Graces to all for to have given hand to me in the resolution of the
problem!!!
Now xcms works fine.
Best
Riccardo
On 16/nov/11, at 21:53, Simon Urbanek wrote:
On Nov 16, 2011, at 3:07 PM, Dan Tenenbaum wrote:
Simo n,
On Tue, Nov 15, 2011 at 7:26 PM, Simon Urbanek
<[email protected]> wrote:
Dan,
static hdf5-1.8.8 and netcdf-4.1.3 are now in http://r.research.att.com/libs/
(and also on the CRAN machine).
Thanks! So far the package does not compile against that but I've
asked the package maintainer to take a look. If you are curious, the
package is ncdfFlow
(http://bioconductor.org/packages/release/bioc/html/ncdfFlow.html)
and
the error I get is:
checking for nc_def_var_deflate in -lnetcdf... no
configure: error: netCDF library not found!
ERROR: configuration failed for package 'ncdfFlow'
Seems like this might be a symbol from zlib.
No, it's using the wrong flags to link NetCDF - it completely
ignores dependencies. It has hard-coded LIBS which is simply wrong.
I would suggest the author uses pkg-config to fetch the relevant
LIBS, e.g. on the CRAN machine it is
hagal:tmp$ pkg-config --libs netcdf
-L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl
so all the above is simply missing.
Cheers,
Simon
Dan
Cheers,
Simon
On Nov 15, 2011, at 9:40 PM, Simon Urbanek wrote:
On Nov 15, 2011, at 8:36 PM, Dan Tenenbaum wrote:
Hi all,
2011/11/15 Hervé Pagès <[email protected]>:
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.
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.
This is fixed now. At the end of our next build cycle (about 1PM
tomorrow, Wednesday, Seattle time), xcms 1.30.1 will be available
which is once again built against the static netcdf library
(version
4.0.1) that Simon provides on his site. Other BioC packages that
use
netcdf (flowWorkspace and mzR) will also be fixed.
Riccardo, this means that all you have to do is wait until the new
package is available and then:
source("http://bioconductor.org/biocLite.R";)
biocLite("xcms")
library(xcms)
You will not need to compile anything. I just tested this on a Mac
without netcdf or any compilers and it worked fine.
Simon: I will be asking for your help but I want to make sure I
have
all my ducks in a row first. I want first to be able to build
things
exactly right, then I can know that I am giving you the right
thing.
That is taking a bit more time than I'd like.
Briefly, the package in question needs netcdf (must be version
4.1.3)
to be linked against hdf5 which in turn needs to link to zlib.
I will contact you when I am able to create a static version of
this
that allows this package to compile.
Note that in libs there is static hdf5 and netcdf 4.1.1 (which
uses hdf5), so the only issue is that the package needs 4.1.3 and
not 4.1.1 -- I wonder why since it's just a patch release ...
Cheers,
Simon
Thanks for your help.
Dan
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
_______________________________________________
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[email protected]
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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
_______________________________________________
R-SIG-Mac mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/r-sig-mac
