[Bioc-devel] error loading Biostrings
Hervé Pagès
hpages at fhcrc.org
Sat Oct 27 01:47:12 CEST 2012
This is fixed in Biostrings 2.27.5. H.
On 10/24/2012 09:36 PM, Hervé Pagès wrote:
> 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
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
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>>>> 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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