking. installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/igraph/libs
Re: Problems trying to use the igraph package
Posted: Sat Dec 08, 2018 2:48 am
by jonathon
oh yup. at the moment we're maintain compatibility with macOS mavericks ... (but probably not for too much longer). so you'll need a version of gfortran compatible with mavericks. i'm using 4.8.2
cheers
jonathon
Re: Problems trying to use the igraph package
Posted: Sun Dec 09, 2018 8:06 pm
by Fhas
Ok that worked!
- Screenshot 2018-12-09 at 17.38.17.png (219.05 KiB) Viewed 11045 times
Is this versioning limit perhaps also related to the error I get when I try to install package proxy:
Code: Select all
Warning message:
package ‘proxy’ is not available (for R version 3.3.0)
Re: Problems trying to use the igraph package
Posted: Sun Dec 09, 2018 9:47 pm
by jonathon
so the R we ship with the macOS version of jamovi is 3.3, where as proxy requires R >= 3.4
in these situations, it's easiest to modify proxy, remove the >= 3.4, install it locally using a matching version of R (3.3.0 for mavericks), then copy the built package to build/R
i appreciate this is a bit of a pain. we will update the R version with ship with macOS at some point, but you wouldn't believe how painful it is to modify R (on macOS) so it can be bundled with an application!
(won't be an issue on windows, we ship 3.4 for that, and 3.5 for linux.)
jonathon
Re: Problems trying to use the igraph package
Posted: Sun Dec 09, 2018 10:04 pm
by Fhas
Ok thanks that's very useful info!
I found an alternative for proxy so it is not urgent, though at some point I'll want to use it again.
Then the easiest solution will be to install R as if it were the good old Mavericks days
, with gfortran 4.8.2
Could be useful to have an 'R setup recommendation' for developers , and if such a thing already exists & I missed it, I will go hide in shame and stop asking for help (for a while
)
Re: Problems trying to use the igraph package
Posted: Fri Dec 14, 2018 9:21 pm
by Fhas
Hi!
That was a huge update, excellent.
However, is there anything I can do to prevent this from happening each time?
- Screenshot 2018-12-14 at 22.12.14.png (146.23 KiB) Viewed 10986 times