[BioC] RWebServices installation

Tue Dec 16 16:51:42 CET 2008

Hi Martin,

thanks a lot. Using 
export PKG_CFLAGS = '-I/usr/lib/jvm/java-6-sun-1.6.0.07/include -I/usr/lib/jvm/java-6-sun-1.6.0.07/include/linux' 
I was able to install RWebServices_1.6.0. I'll try the SVN versions of SJava and RWebservices.

Thanks again for your help.
Bastian

-------- Original-Nachricht --------
> Datum: Mon, 15 Dec 2008 22:47:40 -0800
> Von: Martin Morgan <mtmorgan at fhcrc.org>
> An: "Bastian Angermann" <AngerB at gmx.de>
> CC: bioconductor at stat.math.ethz.ch
> Betreff: Re: [BioC] RWebServices installation

> Hi Bastian --
> 
> "Bastian Angermann" <AngerB at gmx.de> writes:
> 
> > Hi List,
> >
> > I am trying to install RWebServices, but the installation fails
> > because the jni.h include is not found by the c compiler. I have
> > tried numerous variations of giving the option
> > --configure-args,--configure-vars but these don't seem to have any
> > effect since the parameter I provide to them is not passed on to the
> > compiler.  The java settings in R_HOME/etc/Makevars are set and
> > point to the correct location but are not handed to the compiler
> > either. How can I pass the appropriate CFLAGS to the installation
> > procedure?
> 
> The version of RWebServices available in R-2.8.0 does not understand
> --configure-args, etc. Try
> 
> PKG_CFLAGS=-I/usr/lib/jvm/java-6-sun-1.6.0.07/include
> /home/bastian/RWebServices_1.6.0.tar.gz
> 
> There's an updated version of SJava available via svn, at
> 
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SJava
> 
> and in general expect changes (for the better!) in both SJava at the
> above svn and RWebServices as available in the bioc-devel repository.
> 
> Please let me know how this goes.
> 
> Martin
> 
> > Thanks,
> > Bastian Angermann
> >
> > This is the output of one of my installation attempts (I tried both sun
> java 1.5 and 1.6)
> > bastian at laptop1:~$ R CMD INSTALL -d
> --configure-args='CFLAGS=-I/usr/lib/jvm/java-6-sun-1.6.0.07/include/' /home/bastian/RWebServices_1.6.0.tar.gz
> > * Installing to library '/home/bastian//lib64/R/library'
> > 'R CMD INSTALL': in startdir= /home/bastian with tmpdir=
> /tmp/R.INSTALL.y12220
> >    lib= '/home/bastian//lib64/R/library', pkgs= '
> "/tmp/R.INSTALL.y12220/RWebServices"'
> >    before checking lockdir= '/home/bastian/lib64/R/library/00LOCK'
> >    after checking lockdir
> >    build_help_opts= '--debug  --txt --html --latex --example'
> > 'R CMD INSTALL': now doing 'eval ... do_install':
> > * Installing *source* package 'RWebServices' ...
> >
> > Guessing SJava home: /home/bastian/lib64/R/library/SJava
> >
> > configure: creating ./config.status
> > config.status: creating inst/scripts/RWebServicesEnv.properties
> > ** libs
> > + mkdir -p /home/bastian/lib64/R/library/RWebServices/libs
> > + test -f src/Makefile
> > + cd src
> > + ls RWebServicesConverters.c init.c *.cc *.cpp *.f90 *.f95 *.mm
> > + srcs=init.c
> > RWebServicesConverters.c
> > + test -r Makevars
> > + allfiles=init.c
> > RWebServicesConverters.c
> > + cd /home/bastian//lib64/R/bin/exec
> > + ls
> > + archs=R
> > + R_ARCH_keep=
> > + test -n init.c
> > RWebServicesConverters.c
> > + test -x ../configure
> > + test -n
> > + sh /home/bastian//lib64/R/bin/SHLIB -o RWebServices.so init.c
> RWebServicesConverters.c
> > gcc -std=gnu99 -I/home/bastian//lib64/R/include  -I/usr/local/include   
> -fpic  -g -O2 -c init.c -o init.o
> > gcc -std=gnu99 -I/home/bastian//lib64/R/include  -I/usr/local/include   
> -fpic  -g -O2 -c RWebServicesConverters.c -o RWebServicesConverters.o
> > RWebServicesConverters.c:1:17: error: jni.h: No such file or directory
> > RWebServicesConverters.c: In function ‘RCharScalar_JavaString’:
> > RWebServicesConverters.c:26: error: ‘JNIEnv’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:26: error: (Each undeclared identifier is
> reported only once
> > RWebServicesConverters.c:26: error: for each function it appears in.)
> > RWebServicesConverters.c:26: error: ‘env’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:28: error: ‘jobject’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:28: error: expected ‘;’ before ‘value’
> > RWebServicesConverters.c:34: error: ‘value’ undeclared (first use in
> this function)
> > RWebServicesConverters.c: In function ‘RIntegerScalar_JavaInteger’:
> > RWebServicesConverters.c:44: error: ‘JNIEnv’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:44: error: ‘env’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:45: error: ‘jclass’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:45: error: expected ‘;’ before
