Dear list,

I've encountered the following problem when trying to install the package
"oligo" on R-3.0.0 :
On Ubuntu the installation stalls with the message "unable to load shared
object '/linux/biolo/R_surf/R-3.0.0/lib64/R/library/oligo/libs/oligo.so':"
(see details below).
Also, on Windows XP I couldn't install sucessfully, XP tells me that it
can't find the procedure  "sprintf_s" in  "msvcrt.dll". However, this might
rather be an issue of (my?) WinXP installation. So I'd prefer to get "oligo
working" on Ubuntu first.  "affxparser" seems to be installed correctly.
Any hints ?

Here the procedure on Ubuntu (some special/quotation characters in the
message(s) don't show up well on the screen, but this should not have any
functional consequences):

> source("http://www.bioconductor.org/biocLite.R")
> biocLite("oligo")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.12 (BiocInstaller 1.10.1), R version 3.0.0.
Installing package(s) 'oligo'
trying URL '
http://bioconductor.org/packages/2.12/bioc/src/contrib/oligo_1.24.0.tar.gz'
Content type 'application/x-gzip' length 5431248 bytes (5.2 Mb)
opened URL
===================================

[[ ... lots of text on screen, only the end is shown here ...]]

Thread model: posix
gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5.1)
COLLECT_GCC_OPTIONS='-std=gnu99' '-I/biolo/R_surf/R-3.0.0/lib64/R/include'
'-DNDEBUG' '-I/usr/local/include'
'-I/linux/biolo/R_surf/R-3.0.0/lib64/R/library/preprocessCore/include'
'-fpic' '-v' '-c' '-o' 'trimmed.o' '-mtune=generic'
 /usr/lib/gcc/x86_64-linux-gnu/4.4.3/cc1 -quiet -v
-I/biolo/R_surf/R-3.0.0/lib64/R/include -I/usr/local/include
-I/linux/biolo/R_surf/R-3.0.0/lib64/R/library/preprocessCore/include
-DNDEBUG trimmed.c -D_FORTIFY_SOURCE=2 -quiet -dumpbase trimmed.c
-mtune=generic -auxbase-strip trimmed.o -std=gnu99 -version -fpic
-fstack-protector -o /tmp/ccNLIIAr.s
GNU C (Ubuntu 4.4.3-4ubuntu5.1) version 4.4.3 (x86_64-linux-gnu)
        compiled by GNU C version 4.4.3, GMP version 4.3.2, MPFR version
2.4.2-p1.
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"
ignoring nonexistent directory
"/usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../../x86_64-linux-gnu/include"
ignoring nonexistent directory "/usr/include/x86_64-linux-gnu"
ignoring duplicate directory "/usr/local/include"
  as it is a non-system directory that duplicates a system directory
#include "..." search starts here:
#include <...> search starts here:
 /biolo/R_surf/R-3.0.0/lib64/R/include
 /linux/biolo/R_surf/R-3.0.0/lib64/R/library/preprocessCore/include
 /usr/local/include
 /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include
 /usr/lib/gcc/x86_64-linux-gnu/4.4.3/include-fixed
 /usr/include
End of search list.
GNU C (Ubuntu 4.4.3-4ubuntu5.1) version 4.4.3 (x86_64-linux-gnu)
        compiled by GNU C version 4.4.3, GMP version 4.3.2, MPFR version
2.4.2-p1.
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: 462394bb0ac77cba16b6fb6b32589358
COLLECT_GCC_OPTIONS='-std=gnu99' '-I/biolo/R_surf/R-3.0.0/lib64/R/include'
'-DNDEBUG' '-I/usr/local/include'
'-I/linux/biolo/R_surf/R-3.0.0/lib64/R/library/preprocessCore/include'
'-fpic' '-v' '-c' '-o' 'trimmed.o' '-mtune=generic'
 as -V -Qy -o trimmed.o /tmp/ccNLIIAr.s
GNU assembler version 2.20.1 (x86_64-linux-gnu) using BFD version (GNU
Binutils for Ubuntu) 2.20.1-system.20100303
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.4.3/:/usr/lib/gcc/x86_64-linux-gnu/4.4.3/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.4.3/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.4.3/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.4.3/:/usr/lib/gcc/x86_64-linux-gnu/4.4.3/:/usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../../lib/:/lib/../lib/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../:/lib/:/usr/lib/:/usr/lib/x86_64-linux-gnu/
COLLECT_GCC_OPTIONS='-std=gnu99' '-I/biolo/R_surf/R-3.0.0/lib64/R/include'
'-DNDEBUG' '-I/usr/local/include'
'-I/linux/biolo/R_surf/R-3.0.0/lib64/R/library/preprocessCore/include'
'-fpic' '-v' '-c' '-o' 'trimmed.o' '-mtune=generic'
gcc -std=gnu99 -shared -L/usr/local/lib64 -o oligo.so DABG.o ParserGzXYS.o
ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o
rma_common.o trimmed.o -lz -lgfortran -lm
-L/biolo/R_surf/R-3.0.0/lib64/R/lib -lRlapack
-L/biolo/R_surf/R-3.0.0/lib64/R/lib -lRblas
-L/biolo/R_surf/R-3.0.0/lib64/R/lib -lR
installing to /linux/biolo/R_surf/R-3.0.0/lib64/R/library/oligo/libs
** R
** inst
** preparing package for lazy loading
Note: in method for āpm<-ā with signature
āobject="TilingFeatureSet",subset="ANY",target="ANY",value="array"ā:
expanding the signature to include omitted arguments in definition: =
"missing"
Note: in method for āmm<-ā with signature
āobject="TilingFeatureSet",subset="ANY",target="ANY",value="array"ā:
expanding the signature to include omitted arguments in definition: =
"missing"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object
'/linux/biolo/R_surf/R-3.0.0/lib64/R/library/oligo/libs/oligo.so':
  /linux/biolo/R_surf/R-3.0.0/lib64/R/library/oligo/libs/oligo.so:
undefined symbol: gzgetc_
Error: loading failed
Execution halted
ERROR: loading failed
* removing ā/linux/biolo/R_surf/R-3.0.0/lib64/R/library/oligoā

The downloaded source packages are in
        ā/tmp/RtmpVY9MBm/downloaded_packagesā
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
  installation of package āoligoā had non-zero exit status
>
> # for completeness
>
> sessionInfo()
R version 3.0.0 (2013-04-03)
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] affxparser_1.32.1    BiocInstaller_1.10.1

loaded via a namespace (and not attached):

[1] tools_3.0.0
>


Thank's in advance,
Wolfgang

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Wolfgang Raffelsberger, PhD
IGBMC,
1 rue Laurent Fries,  67404 Illkirch  Strasbourg,  France
Tel (+33) 388 65 3300         Fax (+33) 388 65 3201
wolfgang.raffelsberger (at) igbmc.fr

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