[Bioc-devel] error loading Biostrings
Hervé Pagès
hpages at fhcrc.org
Thu Oct 25 06:36:19 CEST 2012
OK I can reproduce this now. The rcont2 C function used to be in the R
C API but was recently moved to the stats package, so it's not
accessible anymore. For it to be accessible stats would need to
register it with REGISTER_CCALLABLE so the C code in other packages
(like Biostrings) would be able to put stats in their LinkingTo field
and then call rcont2.
But the C code in Biostrings trying to call rcont2 is the code behind
an R function (g.test(), non exported) that does a G-test.
This g.test() function is originally from Peter Hurd. See:
https://stat.ethz.ch/pipermail/r-sig-ecology/2008-July/000275.html
It looks very much like stats::chisq.test() and its implementation
is clearly based on the implementation of stats::chisq.test() which
is also based on rcont2.
g.test() should not be implemented in Biostrings to start with so my
question is: does anybody know if there is already such a function
in the stats package or in a CRAN package? Sounds like it belongs to
stats but I cannot find it.
I don't want to copy the rcont2 C code from stats to Biostrings.
If there is no g.test() in stats or on CRAN, then I'd like to drop
support for G-test in dinucleotideFrequencyTest() (will go thru
deprecation first).
Thanks,
H.
On 10/24/2012 08:33 AM, Hervé Pagès wrote:
> Thanks all. I'll take a look at this (need to update my R-devel first).
>
> H.
>
> On 10/24/2012 08:26 AM, Vincent Carey wrote:
>> confirmed on
>>
>>> sessionInfo()
>> R Under development (unstable) (2012-10-24 r61009)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US.ISO8859-1 LC_NUMERIC=C
>> [3] LC_TIME=en_US.ISO8859-1 LC_COLLATE=en_US.ISO8859-1
>> [5] LC_MONETARY=en_US.ISO8859-1 LC_MESSAGES=C
>> [7] LC_PAPER=C LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] BiocInstaller_1.9.4
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.16.0
>>
>>
>> On Wed, Oct 24, 2012 at 10:49 AM, Steve Piccolo <
>> stephen.piccolo at hsc.utah.edu> wrote:
>>
>>> I'm getting the same error on a fresh install of R-devel.
>>>
>>>> sessionInfo()
>>> R Under development (unstable) (2012-10-23 r61007)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> locale:
>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>>> [7] LC_PAPER=C LC_NAME=C
>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> other attached packages:
>>> [1] BiocInstaller_1.9.4
>>>
>>> loaded via a namespace (and not attached):
>>> [1] tools_2.16.0
>>>
>>>
>>>
>>>
>>> On 10/23/2011 Tue, Oct 23, 2011 9:18 AM, "Kasper Daniel Hansen"
>>> <kasperdanielhansen at gmail.com> wrote:
>>>
>>>> I was using
>>>>
>>>> R Under development (unstable) (2012-10-22 r60997) -- "Unsuffered
>>>> Consequences"
>>>> Copyright (C) 2012 The R Foundation for Statistical Computing
>>>> ISBN 3-900051-07-0
>>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>>
>>>> Kasper
>>>>
>>>> On Tue, Oct 23, 2012 at 11:16 AM, Martin Morgan <mtmorgan at fhcrc.org>
>>>> wrote:
>>>>> On 10/23/2012 07:54 AM, Vincent Carey wrote:
>>>>>>
>>>>>> still cannot confirm after update. used biocLite type="source"
>>>>>>
>>>>>> session> sessionInfo()
>>>>>> R Under development (unstable) (2012-10-23 r60999)
>>>>>> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)
>>>>>
>>>>>
>>>>> would seem to be this
>>>>>
>>>>> r60988 | ripley | 2012-10-21 13:57:56 -0700 (Sun, 21 Oct 2012) | 1
>>>>> line
>>>>> Changed paths:
>>>>> M /trunk/doc/NEWS.Rd
>>>>> M /trunk/src/appl/Makefile.in
>>>>> M /trunk/src/appl/Makefile.win
>>>>> D /trunk/src/appl/rcont.c
>>>>> M /trunk/src/include/R_ext/Applic.h
>>>>>
>>>>> remove deprecated entry point rcont2
>>>>>
>>>>> but I don't know why it would still be in the revision Vince mentions.
