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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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

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 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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