[Bioc-devel] error loading Biostrings
Martin Morgan
mtmorgan at fhcrc.org
Tue Oct 23 17:16:27 CEST 2012
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
>>>>
>>>
>>>
>>>
>>
>
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