> ‘thisClass’
> > RWebServicesConverters.c:46: error: ‘jmethodID’ undeclared (first
> use in this function)
> > RWebServicesConverters.c:46: error: expected ‘;’ before
> ‘thisConstructor’
> > RWebServicesConverters.c:47: error: ‘jobject’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:47: error: expected ‘;’ before ‘value’
> > RWebServicesConverters.c:50: error: ‘value’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:50: error: ‘thisClass’ undeclared (first
> use in this function)
> > RWebServicesConverters.c:50: error: ‘thisConstructor’ undeclared
> (first use in this function)
> > RWebServicesConverters.c: In function ‘RNumericScalar_JavaDouble’:
> > RWebServicesConverters.c:61: error: ‘JNIEnv’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:61: error: ‘env’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:62: error: ‘jclass’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:62: error: expected ‘;’ before
> ‘thisClass’
> > RWebServicesConverters.c:63: error: ‘jmethodID’ undeclared (first
> use in this function)
> > RWebServicesConverters.c:63: error: expected ‘;’ before
> ‘thisConstructor’
> > RWebServicesConverters.c:64: error: ‘jobject’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:64: error: expected ‘;’ before ‘value’
> > RWebServicesConverters.c:67: error: ‘value’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:67: error: ‘thisClass’ undeclared (first
> use in this function)
> > RWebServicesConverters.c:67: error: ‘thisConstructor’ undeclared
> (first use in this function)
> > RWebServicesConverters.c: In function ‘RLogicalScalar_JavaBoolean’:
> > RWebServicesConverters.c:78: error: ‘JNIEnv’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:78: error: ‘env’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:79: error: ‘jclass’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:79: error: expected ‘;’ before
> ‘thisClass’
> > RWebServicesConverters.c:80: error: ‘jmethodID’ undeclared (first
> use in this function)
> > RWebServicesConverters.c:80: error: expected ‘;’ before
> ‘thisConstructor’
> > RWebServicesConverters.c:81: error: ‘jobject’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:81: error: expected ‘;’ before ‘value’
> > RWebServicesConverters.c:84: error: ‘value’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:84: error: ‘thisClass’ undeclared (first
> use in this function)
> > RWebServicesConverters.c:84: error: ‘thisConstructor’ undeclared
> (first use in this function)
> > RWebServicesConverters.c: In function ‘RCharVector_JavaStringArray’:
> > RWebServicesConverters.c:95: error: ‘JNIEnv’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:95: error: ‘env’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:97: error: ‘jstring’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:97: error: expected ‘;’ before ‘str’
> > RWebServicesConverters.c:98: error: ‘jobject’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:98: error: expected ‘;’ before ‘value’
> > RWebServicesConverters.c:101: error: ‘value’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:103: error: ‘str’ undeclared (first use in
> this function)
> > RWebServicesConverters.c: In function ‘RList_JavaObjectArray’:
> > RWebServicesConverters.c:116: error: ‘JNIEnv’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:116: error: ‘env’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:118: error: ‘jobject’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:118: error: expected ‘;’ before ‘ele’
> > RWebServicesConverters.c:119: error: expected ‘;’ before ‘value’
> > RWebServicesConverters.c:122: error: ‘value’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:124: error: ‘ele’ undeclared (first use in
> this function)
> > RWebServicesConverters.c: In function ‘RIntegerVector_JavaIntArray’:
> > RWebServicesConverters.c:137: error: ‘JNIEnv’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:137: error: ‘env’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:139: error: ‘jintArray’ undeclared (first
> use in this function)
> > RWebServicesConverters.c:139: error: expected ‘;’ before ‘value’
> > RWebServicesConverters.c:140: error: ‘jint’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:140: error: ‘els’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:141: error: ‘jboolean’ undeclared (first
> use in this function)
> > RWebServicesConverters.c:141: error: expected ‘;’ before