>>>>> Also
>>>>> a little more below...
>>>>>
>>>>>
>>>>>>
>>>>>> locale:
>>>>>> [1]
>>>>>>
>>>>>>
>>>>>> en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US.US-A
>>>>>>
>>>>>> SCII
>>>>>>
>>>>>> attached base packages:
>>>>>> [1] stats graphics grDevices datasets utils tools
>>>>>> methods
>>>>>> [8] base
>>>>>>
>>>>>> other attached packages:
>>>>>> [1] Biostrings_2.27.3 IRanges_1.17.6 BiocGenerics_0.5.0
>>>>>> [4] BiocInstaller_1.9.4 weaver_1.25.0 codetools_0.2-8
>>>>>> [7] digest_0.5.2
>>>>>>
>>>>>> loaded via a namespace (and not attached):
>>>>>> [1] parallel_2.16.0 stats4_2.16.0
>>>>>>
>>>>>>
>>>>>> On Tue, Oct 23, 2012 at 10:07 AM, Vincent Carey
>>>>>> <stvjc at channing.harvard.edu>wrote:
>>>>>>
>>>>>>> aha. i forgot to set useDevel(TRUE) and I assumed that working with
>>>>>>> R-devel would give me devel targets with biocLite. ignore my
>>>>>>> previous
>>>>>>> note, updating now.
>>>>>
>>>>>
>>>>> it would have; probably you have a library that was shared between
>>>>> R-2.15
>>>>> and R-devel, or you installed from svn -- biocLite (and
>>>>> install.packages, I
>>>>> believe) would have found the repository .../2.16/pkg.tgz
>>>>>
>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Tue, Oct 23, 2012 at 9:45 AM, Robert Scharpf
>>>>>>> <rscharpf at jhsph.edu>wrote:
>>>>>>>
>>>>>>>> Hi Vincent, Is there a reason you've installed it this way, as
>>>>>>>> opposed
>>>>>>>> to
>>>>>>>> biocLite(). I notice you have a mix of release and devel
>>>>>>>> packages in
>>>>>>>> your
>>>>>>>> sessionInfo. Nevertheless, I get the loading error using
>>>>>>>> --clean and
>>>>>>>> --preclean from the command line. Below, I've reproduced the
>>>>>>>> error on
>>>>>>>> Mac
>>>>>>>> OSX and have loaded IRanges manually to display the version for
>>>>>>>> this
>>>>>>>> dependency:
>>>>>>>>
>>>>>>>> Rob
>>>>>>>>
>>>>>>>>> biocLite("Biostrings", type="source")
>>>>>>>>
>>>>>>>> BioC_mirror: http://bioconductor.org
>>>>>>>> Using Bioconductor version 2.12 (BiocInstaller 1.9.4), R version
>>>>>>>> 2.16.0.
