[rkward-devel] Trouble loading packages on the Mac

[Frederik Aust]

Hi,

a colleague of mine and I are experiencing problems with the R package 
management in a freshly installed version of RKWard on our Macs.

----------------------------

 > rk.sessionInfo()

RKWard version: 0.6.0
KDE version (runtime): 4.8.3 (4.8.3)
KDE version (compile time): 4.8.3 (4.8.3)
Local KDE directory: /Users/*username*/Library/Preferences/KDE/
RKWard storage directory: /Users/*username*/.rkward/

Debug message file(s) in use (these may contain relevant diagnostic 
output in case of trouble):
/var/folders/zj/8nn45b2d2l9g81zj1hpr08rm0000gq/T/rkward.frontend.M30611
/var/folders/zj/8nn45b2d2l9g81zj1hpr08rm0000gq/T/rkward.rbackend.L30618

R version (compile time): 2.15.1  (2012-06-22 r59600)
R runtime session info:
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin11.4.2/x86_64 (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods base

other attached packages:
[1] rkward_0.6.0

loaded via a namespace (and not attached):
[1] tools_2.15.1

----------------------------

When trying to install the lme4 package into /opt/rkward he is being 
prompted to become root or choose a different directory. When trying to 
become root (pressing the button) the following error is returned:

----------------------------

kdesu(30680)/KSharedDataCache ensureFileAllocated: This system misses 
support for posix_fallocate() -- ensure this partition has room for at 
least 10547296 bytes.

kdesu(30680)/KSharedDataCache: Unable to find an appropriate lock to 
guard the shared cache. This *should* be essentially impossible. :(

kdesu(30680)/KSharedDataCache: Unable to perform initial setup, this 
system probably does not really support process-shared pthreads or 
semaphores, even though it claims otherwise.

kdesu(30680)/KSharedDataCache: Unable to unmap shared memory segment 
0x113767000

kdesu(30680)/kdesu (kdelibs) KDESu::findDaemon: [ 
/opt/rkward/var/macports/build/_opt_rkward_var_macports_sources_rsync.macports.org_release_tarballs_ports_kde_kdelibs4/kdelibs4/work/kdelibs-4.8.3/kdesu/client.cpp 
: 408 ] daemon not found.

kdesu(30680) startApp: Daemon not safe (not sgid), not using it.



FAILURE (KCmdLineArgs):

Application requests for isSet("attach") but the "attach" option

has never been specified via addCmdLineOptions( ... )



Installation process died with exit code 255

----------------------------

Next, we tried to switch to the suggested user specific directory 
'/Users/*username*/.rkward/library'. The installation of the package 
reported no errors, but loading the package fails.

----------------------------

 > library("lme4")

Loading required package: Matrix
Loading required package: lattice
Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared object 
'/Users/*username*/.rkward/library/lme4/libs/x86_64/lme4.so':
dlopen(/Users/*username*/.rkward/library/lme4/libs/x86_64/lme4.so, 6): 
Symbol not found: _libintl_dgettext
   Referenced from: 
/Users/*username*/.rkward/library/lme4/libs/x86_64/lme4.so
   Expected in: /opt/rkward/lib/R/lib/x86_64/libR.dylib

Error: package/namespace load failed for 'lme4'
Error: package/namespace load failed for 'lme4'

----------------------------

I have been able to replicate this problem on my machine as well. I got 
a slightly different error, though:

----------------------------

 > library("lme4")

Loading required package: Matrix
Loading required package: lattice
Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared object 
'/Users/*username*/R/x86_64-apple-darwin11.4.2-library/2.15/lme4/libs/x86_64/lme4.so':
 
dlopen(/Users/*username*/R/x86_64-apple-darwin11.4.2-library/2.15/lme4/libs/x86_64/lme4.so, 
6): Library not loaded: 
/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib
   Referenced from: 
/Users/*username*/R/x86_64-apple-darwin11.4.2-library/2.15/lme4/libs/x86_64/lme4.so
   Reason: image not found
Error: package/namespace load failed for 'lme4'
Error: package/namespace load failed for 'lme4'

----------------------------

I installed using the R console, while my colleague used the GUI.

Any ideas what's going on here? So far I have not had any trouble 
installing packages on my Macs. I'm suspecting it might have something 
to do with the OS X version. We are having trouble on Macs running 
Mountain Lion (10.8.2) while I'm running Lion (10.7.5) on my other 
computers that didn't give me any trouble.

Regards,
Frederik


-- 
Frederik Aust, Dipl.-Psych.

Leibniz Research Center for Working Environment and Human Factors
Research Group: Perceptual cybernetics
Ardeystr. 67
44139 Dortmund
Germany

E-mail: AustF at ifado.de
Tel.:   +49 / 231 1084 382
Web:    http://www.ifado.de/