[BioC] difficulty loading rsbml

Vincent Carey stvjc at channing.harvard.edu
Mon Feb 7 03:51:24 CET 2011 

I just built, from source, libsbml 5.0.0-b1 and then did biocLite to
get rsbml installed from source.  i needed to set PKG_CONFIG_PATH to
know where the libsbml.pc was and all was well

> dom <- rsbml_dom(doc)
> sapply(species(model(dom)), id)
                    Glucose         Glucose_6_phosphate
                  "Glucose"       "Glucose_6_phosphate"
       Fructose_6_phosphate   Fructose_1_6_bisphosphate
     "Fructose_6_phosphate" "Fructose_1_6_bisphosphate"
  Dihydroxyacetonephosphate   Glyceraldehyd_3_phosphate
"Dihydroxyacetonephosphate" "Glyceraldehyd_3_phosphate"
   _1_3_Bisphosphoglycerate         _3_Phosphoglycerate
 "_1_3_Bisphosphoglycerate"       "_3_Phosphoglycerate"
        _2_Phosphoglycerate         Phosphoenolpyruvate
      "_2_Phosphoglycerate"       "Phosphoenolpyruvate"
                   Pyruvate                         ATP
                 "Pyruvate"                       "ATP"
                        ADP                          H_
                      "ADP"                        "H_"
                       NAD_                        NADH
                     "NAD_"                      "NADH"
                        H2O                          Pi
                      "H2O"                        "Pi"
> sessionInfo()
R version 2.13.0 Under development (unstable) (2010-12-18 r53869)
Platform: x86_64-apple-darwin10.4.0/x86_64 (64-bit)

locale:
[1] C

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

other attached packages:
[1] Biobase_2.11.6  rsbml_2.9.1     weaver_1.17.0   codetools_0.2-6
[5] digest_0.4.2

loaded via a namespace (and not attached):
[1] graph_1.29.0

Perhaps Paul and I can take this off line if a similar configuration
is not working for him... and then get back to the list.

On Sun, Feb 6, 2011 at 7:20 PM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> Probably because your libsbml version is too new. rsbml only supports
> libsbml 3.x. If anyone wants to volunteer to fix that, please let me know.
> SBML falls too far outside the scope of my current work.
>
> Thanks,
> Michael
>
> On Sun, Feb 6, 2011 at 8:19 AM, Paul Shannon <pshannon at systemsbiology.org>wrote:
>
>> Thanks for your replies, Dan and Martin.
>>
>> My original post mostly concealed that I do have libsbml installed.  A
>> quick test from python shows that it works: python can read the latest, full
>> yeastNet sbml file.  So the problem appears to be that something I have
>> done, or not done, leads to rsbml not being able to find libsbml.
>>
>> I thought that perhaps the macos version of LD_LIBRARY_PATH (which is
>> 'DYLD_LIBRARY_PATH') might not be properly set.
>> Here's what I tried.  Maybe wiser heads than my own can see what I am doing
>> wrong.
>>
>>  bash> export DYLD_LIBRARY_PATH=/usr/local/lib
>>  bash> R
>>  > env = Sys.getenv ()
>>  > env [grep ('DYLD', names (env))]  # find out the value of this path to
>> the running R process
>>                                                       DYLD_LIBRARY_PATH
>>    "/Library/Frameworks/R.framework/Resources/lib/x86_64:/usr/local/lib"
>>
>>  > grep ('libsbml', list.files ('/usr/local/lib'), value=TRUE)   # is
>> libsbml findable down that path?
>>     [1] "libsbml.4.2.0.dylib" "libsbml.4.dylib"     "libsbml.a"
>> "libsbml.dylib"       "libsbml.la"          "libsbmlj.jnilib"
>>
>>  > library (rsbml)   # try to load.  as rsbml.so loads, it looks for, but
>> cannot find, libsbml (apparently)
>>     Error : .onLoad failed in loadNamespace() for 'rsbml', details:
>>    call: dyn.load(file, DLLpath = DLLpath, ...)
>>    error: unable to load shared object
>> '/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rsbml/libs/x86_64/rsbml.so':
>>
>>  dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rsbml/libs/x86_64/rsbml.so,
>> 6): Symbol not found: _ASTNode_addChild
>>    Referenced from:
>> /Library/Frameworks/R.framework/Versions/2.12/Resources/library/rsbml/libs/x86_64/rsbml.so
>>    Expected in: dynamic lookup
>>
>>   Error: package/namespace load failed for 'rsbml'
>>
>> Any suggestions?
>>
>> Thanks!
>>
>>  - Paul
>>
>> sessionInfo ()
>> R version 2.12.1 (2010-12-16)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>
>> 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
>>
>> loaded via a namespace (and not attached):
>> [1] graph_1.29.2 tools_2.12.1
>>
>>
>>
>>
>>
>>
>> On Feb 6, 2011, at 12:12 AM, Dan Tenenbaum wrote:
>>
>> >
>> >
>> > On Sat, Feb 5, 2011 at 8:23 PM, Paul Shannon <
>> pshannon at systemsbiology.org> wrote:
>> > The specific error is see (text below) suggests that libsbml is not being
>> found.  ASTNode appears to be a symbol in libsbml
>> >
>> >  biocLite ('rbsml')
>> >  installing /usr/local/lib/libsbml.4.2.0.dylib
>> >  export DYLD_LIBRARY_PATH=/usr/local/lib
>> >  R
>> >  > library (rsbml)
>> >
>> > I get this error message:
>> >
>> > Error : .onLoad failed in loadNamespace() for 'rsbml', details:
>> >  call: dyn.load(file, DLLpath = DLLpath, ...)
>> >  error: unable to load shared object
>> '/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rsbml/libs/x86_64/rsbml.so':
>> >
>>  dlopen(/Library/Frameworks/R.framework/Versions/2.12/Resources/library/rsbml/libs/x86_64/rsbml.so,
>> 6): Symbol not found: _ASTNode_addChild
>> >  Referenced from:
>> /Library/Frameworks/R.framework/Versions/2.12/Resources/library/rsbml/libs/x86_64/rsbml.so
>> >  Expected in: dynamic lookup
>> >
>> > Error: package/namespace load failed for 'rsbml'
>> >
>> > rsbml.so is where it is supposed to be:
>> >
>> >
>>  /Library/Frameworks/R.framework/Versions/2.12/Resources/library/rsbml/libs/x86_64:
>> >     -rwxr-xr-x  1 pshannon  admin  95328 Oct 19 22:08 rsbml.so
>> >
>> > Any suggestions?  Thanks.
>> >
>> >  - Paul
>> >
>> >
>> >
>> > Hi Paul,
>> >
>> > rsbml requires that you install libsbml. rsbml does not do this for you.
>> >
>> > You can get libsbml from http://www.sbml.org.
>> >
>> > Dan
>> >
>> >
>> > > sessionInfo ()
>> > R version 2.12.1 (2010-12-16)
>> > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>> >
>> > 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
>> >
>> > loaded via a namespace (and not attached):
>> > [1] graph_1.29.2 tools_2.12.1
>> > _______________________________________________
>> > Bioconductor mailing list
>> > Bioconductor at r-project.org
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>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>>
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