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

Fri Oct 2 15:56:40 CEST 2009

Martin

Thanks, I'll give it a go.

Mike
On Oct 1, 2009, at 8:08 PM, Martin Morgan wrote:

> 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

Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806