[Bioc-sig-seq] Trouble loading development version of ShortRead on OS X
Martin Morgan
mtmorgan at fhcrc.org
Fri Oct 2 03:08:58 CEST 2009
Hi Mike --
Michael Muratet wrote:
> 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?
Probably the problem is that your version of ShortRead and of the other
Bioconductor packages are not in sync. Probably what you want to do is
use the 'svn' version control system, and 'check out' the relevant
packages from the bioconductor code repository, and use the checked out
copies for installation instead of biocLite(). Then copy your changed
files into the repository and go from there. Very roughly
cd some/directory
svn co -N https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks
cd Rpacks
svn up IRanges Biostrings BSgenome ShortRead
R CMD INSTALL --clean IRanges Biostrings BSgenome
cp my/modified/ShortRead/R/AllClasses.R ShortRead/R/AllClasses
R CMD INSTALL --clean ShortRead
Use
svn add ShortRead/R/new-file.R
to add a file to svn's manifest of files that it is tracking.
svn stat ShortRead
will show you which files are new / modified and
svn diff ShortRead
will show you the changes. Finally,
svn diff ShortRead > ShortRead.patch
will summarize the differences into a file that can be used by the
package maintainer to update ShortRead. You can periodically, from
within the Rpacks directory,
svn up IRanges Biostrings BSgenome ShortRead
R CMD INSTALL --clean IRanges Biostrings BSgenome ShortRead
to sync up with the latest versions in the repository. There are
additional instructions on the Bioconductor developer wiki, at
http://wiki.fhcrc.org/bioc/SvnHowTo
The instructions I gave in this email checks out the top-level 'Rpacks'
directory of the Bioconductor repository, and then specific packages in
the repository; this is not such a good idea if you're interested in a
long-term relationship with svn and Bioconductor, you'd probably want to
check out the entire directory structure.
Martin
>
> 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)
>
>
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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