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, class...@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
[email protected]
(256) 327-0473 (p)
(256) 327-0966 (f)
Room 4005
601 Genome Way
Huntsville, Alabama 35806
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