[BioC] flowClust Installation Help

[Aric Gregson]

Hello,

I am having difficulty with the installation of flowClust on Solaris 
Nevada (SXCE build 121) and R 2.9.2. All are built with similar command 
line arguments in 64-bit. Any help will be greatly appreciated! Thanks 
in advance.

I receive the following error upon loading flowClust:

Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared library 
'/opt/R/lib/R/library/flowClust/libs/flowClust.so':
   ld.so.1: R: fatal: relocation error: file 
/opt/R/lib/R/library/flowClust/libs/flowClust.so: symbol 
gsl_root_fsolver_brent: referenced symbol not found
============
It appears that it is not linking properly? My gsl installation is in 
/opt/local and I appear to have been able to install gsl R package OK:

require(gsl)
Loading required package: gsl
Attaching package: 'gsl'
     The following object(s) are masked from package:stats :
      sd
=============
/opt/local is in my ld.config path:

Configuration file [version 4]: /var/ld/ld.config
   Platform:     32-bit LSB 80386
   Default Library Path (ELF):   /lib:/usr/lib:/opt/local/lib
   Trusted Directories (ELF):    /lib/secure:/usr/lib/secure  (system 
default)
=============
I have tried various combinations of the following in an attempt to get 
flowClust to install properly:

./R CMD INSTALL --configure-args="CC='/opt/sunstudio12.1/bin/cc -m64' 
CPPFLAGS='-I/usr/gnu/include -I/opt/local/include -I/usr/include -I/
usr/sfw/include -R/usr/gnu/include -R/usr/include -R/usr/sfw/include 
-R/opt/local/include' CFLAGS='-xO5 -xc99 -xlibmieee -xlibmil -nofstore' 
LDFLAGS='-L/opt/local/lib -L/usr/gnu/lib -L/usr/sfw/lib/amd64 
-L/usr/lib/amd64 -L/usr/lib -R/usr/sfw/lib/amd64 -R/usr/lib/amd64 
-R/usr/lib -R/usr/gnu/lib -R/opt/local/lib' LIBS='-L/opt/local/lib' 
LD_LIBRARY_PATH=/opt/local/lib:$LD_LIBRARY_PATH" ~/downloads/flowClust
Loading required package: fortunes
* Installing to library '/export/pei/src/R-2.9.2/library'
* Installing *source* package 'flowClust' ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
/opt/sunstudio12.1/bin/cc -m64 -I/export/pei/src/R-2.9.2/include 
-I/usr/gnu/include -I/opt/local/include -I/usr/include 
-I/usr/sfw/include -I/usr/postgres/8.3/include -R/usr/gnu/include 
-R/usr/include -R/usr/sfw/include -R/opt/local/include 
-R/usr/postgres/8.3/include    -KPIC  -xO5 -xc99 -xlibmieee -xlibmil 
-nofstore -c BoxCox.c -o BoxCox.o
/opt/sunstudio12.1/bin/cc -m64 -I/export/pei/src/R-2.9.2/include 
-I/usr/gnu/include -I/opt/local/include -I/usr/include 
-I/usr/sfw/include -I/usr/postgres/8.3/include -R/usr/gnu/include 
-R/usr/include -R/usr/sfw/include -R/opt/local/include 
-R/usr/postgres/8.3/include    -KPIC  -xO5 -xc99 -xlibmieee -xlibmil 
-nofstore -c Nu.c -o Nu.o
/opt/sunstudio12.1/bin/cc -m64 -I/export/pei/src/R-2.9.2/include 
-I/usr/gnu/include -I/opt/local/include -I/usr/include 
-I/usr/sfw/include -I/usr/postgres/8.3/include -R/usr/gnu/include 
-R/usr/include -R/usr/sfw/include -R/opt/local/include 
-R/usr/postgres/8.3/include    -KPIC  -xO5 -xc99 -xlibmieee -xlibmil 
-nofstore -c flowClust.c -o flowClust.o
/opt/sunstudio12.1/bin/cc -m64 -I/export/pei/src/R-2.9.2/include 
-I/usr/gnu/include -I/opt/local/include -I/usr/include 
-I/usr/sfw/include -I/usr/postgres/8.3/include -R/usr/gnu/include 
-R/usr/include -R/usr/sfw/include -R/opt/local/include 
-R/usr/postgres/8.3/include    -KPIC  -xO5 -xc99 -xlibmieee -xlibmil 
-nofstore -c flowClustGaussian.c -o flowClustGaussian.o
/opt/sunstudio12.1/bin/cc -m64 -I/export/pei/src/R-2.9.2/include 
-I/usr/gnu/include -I/opt/local/include -I/usr/include 
-I/usr/sfw/include -I/usr/postgres/8.3/include -R/usr/gnu/include 
-R/usr/include -R/usr/sfw/include -R/opt/local/include 
-R/usr/postgres/8.3/include    -KPIC  -xO5 -xc99 -xlibmieee -xlibmil 
-nofstore -c ranMVNT.c -o ranMVNT.o
/opt/sunstudio12.1/bin/cc -m64 -G -L/usr/gnu/lib -L/usr/sfw/lib/amd64 
-L/usr/lib/amd64 -L/opt/local/lib -L/opt/local/lib/amd64 -L/usr/lib 
-L/usr/postgres/8.3/lib -R/usr/sfw/lib/amd64 -R/usr/lib/amd64 -R/usr/lib 
-R/usr/gnu/lib -R/opt/local/lib -R/opt/local/lib/amd64 
-R/usr/postgres/8.3/lib -o flowClust.so BoxCox.o Nu.o flowClust.o 
flowClustGaussian.o ranMVNT.o
** R
** data
** inst
** preparing package for lazy loading
by using mclust, you accept the license agreement in the LICENSE file
and at http://www.stat.washington.edu/mclust/license.txt

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()'. To cite Bioconductor, see
    'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: rrcov
Loading required package: robustbase
Loading required package: pcaPP
Loading required package: mvtnorm
pcaPP 0.1-1 loaded
Scalable Robust Estimators with High Breakdown Point (version 0.5-02)

Attaching package: 'flowCore'


          The following object(s) are masked from package:stats :

           alias,
           filter

Warning in .findOrCopyClass(class2, classDef2, where, "subclass") :
    Class "Ulist" is defined (with package slot "rrcov") but no metadata 
object found to revise subclass information---not exported?  Making a 
copy in package "flowClust"
Warning in .findOrCopyClass(class2, classDef2, where, "subclass") :
    Class "Uvector" is defined (with package slot "rrcov") but no 
metadata object found to revise subclass information---not exported? 
Making a copy in package "flowClust"
** help
*** installing help indices
   >>> Building/Updating help pages for package 'flowClust'
       Formats: text html latex example
** building package indices ...
* DONE (flowClust)