[Bioc-sig-seq] Trouble loading development version of ShortRead on OS X

[Michael Muratet]

Greetings

I have been working on incorporating the new Illumina SCS v2.4 file  
structure into the ShortRead package. I downloaded and built the R- 
devel version 2.10.0 (2009-09-09 r49643) and then installed  
BioConductor from it. I have a version of ShortRead that I wanted to  
test, so I built in the tree I have locally (output at the end of this  
message). I started my dev. version of R and tried to load ShortRead  
and got:

Loading required package: Biostrings
Loading required package: BSgenome
Loading required package: lattice
Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared library '/Users/mmuratet/Downloads/R-devel/ 
library/ShortRead/libs/ShortRead.so':
   dlopen(/Users/mmuratet/Downloads/R-devel/library/ShortRead/libs/ 
ShortRead.so, 6): Symbol not found: _cache_XStringSet
   Referenced from: /Users/mmuratet/Downloads/R-devel/library/ 
ShortRead/libs/ShortRead.so
   Expected in: dynamic lookup

Error: package/namespace load failed for 'ShortRead'

I suspect an issue with the Biostrings lib, and _cache_XStringSet is a  
symbol in Biostrings.so. Shouldn't this be loaded already?

Can anyone suggest a place where I may have gone wrong?

Session info follows.

Thanks

Mike

SessionInfo():

 > sessionInfo()
R version 2.10.0 Under development (unstable) (2009-09-09 r49643)
i386-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] lattice_0.17-25    BSgenome_1.13.11   Biostrings_2.13.37  
IRanges_1.3.71

loaded via a namespace (and not attached):
[1] Biobase_2.5.6 grid_2.10.0   hwriter_1.1

Output from ShortRead build:

Macintosh-8:~ mmuratet$ Downloads/R-devel/bin/R CMD INSTALL ShortRead
* installing to library ‘/Users/mmuratet/Downloads/R-devel/library’
* installing *source* package ‘ShortRead’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gzeof in -lz... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/Users/mmuratet/Downloads/R-devel/include  -I/sw/ 
include -I/usr/local/include -I"/Users/mmuratet/Downloads/R-devel/ 
library/IRanges/include" -I"/Users/mmuratet/Downloads/R-devel/library/ 
Biostrings/include"   -fPIC  -g -O2 -c alphabet.c -o alphabet.o
gcc -std=gnu99 -I/Users/mmuratet/Downloads/R-devel/include  -I/sw/ 
include -I/usr/local/include -I"/Users/mmuratet/Downloads/R-devel/ 
library/IRanges/include" -I"/Users/mmuratet/Downloads/R-devel/library/ 
Biostrings/include"   -fPIC  -g -O2 -c io.c -o io.o
gcc -std=gnu99 -I/Users/mmuratet/Downloads/R-devel/include  -I/sw/ 
include -I/usr/local/include -I"/Users/mmuratet/Downloads/R-devel/ 
library/IRanges/include" -I"/Users/mmuratet/Downloads/R-devel/library/ 
Biostrings/include"   -fPIC  -g -O2 -c io_bowtie.c -o io_bowtie.o
gcc -std=gnu99 -I/Users/mmuratet/Downloads/R-devel/include  -I/sw/ 
include -I/usr/local/include -I"/Users/mmuratet/Downloads/R-devel/ 
library/IRanges/include" -I"/Users/mmuratet/Downloads/R-devel/library/ 
Biostrings/include"   -fPIC  -g -O2 -c io_soap.c -o io_soap.o
gcc -std=gnu99 -I/Users/mmuratet/Downloads/R-devel/include  -I/sw/ 
include -I/usr/local/include -I"/Users/mmuratet/Downloads/R-devel/ 
library/IRanges/include" -I"/Users/mmuratet/Downloads/R-devel/library/ 
Biostrings/include"   -fPIC  -g -O2 -c pileup.c -o pileup.o
g++ -I/Users/mmuratet/Downloads/R-devel/include  -I/sw/include -I/usr/ 
local/include -I"/Users/mmuratet/Downloads/R-devel/library/IRanges/ 
include" -I"/Users/mmuratet/Downloads/R-devel/library/Biostrings/ 
include"   -fPIC  -g -O2 -c readBfaToc.cc -o readBfaToc.o
g++ -I/Users/mmuratet/Downloads/R-devel/include  -I/sw/include -I/usr/ 
local/include -I"/Users/mmuratet/Downloads/R-devel/library/IRanges/ 
include" -I"/Users/mmuratet/Downloads/R-devel/library/Biostrings/ 
include"   -fPIC  -g -O2 -c read_maq_map.cc -o read_maq_map.o
gcc -std=gnu99 -I/Users/mmuratet/Downloads/R-devel/include  -I/sw/ 
include -I/usr/local/include -I"/Users/mmuratet/Downloads/R-devel/ 
library/IRanges/include" -I"/Users/mmuratet/Downloads/R-devel/library/ 
Biostrings/include"   -fPIC  -g -O2 -c util.c -o util.o
gcc -std=gnu99 -I/Users/mmuratet/Downloads/R-devel/include  -I/sw/ 
include -I/usr/local/include -I"/Users/mmuratet/Downloads/R-devel/ 
library/IRanges/include" -I"/Users/mmuratet/Downloads/R-devel/library/ 
Biostrings/include"   -fPIC  -g -O2 -c xsnap.c -o xsnap.o
g++ -dynamiclib -Wl,-headerpad_max_install_names -undefined  
dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -L/ 
usr/local/lib -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o  
R_init_ShortRead.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o  
readBfaToc.o read_maq_map.o util.o xsnap.o -lz -L/Users/mmuratet/ 
Downloads/R-devel/lib -lR -dylib_file libRblas.dylib:/Users/mmuratet/ 
Downloads/R-devel/lib/libRblas.dylib -lintl -liconv -lc -Wl,-framework  
-Wl,CoreFoundation
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'


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

	 Map,
	 cbind,
	 mapply,
	 order,
	 pmax,
	 pmax.int,
	 pmin,
	 pmin.int,
	 rbind,
	 rep.int,
	 table

Warning in .reportSuperclassConflicts(Class, classDef at contains, where) :
   unable to find a consistent ordering of superclasses for class  
"ArrayIntensity": order chosen is inconsistent with the superclasses  
of "array"
** help
*** installing help indices
** building package indices ...
* DONE (ShortRead)