I am running Linux Mandrake 7.2 with the following:
platform i586-pc-linux-gnu
arch i586
os linux-gnu
system i586, linux-gnu
status
major 1
minor 2.3
year 2001
month 04
day 26
language R
To build a package I ran R CMD build Hmisc, apparently with success:
* checking for file `Hmisc/DESCRIPTION' ... OK
* preparing `Hmisc':
* cleaning src
* checking whether `INDEX' is up-to-date ... NO
* use `--force' to overwrite the existing `INDEX'
* removing junk files
* building `Hmisc_1.0.tar.gz'
The source directory had a single large R source file under R
and many .Rd files under man. It did not have a test directory,
and it have an extraneous s directory and an extraneous text
file in its root area.
Then I ran, under root, R CMD INSTALL Hmisc_1.0.tar.gz, and got:
Installing source package `Hmisc' ...
libs
g77 -fPIC -O3 -fomit-frame-pointer -pipe -s -march=pentium
-ffast-math -fexpensive-optimizations -fno-fast-math -c cidxcn.f -o
cidxcn.o
g77 -fPIC -O3 -fomit-frame-pointer -pipe -s -march=pentium
-ffast-math -fexpensive-optimizations -fno-fast-math -c cidxcp.f -o
cidxcp.o
g77 -fPIC -O3 -fomit-frame-pointer -pipe -s -march=pentium
-ffast-math -fexpensive-optimizations -fno-fast-math -c hoeffd.f -o
hoeffd.o
g77 -fPIC -O3 -fomit-frame-pointer -pipe -s -march=pentium
-ffast-math -fexpensive-optimizations -fno-fast-math -c largrec.f -o
largrec.o
gcc -I/usr/lib/R/include -I/usr/local/include -mieee-fp
-D__NO_MATH_INLINES -fPIC -O3 -fomit-frame-pointer -pipe -s
-march=pentium -ffast-math -fexpensive-optimizations -fno-fast-math -c
ranksort.c -o ranksort.o
g77 -fPIC -O3 -fomit-frame-pointer -pipe -s -march=pentium
-ffast-math -fexpensive-optimizations -fno-fast-math -c rcorr.f -o
rcorr.o
gcc -shared -o Hmisc.so cidxcn.o cidxcp.o hoeffd.o largrec.o ranksort.o
rcorr.o -L/usr/local/lib -lg2c -lm
-L/usr/lib/gcc-lib/i586-mandrake-linux/2.95.3
-L/usr/i586-mandrake-linux/lib -lm
R
At this point the install program became stuck. It had created
/tmp/R.INSTALL.xxxx/Hmisc OK, apparently, with a file
Hmisc.so in Hmisc/src that appears valid, and several .o files.
I would appreciate advice on how to best debug this.
Thanks -Frank
--
Frank E Harrell Jr Prof. of Biostatistics & Statistics
Div. of Biostatistics & Epidem. Dept. of Health Evaluation Sciences
U. Virginia School of Medicine http://hesweb1.med.virginia.edu/biostat
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On Sun, 3 Jun 2001 fharrell at virginia.edu wrote:> I am running Linux Mandrake 7.2 with the following: > > platform i586-pc-linux-gnu > arch i586 > os linux-gnu > system i586, linux-gnu > status > major 1 > minor 2.3 > year 2001 > month 04 > day 26 > language R > > To build a package I ran R CMD build Hmisc, apparently with success: > > * checking for file `Hmisc/DESCRIPTION' ... OK > * preparing `Hmisc': > * cleaning src > * checking whether `INDEX' is up-to-date ... NO > * use `--force' to overwrite the existing `INDEX' > * removing junk files > * building `Hmisc_1.0.tar.gz' > > The source directory had a single large R source file under RWith what extension? At that point in the install process we have if test -d R; then echo " R" mkdir -p ${lib}/${pkg}/R cat `ls R/*.[RSqrs] R/unix/*.[RSqrs] 2>/dev/null` \ > ${lib}/${pkg}/R/${pkg} fi This will get stuck if there is an R directory, but the files in it do not have extensions R S q r or s. See section 1.1.3 of `Writing R extensions' for the rules. That's a bug (getting stuck) fixed in R-devel and hence will be fixed in 1.3.0: from the CVS logs revision 1.61 date: 2001/05/03 07:18:41; author: ripley; state: Exp; lines: +6 -4 INSTALL failed if dir R was empty or had no suitable files As a more general comment, R CMD build is intended to be the last stage of the process, used after R CMD check (which checks that installation works). When developing a package I tend to INSTALL it several times and run a few tests each time, then use R CMD check --no-clean to refine it (not re-installing from scratch each time), and finally R CMD check then R CMD build. Brian -- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272860 (secr) Oxford OX1 3TG, UK Fax: +44 1865 272595 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or "[un]subscribe" (in the "body", not the subject !) To: r-help-request at stat.math.ethz.ch _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._