>>>>>>>> Installing package(s) 'Biostrings'
>>>>>>>>
>>>>>>>> <SNIP>
>>>>>>>>
>>>>>>>> *** installing help indices
>>>>>>>> ** building package indices
>>>>>>>> ** installing vignettes
>>>>>>>> 'Biostrings2Classes.Rnw'
>>>>>>>> 'MultipleAlignments.Rnw'
>>>>>>>> 'PairwiseAlignments.Rnw'
>>>>>>>> 'matchprobes.Rnw'
>>>>>>>> ** testing if installed package can be loaded
>>>>>>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>>>>>> unable to load shared object
>>>>>>>>
>>>>>>>>
>>>>>>>> '/Users/rscharpf/Library/R/2.16-bioc-devel/library/Biostrings/libs/x86
>>>>>>>>
>>>>>>>> _64/Biostrings.so':
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> dlopen(/Users/rscharpf/Library/R/2.16-bioc-devel/library/Biostrings/li
>>>>>>>>
>>>>>>>> bs/x86_64/Biostrings.so,
>>>>>>>> 6): Symbol not found: _rcont2
>>>>>>>> Referenced from:
>>>>>>>>
>>>>>>>>
>>>>>>>> /Users/rscharpf/Library/R/2.16-bioc-devel/library/Biostrings/libs/x86_
>>>>>>>>
>>>>>>>> 64/Biostrings.so
>>>>>>>> Expected in: flat namespace
>>>>>>>> in
>>>>>>>>
>>>>>>>>
>>>>>>>> /Users/rscharpf/Library/R/2.16-bioc-devel/library/Biostrings/libs/x86_
>>>>>>>>
>>>>>>>> 64/Biostrings.so
>>>>>>>> Error: loading failed
>>>>>>>>
>>>>>>>>> library(IRanges)
>>>>>>>>> sessionInfo()
>>>>>>>>
>>>>>>>>
>>>>>>>> R Under development (unstable) (2012-10-21 r60988)
>>>>>>>> Platform: x86_64-apple-darwin12.2.0/x86_64 (64-bit)
>>>>>>>>
>>>>>>>> locale:
>>>>>>>> [1]
>>>>>>>>
>>>>>>>>
>>>>>>>> en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US.US
>>>>>>>>
>>>>>>>> -ASCII
>>>>>>>>
>>>>>>>> attached base packages:
>>>>>>>> [1] stats graphics grDevices utils datasets methods
>>>>>>>> base
>>>>>>>>
>>>>>>>> other attached packages:
>>>>>>>> [1] IRanges_1.17.6 BiocGenerics_0.5.0 BiocInstaller_1.9.4
>>>>>>>>
>>>>>>>> loaded via a namespace (and not attached):
>>>>>>>> [1] parallel_2.16.0 stats4_2.16.0 tools_2.16.0
>>>>>>>>
>>>>>>>>
>>>>>>>> On Oct 23, 2012, at 9:23 AM, Vincent Carey
>>>>>>>> <stvjc at channing.harvard.edu>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>> can't confirm on either linux or macosx with Oct 23 R-devel build
>>>>>>>>
>>>>>>>> Here installed Biostrings from source folder with --clean
>>>>>>>> --preclean
>>>>>>>>
>>>>>>>>> library(Biostrings)
>>>>>>>>
>>>>>>>> Loading required package: BiocGenerics
>>>>>>>>
>>>>>>>> Attaching package: 'BiocGenerics'
>>>>>>>>
>>>>>>>> The following object is masked from 'package:stats':
>>>>>>>>
>>>>>>>> xtabs
>>>>>>>>
>>>>>>>> The following objects are masked from 'package:base':
>>>>>>>>
>>>>>>>> anyDuplicated, cbind, colnames, duplicated, eval, Filter,
>>>>>>>> Find,
>>>>>>>> get, intersect, lapply, Map, mapply, mget, order, paste,
>>>>>>>> pmax,
>>>>>>>> pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
>>>>>>>> rownames, sapply, setdiff, table, tapply, union, unique
>>>>>>>>
>>>>>>>> Loading required package: IRanges
>>>>>>>> sessionI> sessionInfo()
>>>>>>>> R Under development (unstable) (2012-10-23 r61000)
>>>>>>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>>>>>>
>>>>>>>> locale:
>>>>>>>> [1] LC_CTYPE=en_US.ISO8859-1 LC_NUMERIC=C
>>>>>>>> [3] LC_TIME=en_US.ISO8859-1 LC_COLLATE=en_US.ISO8859-1
>>>>>>>> [5] LC_MONETARY=en_US.ISO8859-1 LC_MESSAGES=C
>>>>>>>> [7] LC_PAPER=C LC_NAME=C
>>>>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>>>>>>> [11] LC_MEASUREMENT=en_US.iso88591 LC_IDENTIFICATION=C
