[BioC] RMAGEML installation and ArrayExpress database

[Martin Morgan]

Hi John --

"John Lande" <john.lande77 at gmail.com> writes:

> dear all,
>
> I need to import data from ArrayExpress, and I am tring RMAGEML.
> unluckly I retrive the following error during installation. what do I miss?

RMAGEML is expecting an environment variable JAVA_HOME, e.g,

export JAVA_HOME=/usr/lib64/jvm/java-1.5.0-sun-1.5.0_update16

RMAGEML produced a segmentation fault (in the second chunk of the
vignette)

 *** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: .Call("getVoidVoid", "init", mageOM, ..rmagemlJVM at jvmptr, PACKAGE = "RMAGEML")
 2: importMAGEML(directory = datadir, package = "marray", arrayID = "A-MEXP-14",     DED = "DED:707", QTD = "QTD:707", name.Rf = "QT:F635 Mean",     name.Rb = "QT:B635 Median", name.Gf = "QT:F532 Mean", name.Gb = "QT:B532 Median")

on one of the systems I have access to so this might not be a short
road that you are starting down.

Martin

> is there any other package to andle ArrayExpress Data?
>
>
>> install.packages("RMAGEML")
> trying URL '
> http://www.bioconductor.org/packages/2.2/bioc/src/contrib/RMAGEML_2.14.0.tar.gz
> '
> Content type 'application/x-gzip' length 4912894 bytes (4.7 Mb)
> opened URL
> ==================================================
> downloaded 4.7 Mb
>
> * Installing *source* package 'RMAGEML' ...
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> During startup - Warning messages:
> 1: Setting LC_CTYPE failed, using "C"
> 2: Setting LC_TIME failed, using "C"
> 3: Setting LC_MESSAGES failed, using "C"
> 4: Setting LC_PAPER failed, using "C"
> 5: Setting LC_MEASUREMENT failed, using "C"
> gcc -std=gnu99 -I/usr/local/lib64/R/include -I/include -I/include/linux
> -I/usr/local/include    -fpic  -g -O2 -c rmageml.c -o rmageml.o
> rmageml.c: In function 'updateMAGEML':
> rmageml.c:599: warning: cast from pointer to integer of different size
> gcc -std=gnu99 -shared -L/usr/local/lib64 -o RMAGEML.so rmageml.o
> -L/jre/lib/amd64 -L/jre/lib/i386 -ljava -L/jre/lib/amd64/server
> -L/jre/lib/i386/client -ljvm
> /usr/bin/ld: cannot find -ljava
> collect2: ld returned 1 exit status
> make: *** [RMAGEML.so] Error 1
> chmod: cannot access `/usr/local/lib64/R/library/RMAGEML/libs/*': No such
> file or directory
> ERROR: compilation failed for package 'RMAGEML'
> ** Removing '/usr/local/lib64/R/library/RMAGEML'
>
> The downloaded packages are in
>     /tmp/RtmpEZsArx/downloaded_packages
> Updating HTML index of packages in '.Library'
> Warning message:
> In install.packages("RMAGEML") :
>   installation of package 'RMAGEML' had non-zero exit status
>
>> sessionInfo()
> R version 2.7.2 (2008-08-25)
> x86_64-unknown-linux-gnu
>
> locale:
> C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] tools_2.7.2
>
> 	[[alternative HTML version deleted]]
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793