Dear Bioconductor community,
I'm a biologist and a quite new, R user. Thus I apologize in advance for improper lexicon and personal naivety.
I'm encountering difficulties in loading the BiGGR pckg.
If I've understood correctly I need:
- libSBML
- rsbml
- BiGGR
libSBML is downloaded and installed successfully, following instructions found here:
http://sbml.org/Software/libSBML/Downloading_libSBML
for R language, using shell command.
rsmbl is then downloaded as follow:
BiocInstaller::biocLite("rsbml")
with the following result:
BioC_mirror: http://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.3), R 3.2.1 (2015-06-18).
Installing package(s) ‘rsbml’
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0100 1102k 100 1102k 0 0 2971k 0 --:--:-- --:--:-- --:--:-- 3139k
The downloaded binary packages are in
/var/folders/21/_9mqw7tx7jxc0yw8b8wnxh680000gn/T//RtmpEZvXYc/downloaded_packages
when I load rsbml via:
library(rsbml)
the following error arises:
Error : .onLoad failed in loadNamespace() for 'rsbml', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rsbml/libs/rsbml.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rsbml/libs/rsbml.so, 6): Library not loaded: /usr/local/lib/libsbml.5.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rsbml/libs/rsbml.so
Reason: Incompatible library version: rsbml.so requires version 16.0.0 or later, but libsbml.5.dylib provides version 5.0.0
Inoltre: Warning message:
package ‘rsbml’ was built under R version 3.2.2
Errore: package or namespace load failed for ‘rsbml’
traceback()
2: stop(gettextf("package or namespace load failed for %s", sQuote(package)),
call. = FALSE, domain = NA)
1: library(rsbml)
and I cannot get through this.
sessioninfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
Running under: OS X 10.8.5 (Mountain Lion)
locale:
[1] it_IT.UTF-8/it_IT.UTF-8/it_IT.UTF-8/C/it_IT.UTF-8/it_IT.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] libSBML_5.13.0 BiocGenerics_0.16.1
loaded via a namespace (and not attached):
[1] BiocInstaller_1.20.3 tools_3.2.1 stats4_3.2.1 graph_1.48.0
Any kind of help would be very appreciated.
Thank you in advance.
Enrico
Which version of libsbml? Looks like it's older than the one on the Bioc build machine.
Yes, you're right. However it is the latest I've found so far.
So I guess you're using libsbml 5.13? Dan could comment on what the Bioc build machine is using. I also noticed that you have a "libSBML" package attached. Perhaps that is causing some sort of conflict.
The build macs use version 5.10.x
Yes,it is correct, I've downloaded and installed libSBML 5.13.0. If I've understood correctly you're suggesting to downgrade to e.g. libSBML 5.10.2, and retry? Now I've also tried to load "rsbml" package without "libSBML" package attached and I get the same error reported in the original question. I think the core of the problem is "Reason: Incompatible library version: rsbml.so requires version 16.0.0 or later, but libsbml.5.dylib provides version 5.0.0" , but it is not clear to me from where can I obtain v16
Sorry, I have no idea why it would require v16, which seems too far beyond v5 to make sense.
Yeah, something sounds wrong. According to http://sbml.org/Software/libSBML, the latest stable version is 5.13.0. Please thoroughly remove libsbml and then install version 5.10 from here.