[R] Re: unix R CMD check problem
Tim Hoar
thoar at cgd.ucar.edu
Mon Jun 4 18:56:35 CEST 2001
Doh!
turns out I was using a newer feature of S-PLUS that is not supported in R,
or at least was generating the parse error.
replace all
a = b
with
a <- b
(except in arguments, naturally ...)
Sorry to bother anyone ... smooth sailing ahead.
> Date: Mon, 4 Jun 2001 10:03:56 -0600 (MDT)
> From: Tim Hoar <thoar at cgd.ucar.edu>
> Reply-To: Tim Hoar <thoar at ucar.edu>
> To: r-help at lists.R-project.org
> Subject: unix R CMD check problem
>
> I am just getting familiar with R and am running into a problem.
>
> I have several S functions I would like to port to R and _almost_ have
> it. I am running on Solaris 5.6 Generic_105181-17 sun4u sparc SUNW,Ultra-60
> with the Sun performance compilers (which are not the problem):
>
> I am starting out small and am having problems with "undocumented objects"
> in the following code structure (I am including the structure first, then
> the result of "R CMD check"):
>
> 0[218]0 nightingale:~/Snackbar > ls -R
> .:
> DESCRIPTION R man src
>
> ./R:
> unix
>
> ./R/unix:
> direct.read.R flat.read.R getncvar.R zzz.R
> direct.write.R flat.write.R strpos.R
>
> ./man:
> direct.read.Rd flat.read.Rd getncvar.Rd
> direct.write.Rd flat.write.Rd strpos.Rd
>
> ./src:
> Makevars dflatread.f flatread.f iflatread.f strpos.f
> Snackbar.so dflatwrite.f flatwrite.f iflatwrite.f
> ddirectread.f directread.f idirectread.f inpoly.f
> ddirectwrite.f directwrite.f idirectwrite.f ncgetvar.f
> 0[224]0 nightingale:~/Snackbar >
>
> The R code has logical sections to call several of the Fortran sources.
> Each Fortran source has exactly one routine.
>
> ------------ results of R CMD check ----------------------
>
> 1[204]0 nightingale:~ > R CMD check Snackbar
> * checking for working latex ... OK
> * using log directory /home/thoar/Snackbar.Rcheck
>
> Installing source package `Snackbar' ...
> libs
> /opt/SUNWspro/bin/f90 -O3 -I/opt/local/include -PIC -O3 -c ddirectread.f -o
> ddirectread.o
> /opt/SUNWspro/bin/f90 -O3 -I/opt/local/include -PIC -O3 -c ddirectwrite.f -o
> ddirectwrite.o
> /opt/SUNWspro/bin/f90 -O3 -I/opt/local/include -PIC -O3 -c dflatread.f -o
> dflatread.o
> /opt/SUNWspro/bin/f90 -O3 -I/opt/local/include -PIC -O3 -c dflatwrite.f -o
> dflatwrite.o
> /opt/SUNWspro/bin/f90 -O3 -I/opt/local/include -PIC -O3 -c directread.f -o
> directread.o
> /opt/SUNWspro/bin/f90 -O3 -I/opt/local/include -PIC -O3 -c directwrite.f -o
> directwrite.o
> /opt/SUNWspro/bin/f90 -O3 -I/opt/local/include -PIC -O3 -c flatread.f -o
> flatread.o
> /opt/SUNWspro/bin/f90 -O3 -I/opt/local/include -PIC -O3 -c flatwrite.f -o
> flatwrite.o
> /opt/SUNWspro/bin/f90 -O3 -I/opt/local/include -PIC -O3 -c idirectread.f -o
> idirectread.o
> /opt/SUNWspro/bin/f90 -O3 -I/opt/local/include -PIC -O3 -c idirectwrite.f -o
> idirectwrite.o
> /opt/SUNWspro/bin/f90 -O3 -I/opt/local/include -PIC -O3 -c iflatread.f -o
> iflatread.o
> /opt/SUNWspro/bin/f90 -O3 -I/opt/local/include -PIC -O3 -c iflatwrite.f -o
> iflatwrite.o
> /opt/SUNWspro/bin/f90 -O3 -I/opt/local/include -PIC -O3 -c inpoly.f -o
> inpoly.o
> /opt/SUNWspro/bin/f90 -O3 -I/opt/local/include -PIC -O3 -c ncgetvar.f -o
> ncgetvar.o
> /opt/SUNWspro/bin/f90 -O3 -I/opt/local/include -PIC -O3 -c strpos.f -o
> strpos.o
> /opt/SUNWspro/bin/cc -G -o Snackbar.so ddirectread.o ddirectwrite.o
> dflatread.o dflatwrite.o directread.o directwrite.o flatread.o flatwrite.o
> idirectread.o idirectwrite.o iflatread.o iflatwrite.o inpoly.o ncgetvar.o
> strpos.o -L/usr/local/lib -L/opt/local/lib -lnetcdf -R/opt/SUNWspro/lib
> -L/opt/SUNWspro/lib -L/opt/SUNWspro/WS6U1/lib -L/usr/ccs/lib -L/usr/lib -lfui
> -lfai -lfai2 -lfsumai -lfprodai -lfminlai -lfmaxlai -lfminvai -lfmaxvai -lfsu
> -lsunmath -lm
> R
> help
> >>> Building/Updating help pages for package `Snackbar'
> Formats: text html latex example
> direct.read text html latex
> direct.write text html latex
> flat.read text html latex
> flat.write text html latex
> getncvar text html latex
> strpos text html latex
> DONE (Snackbar)
>
> DONE (INSTALL)
>
> * checking for file `Snackbar/DESCRIPTION' ... OK
> * checking package directory ... OK
> * checking DESCRIPTION Package field ... OK
> * checking DESCRIPTION Version field ... OK
> * checking DESCRIPTION Title field ... OK
> * checking DESCRIPTION License field ... OK
> * checking DESCRIPTION Author field ... OK
> * checking DESCRIPTION Maintainer field ... OK
> * checking Rd files ... OK
> * checking for undocumented objects ... ERROR
> * in parse(file, n, text, prompt) : syntax error on line 28
>
> ------------ question ----------------------
>
> Looks like the help files are OK ... and the compiles are OK ...
> but something somewhere is going astray. Any help?
>
> I have included a TAR file of the pertinent parts ... just in case someone
> wants to see _exactly_ ...
>
> Any help would be appreciated.
>
> Tim
>
>
>
> ## Tim Hoar, Associate Scientist email: thoar at ucar.edu ##
> ## Geophysical Statistics Project phone: 303-497-1708 ##
> ## National Center for Atmospheric Research FAX : 303-497-1333 ##
> ## Boulder, CO 80307 http://www.cgd.ucar.edu/~thoar ##
>
## Tim Hoar, Associate Scientist email: thoar at ucar.edu ##
## Geophysical Statistics Project phone: 303-497-1708 ##
## National Center for Atmospheric Research FAX : 303-497-1333 ##
## Boulder, CO 80307 http://www.cgd.ucar.edu/~thoar ##
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