>>>>>>>>
>>>>>>>> attached base packages:
>>>>>>>> [1] stats graphics grDevices datasets tools utils
>>>>>>>> methods
>>>>>>>> [8] base
>>>>>>>>
>>>>>>>> other attached packages:
>>>>>>>> [1] Biostrings_2.27.3 IRanges_1.16.3 BiocGenerics_0.4.0
>>>>>>>> [4] weaver_1.24.0 codetools_0.2-8 digest_0.5.2
>>>>>>>> [7] BiocInstaller_1.8.2
>>>>>>>>
>>>>>>>> loaded via a namespace (and not attached):
>>>>>>>> [1] parallel_2.16.0 stats4_2.16.0
>>>>>>>>
>>>>>>>>
>>>>>>>> On Tue, Oct 23, 2012 at 7:27 AM, Robert Scharpf
>>>>>>>> <rscharpf at jhsph.edu>wrote:
>>>>>>>>
>>>>>>>>> Hello,
>>>>>>>>>
>>>>>>>>> I'm having trouble loading the Biostrings package (the
>>>>>>>>> Biostrings.so
>>>>>>>>> shared library) after installation of the most recent R-devel (Oct
>>>>>>>>> 22).
>>>>>>>>> There is no error on the BioC build report, but BioC is
>>>>>>>>> building
>>>>>>>>> packages
>>>>>>>>> from the Oct 5 R-devel.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> Rob
>>>>>>>>>
>>>>>>>>> biocLite("Biostrings", type="source")
>>>>>>>>> [...]
>>>>>>>>>
>>>>>>>>> *** installing help indices
>>>>>>>>> ** building package indices
>>>>>>>>> ** installing vignettes
>>>>>>>>> 'Biostrings2Classes.Rnw'
>>>>>>>>> 'MultipleAlignments.Rnw'
>>>>>>>>> 'PairwiseAlignments.Rnw'
>>>>>>>>> 'matchprobes.Rnw'
>>>>>>>>> ** testing if installed package can be loaded
>>>>>>>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>>>>>>> unable to load shared object
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> '/home/bst/student/rscharpf/Library/R/2.16-bioc-devel/library/Biostri
>>>>>>>>>
>>>>>>>>> ngs/libs/Biostrings.so':
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> /home/bst/student/rscharpf/Library/R/2.16-bioc-devel/library/Biostrin
>>>>>>>>>
>>>>>>>>> gs/libs/Biostrings.so:
>>>>>>>>> undefined symbol: rcont2
>>>>>>>>> Error: loading failed
>>>>>>>>>
>>>>>>>>> Session info:
>>>>>>>>>
>>>>>>>>> R Under development (unstable) (2012-10-22 r60997)
>>>>>>>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>>>>>>>
>>>>>>>>> locale:
>>>>>>>>> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
>>>>>>>>> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
>>>>>>>>> [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
>>>>>>>>> [7] LC_PAPER=C LC_NAME=C
>>>>>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>>>>>>>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>>>>>>>>>
>>>>>>>>> attached base packages:
>>>>>>>>> [1] stats graphics grDevices datasets utils methods
>>>>>>>>> base
>>>>>>>>>
>>>>>>>>> other attached packages:
>>>>>>>>> [1] BiocInstaller_1.9.4
>>>>>>>>>
>>>>>>>>> loaded via a namespace (and not attached):
>>>>>>>>> [1] tools_2.16.0
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Bioc-devel at r-project.org mailing list
>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>> [[alternative HTML version deleted]]
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioc-devel at r-project.org mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>> _______________________________________________
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>>
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>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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