[Bioc-devel] error loading Biostrings
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Tue Oct 23 17:18:35 CEST 2012
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-ASCII
>>
>> 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/libs/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/Biostrings/libs/Biostrings.so':
>>>>>
>>>>>
>>>>> /home/bst/student/rscharpf/Library/R/2.16-bioc-devel/library/Biostrings/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
>>
>
>
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