[Bioc-devel] error loading Biostrings
Hervé Pagès
hpages at fhcrc.org
Wed Oct 24 17:33:52 CEST 2012
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
>>>>>
>>>>
>>>>
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>>>>
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>>>>
>>>>
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>>>
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>>
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>
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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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