[Rd] possibly stupid question about RPM building

From: Ben Bolker <bolker_at_zoo.ufl.edu>
Date: Tue 18 Jul 2006 - 22:32:19 GMT

  I'm trying to build an RPM of R 2.3.1 on a very old RedHat system (specifically, a ROCKS 3.3.0 cluster which is built on RH enterprise 3 (I think??))

  I downloaded R-2.3.1.tgz from CRAN; downloaded the R.spec file cran.r-project.org/http://cran.r-project.org/bin/linux/redhat/SRPMS/ ; and ran rpmbuild -ba R.specs.

  Everything goes along fine until ...

make[5]: Entering directory
`/usr/src/redhat/BUILD/R-2.3.1/src/library/tools/src'

gcc -I../../../../include -I../../../../include  -I/usr/local/include

-fpic -O2 -g -march=i386 -mcpu=i686 -c text.c -o text.o
gcc -I../../../../include -I../../../../include -I/usr/local/include
-fpic -O2 -g -march=i386 -mcpu=i686 -c init.c -o init.o
gcc -I../../../../include -I../../../../include -I/usr/local/include
-fpic -O2 -g -march=i386 -mcpu=i686 -c Rmd5.c -o Rmd5.o
gcc -I../../../../include -I../../../../include -I/usr/local/include

-fpic -O2 -g -march=i386 -mcpu=i686 -c md5.c -o md5.o
gcc -shared -L/usr/local/lib -o tools.so text.o init.o Rmd5.o md5.o
-L../../../../lib -lR

mkdir -p -- ../../../../library/tools/libs make[5]: Leaving directory
`/usr/src/redhat/BUILD/R-2.3.1/src/library/tools/src' make[4]: Leaving directory
`/usr/src/redhat/BUILD/R-2.3.1/src/library/tools/src' Warning message:
package seems to be using lazy loading already in: makeLazyLoading("tools") Error in lazyLoadDBfetch(key, datafile, compressed, envhook) :

        internal error in R_decompress1
Execution halted

Thereafter, going to /usr/src/redhat/BUILD/R-2.3.1/src/library/tools and executing "make" gives essentially the same result.

  digging deeper finds the error message within library/tools/R/makeLazyLoad.R:

  if (file.info(codeFile)["size"] == file.info(loaderFile)["size"])

        warning("package seems to be using lazy loading already")

hacking this file to produce more output identifies codeFile as /usr/lib/R/library/tools/R/tools and loaderFile as below:

[root@bolker-cluster tools]# ls -l
/usr/src/redhat/BUILD/R-2.3.1/share/R/nspackloader.R
-rw-r--r-- 1 root root 384 Jul 18 18:29
/usr/src/redhat/BUILD/R-2.3.1/share/R/nspackloader.R [root@bolker-cluster tools]# ls -l /usr/lib/R/library/tools/R/tools
-rw-r--r-- 1 root root 384 Jul 18 17:33
/usr/lib/R/library/tools/R/tools

  ?? I am at the edge of my comprehension here ...

  Searching for "R_decompress1", "internal error", etc., on Google/RSiteSearch gave nothing

Searching on "package seems to be using lazy loading already" finds a few old hits, but no solutions.

  I have 252M free space (the first time this happened I had only 50M ...)

  Could this possibly be related to having another (old) instance of R running at the same time? Seems unlikely but ...

  does anyone have any hints?

  sincerely
    Ben Bolker

--

620B Bartram Hall                            bolker@zoo.ufl.edu
Zoology Department, University of Florida    http://www.zoo.ufl.edu/bolker
Box 118525                                   (ph)  352-392-5697
Gainesville, FL 32611-8525                   (fax) 352-392-3704

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