[Bioc-devel] error loading Biostrings

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

        [[alternative HTML version deleted]]

--
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