From therneau at mayo.edu  Thu Apr  6 15:51:31 2017
From: therneau at mayo.edu (Therneau, Terry M., Ph.D.)
Date: Thu, 06 Apr 2017 08:51:31 -0500
Subject: [Rd] failure of make check-all
In-Reply-To: <E86596A7-C098-411A-AB0B-2A37EF64D9BF@gmail.com>
References: <47cabe$662clt@ironport10.mayo.edu>
 <E86596A7-C098-411A-AB0B-2A37EF64D9BF@gmail.com>
Message-ID: <47cabe$6636cc@ironport10.mayo.edu>

Peter,
   Retry how much of it?  That is, where does it go in the sequence from svn up to make 
check?  I'll update my notes so as to do it correctly.

In any case, I put it first and reran the whole command chain.  I had recently upgraded 
linux from 14.xx LTS to 16.04 LTS so it makes sense to start over.  This removed the large 
diff in base-Ex.Rout from the first part of the log, but the terminal error still remains:

make[3]: Leaving directory '/usr/local/src/R-devel/tests'
make[3]: Entering directory '/usr/local/src/R-devel/tests'
running code in 'reg-tests-3.R' ... OK
   comparing 'reg-tests-3.Rout' to './reg-tests-3.Rout.save' ... OK
running code in 'reg-examples3.R' ...Makefile.common:98: recipe for target 
'reg-examples3.Rout' failed
make[3]: *** [reg-examples3.Rout] Error 1
make[3]: Leaving directory '/usr/local/src/R-devel/tests'
Makefile.common:273: recipe for target 'test-Reg' failed

Here are lines 97-100 of tests/Makefile.common:

.R.Rout:
     @rm -f $@ $@.fail $@.log
     @$(ECHO) $(ECHO_N) "running code in '$<' ...$(ECHO_C)" > $@.log
     @$(R) < $< > $@.fail 2>&1 || (cat $@.log && rm $@.log && exit 1)


There is one complier warning message, it prints in pink so as not to miss it!

main.c: In function ?dummy_ii?:
main.c:1669:12: warning: function returns address of local variable [-Wreturn-local-addr]
      return (uintptr_t) &ii;

-------------

So as to be more complete I did "cd tests; R" and source("reg-examples3.R"), and lo and 
behold the error is

> source('reg-examples3.R')
Loading required package: MASS
Loading required package: survival
Error in fitter(X, Y, strats, offset, init, control, weights = weights,  :
   object 'Ccoxmart2' not found

Looking at src/coxmart2.c and src/init.c I don't see anything different than the other 
dozen .C routines in my survival package.  The file tests/book7.R in the package exercises 
this routine, and CMD check passes.

Hints?

Terry T.






On 04/06/2017 07:52 AM, peter dalgaard wrote:
> You may want to retry that after a make distclean, in case anything changed in the toolchain.
>
> -pd
>



[Rd] failure of make check-all
Therneau, Terry M., Ph.D.