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checking whether sigsetjmp is declared... yes

checking whether siglongjmp is declared... yes

checking Java support in R... present:

interpreter : '/usr/lib/jvm/default-java/jre/bin/java'

archiver : '/usr/lib/jvm/default-java/bin/jar'

compiler : '/usr/lib/jvm/default-java/bin/javac'

header prep.: '/usr/lib/jvm/default-java/bin/javah'

cpp flags : '-I/usr/lib/jvm/default-java/include'

java libs : '-L/usr/lib/jvm/default-java/jre/lib/amd64/server -ljvm'

checking whether Java run-time works...

./configure: line 3736: /usr/lib/jvm/default-java/jre/bin/java: No such file or directory no configure: error: Java interpreter '/usr/lib/jvm/default-java/jre/bin/java' does not work

ERROR: configuration failed for package ‘rJava’ * removing ‘/home/farshid/R/x86_64-pc-linux-gnu-library/3.2/rJava’

Warning in install.packages :

installation of package ‘rJava’ had non-zero exit status ERROR: dependency ‘rJava’ is not available for package ‘rcdklibs’

  • removing ‘/home/farshid/R/x86_64-pc-linux-gnu-library/3.2/rcdklibs’

Warning in install.packages : installation of package ‘rcdklibs’ had non-zero exit status ERROR: dependencies ‘rJava’, ‘rcdklibs’ are not available for package ‘rcdk’ *

removing ‘/home/farshid/R/x86_64-pc-linux-gnu-library/3.2/rcdk’

Warning in install.packages : installation of package ‘rcdk’ had non-zero exit status

The downloaded source packages are in ‘/tmp/RtmpcTxYBJ/downloaded_packages’

Farshid Rayhan
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  • Maybe you don't have java virtual machine or jre installed? – lbusett Oct 07 '16 at 17:19
  • The problem seems to be with installation of rJava. Trying installing rJava package before this one might be worthwhile. If you are on ubuntu you can try the method here : http://stackoverflow.com/questions/3311940/r-rjava-package-install-failing . – R.S. Oct 07 '16 at 17:28

1 Answers1

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Install rJave before you install rcdklibs. You can also type "dependencies = TRUE" in the install.packages function.

Aaron Baker
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