[Bioc-devel] error loading Biostrings
Steve Piccolo
stephen.piccolo at hsc.utah.edu
Wed Oct 24 16:49:04 CEST 2012
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
>>>
>>
>>
>> --
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>>
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>>
>>
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>
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