On 11-11-15 07:26 AM, Simon Urbanek wrote:
On Nov 15, 2011, at 10:18 AM, Hervé Pagès wrote:
On 11-11-15 06:26 AM, Simon Urbanek wrote:
On Nov 15, 2011, at 1:29 AM, Hervé Pagès wrote:
On 11-11-12 11:30 PM, Prof Brian Ripley wrote:
On Sun, 13 Nov 2011, Riccardo Romoli wrote:
Hi, I have already installed R 2.14.0 and I have some problem to load
several packages, in particular xcms package. I installed it directly
from the GUI and when I try to load it the R I have:
library(xcms)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object
'/Users/riccardoromoli/Library/R/2.14/library/xcms/libs/x86_64/xcms.so':
dlopen(/Users/riccardoromoli/Library/R/2.14/library/xcms/libs/x86_64/xcms.so,
6): Library not loaded: /usr/local/lib/libnetcdf.7.dylib
Referenced from:
/Users/riccardoromoli/Library/R/2.14/library/xcms/libs/x86_64/xcms.so
Reason: image not found
Inoltre: Warning message:
In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc
= lib.loc) :
there is no package called ‘digest’
Errore: package/namespace load failed for ‘xcms’
I think the error is the absence of ibnetcdf.7.dylib. Do you have any
idea how can I correct this error??
1) Ask BioC to build the package correctly, or
2) Build from the sources yourself, preferably using a static netcdf
library.
People should not be distributing Mac binary packages with hardcoded
paths to dependencies not in the R framework: CRAN does not.
Not true. rggobi, Cairo and other Mac binaries on CRAN have hardcoded paths to
a bunch of stuff that is not in the R framework.
The above statement is false.
All binaries that involve just libraries (like Cairo) are linked statically and
have no dependencies (see otool -L).
There are very few exceptions where it doesn't involve a library but an entire
system: gtk, ggobi and tcltk. For those there is no other option since just
linking them statically is not sufficient as they rely on other external files.
For those we provide the binaries for download along with the package.
I'm aware of that and thanks for providing those binaries.
Also thanks for confirming that Ripley's original statement was wrong.
Just to clarify on my end: in my e-mail "The above statement" was referring to
your statement, not Brian's. Whatever you make out of the rest is up to you ;).
Just to clarify here too: the fact that you mentioned that there are
exceptions to the "no hardcoded paths to dependencies not in the R
framework" was a useful and honest clarification. So again, thanks!
H.
The problem in BioC is that not only it uses unnecessary dependent libraries
(it didn't use to when you were running it ;)), it doesn't even provide the
needed dependencies for download with the package. That makes the repository
useless for the user since the packages simply don't work.
We used to use your static netcdf from here
http://r.research.att.com/libs/
and that's what we should use. For whatever reason another netcdf (non-static)
ended up being installed on our build machine. We'll fix
that.
Great. Dan mentioned something about more recent netcdf and special handling, but didn't
get back to me yet. I can build more recent netcdf if needed, but i need to know what the
"specially built" exactly means and which package he was referring to so I can
test it.
Thanks,
Simon
Cheers,
H.
Cheers,
Simon
In
particular, /usr/local/lib need administrative privileges to populate.
Note that installing the external stuff needed by rggobi, Cairo etc
also requires administrative privileges.
Cheers,
H.
Best
Riccardo
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: [email protected]
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
R-SIG-Mac mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: [email protected]
Phone: (206) 667-5791
Fax: (206) 667-1319
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: [email protected]
Phone: (206) 667-5791
Fax: (206) 667-1319
_______________________________________________
R-SIG-Mac mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
