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@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@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@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@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@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@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@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@r-project.org mailing list
> >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>
> >>>         [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> Bioc-devel@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@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >_______________________________________________
> >Bioc-devel@r-project.org mailing list
> >https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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