[BioC] RWebServices installation

Mon Dec 15 22:53:57 CET 2008

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?

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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