unix R CMD check problem

Tim Hoar

Mon, Jun 4, 2001 9:56 AM

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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