[BioC] RWebServices installation

Tue Dec 16 07:47:40 CET 2008

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
>
> -- 
> Sensationsangebot verlängert: GMX FreeDSL - Telefonanschluss + DSL 
> für nur 16,37 Euro/mtl.!* http://dsl.gmx.de/?ac=OM.AD.PD003K1308T4569a
>
> _______________________________________________
> 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