Paul Johnson
2012-May-23 01:56 UTC
[R] Build error on RedHat EL 5.5: byte-compiling package 'compiler'
Greetings R-help! In case anybody has worked on an old Redhat system lately, can you remember what is the cause of this problem? I don't think this is a fatal problem, because I can get around it by uninstalling all of the R RPM packages and re-running the build. But if R is installed, the build fails while byte-compiling as seen below. A *guessed* removing the installed R stuff might make a difference, and it did! The build directory is /tmp/BUILD/R-2.15.0/ but the compile process jumps out and tries to grab files in /usr/lib64... make[6]: Entering directory `/tmp/BUILD/R-2.15.0/src/library/tools/src' make[6]: `Makedeps' is up to date. make[6]: Leaving directory `/tmp/BUILD/R-2.15.0/src/library/tools/src' make[6]: Entering directory `/tmp/BUILD/R-2.15.0/src/library/tools/src' mkdir -p -- ../../../../library/tools/libs make[6]: Leaving directory `/tmp/BUILD/R-2.15.0/src/library/tools/src' make[5]: Leaving directory `/tmp/BUILD/R-2.15.0/src/library/tools/src' make[4]: Leaving directory `/tmp/BUILD/R-2.15.0/src/library/tools' make[3]: Leaving directory `/tmp/BUILD/R-2.15.0/src/library/tools' make[3]: Entering directory `/tmp/BUILD/R-2.15.0/src/library/compiler' building package 'compiler' mkdir -p -- ../../../library/compiler make[4]: Entering directory `/tmp/BUILD/R-2.15.0/src/library/compiler' mkdir -p -- ../../../library/compiler/R mkdir -p -- ../../../library/compiler/po make[4]: Leaving directory `/tmp/BUILD/R-2.15.0/src/library/compiler' make[4]: Entering directory `/tmp/BUILD/R-2.15.0/src/library/compiler' byte-compiling package 'compiler' Warning in file(datafile, "wb") : cannot open file '/usr/lib64/R/library/compiler/R/compiler.rdb': Permission denied Error in file(datafile, "wb") : cannot open the connection Calls: <Anonymous> -> code2LazyLoadDB -> makeLazyLoadDB -> close -> file Execution halted make[4]: *** [../../../library/compiler/R/compiler.rdb] Error 1 make[4]: Leaving directory `/tmp/BUILD/R-2.15.0/src/library/compiler' make[3]: *** [all] Error 2 make[3]: Leaving directory `/tmp/BUILD/R-2.15.0/src/library/compiler' make[2]: *** [R] Error 1 make[2]: Leaving directory `/tmp/BUILD/R-2.15.0/src/library' make[1]: *** [R] Error 1 make[1]: Leaving directory `/tmp/BUILD/R-2.15.0/src' make: *** [R] Error 1 error: Bad exit status from /var/tmp/rpm-tmp.5874 (%build) The command line that initiates the RPM build is rpmbuild -ba R-2.15-pj.spec --define "dist=kurocks" > Rbuild.txt 2>&1 & and I uploaded the full script of the build process here: http://pj.freefaculty.org/R/Rbuild.txt I searched the archive and find a 2006 mention of the same problem, and the solution was that the user had R_LIBS defined in the environment. I don't have anything like that in the output of "env", but obviously, I'm getting something that confuses the build from the R envionment. I am just a little curious if somebody can explain what's going wrong. pj -- Paul E. Johnson Professor, Political Science ? ?Assoc. Director 1541 Lilac Lane, Room 504 ? ? Center for Research Methods University of Kansas ? ? ? ? ? ? ? University of Kansas http://pj.freefaculty.org ? ? ? ? ? ?http://quant.ku.edu
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