> ‘isCopy’
> > RWebServicesConverters.c:144: error: ‘value’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:145: error: ‘isCopy’ undeclared (first use
> in this function)
> > RWebServicesConverters.c: In function
> ‘RNumericVector_JavaDoubleArray’:
> > RWebServicesConverters.c:159: error: ‘JNIEnv’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:159: error: ‘env’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:161: error: ‘jdoubleArray’ undeclared
> (first use in this function)
> > RWebServicesConverters.c:161: error: expected ‘;’ before ‘value’
> > RWebServicesConverters.c:162: error: ‘jdouble’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:162: error: ‘els’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:163: error: ‘jboolean’ undeclared (first
> use in this function)
> > RWebServicesConverters.c:163: error: expected ‘;’ before
> ‘isCopy’
> > RWebServicesConverters.c:166: error: ‘value’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:167: error: ‘isCopy’ undeclared (first use
> in this function)
> > RWebServicesConverters.c: In function
> ‘RLogicalVector_JavaBooleanArray’:
> > RWebServicesConverters.c:181: error: ‘JNIEnv’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:181: error: ‘env’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:183: error: ‘jbooleanArray’ undeclared
> (first use in this function)
> > RWebServicesConverters.c:183: error: expected ‘;’ before ‘value’
> > RWebServicesConverters.c:184: error: ‘jboolean’ undeclared (first
> use in this function)
> > RWebServicesConverters.c:184: error: ‘els’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:185: error: expected ‘;’ before
> ‘isCopy’
> > RWebServicesConverters.c:188: error: ‘value’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:189: error: ‘isCopy’ undeclared (first use
> in this function)
> > RWebServicesConverters.c: In function ‘RRawVector_JavaByteArray’:
> > RWebServicesConverters.c:203: error: ‘JNIEnv’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:203: error: ‘env’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:205: error: ‘jbyteArray’ undeclared (first
> use in this function)
> > RWebServicesConverters.c:205: error: expected ‘;’ before ‘value’
> > RWebServicesConverters.c:206: error: ‘jbyte’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:206: error: ‘els’ undeclared (first use in
> this function)
> > RWebServicesConverters.c:207: error: ‘jboolean’ undeclared (first
> use in this function)
> > RWebServicesConverters.c:207: error: expected ‘;’ before
> ‘isCopy’
> > RWebServicesConverters.c:210: error: ‘value’ undeclared (first use
> in this function)
> > RWebServicesConverters.c:211: error: ‘isCopy’ undeclared (first use
> in this function)
> > make: *** [RWebServicesConverters.o] Error 1
> > + has_error=true
> > + chmod 755 /home/bastian/lib64/R/library/RWebServices/libs/*
> > chmod: cannot access
> `/home/bastian/lib64/R/library/RWebServices/libs/*': No such file or directory
> > + cd ..
> > + true
> > + error compilation failed for package 'RWebServices'
> > + echo ERROR: compilation failed for package 'RWebServices'
> > ERROR: compilation failed for package 'RWebServices'
> > + do_exit_on_error
> > + remove_R_package_dir=yes
> > + test -n /tmp/R.INSTALL.y12220/RWebServices
> > + get_dcf_field Contains /tmp/R.INSTALL.y12220/RWebServices/DESCRIPTION
> > + ws=[  ]
> > + /bin/sed -n /^Contains:/,/^[^ ]/p
> /tmp/R.INSTALL.y12220/RWebServices/DESCRIPTION
> > + /bin/sed -n 1s/^Contains:[    ]*//p; /^[      ]/p
> > ]*$//n/sed /^[  ]/s/^[  ]*//; s/[
> > + bundlepkg=
> > + test -z
> > + bundlepkg=RWebServices
> > + false
> > + pkgdir=/home/bastian/lib64/R/library/RWebServices
> > + test yes = yes
> > + test -n /home/bastian/lib64/R/library/RWebServices
> > + message Removing '/home/bastian/lib64/R/library/RWebServices'
> > + echo ** Removing '/home/bastian/lib64/R/library/RWebServices'
> > ** Removing '/home/bastian/lib64/R/library/RWebServices'
> > + rm -rf /home/bastian/lib64/R/library/RWebServices
> > + test -n RWebServices
> > + test -d /home/bastian/lib64/R/library/00LOCK/RWebServices
> > + do_cleanup
> > + do_cleanup_tmpdir
> > + cd /home/bastian
> > + test -d /tmp/R.INSTALL.y12220
> > + rm -rf /tmp/R.INSTALL.y12220
> > + test yes = no
> > + true
> > + rm -rf /home/bastian/lib64/R/library/00LOCK
> > + exit 1
> >
> > -- 
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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
> 
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