[Rd] Rcmd SHLIB error

Gabor Grothendieck ggrothendieck at gmail.com
Sun Dec 19 16:04:02 CET 2010

On Sun, Dec 19, 2010 at 9:07 AM, Duncan Murdoch
<murdoch.duncan at gmail.com> wrote:
> On 19/12/2010 7:01 AM, Gabor Grothendieck wrote:
>> On Sun, Dec 19, 2010 at 6:39 AM, Duncan Murdoch
>> <murdoch.duncan at gmail.com>  wrote:
>>> On 19/12/2010 6:06 AM, Gabor Grothendieck wrote:
>>>> On Sat, Dec 18, 2010 at 8:23 PM, Dominick Samperi<djsamperi at gmail.com>
>>>>  wrote:
>>>>> On Sat, Dec 18, 2010 at 5:24 PM, Gabor Grothendieck
>>>>> <ggrothendieck at gmail.com>    wrote:
>>>>>> I am getting this error message when I try to run Rcmd SHLIB myprog.c.
>>>>>>  There appears to be a missing / between etc and i386 in the path.  I
>>>>>> am on Windows Vista and am using R version 2.12.1 Patched (2010-12-16
>>>>>> r53864) and just downloaded Rtools 2.12 today.   Is this a bug in R?
>>>>>> How can I resolve this?
>>>>> This is due to new behavior in CYGWIN (the basis for Rtools). The
>>>>> new CYGWIN does not like non-standard paths that have C: in them.
>>>>> Some CYGWIN programs will not work when fed file names using
>>>>> this syntax, but normally this is just a warning. The warning can be
>>>>> suppressed by using the Control Panel to set CYGWIN=nodosfilewarning.
>>>>> Another solution is to use POSIX equivalent paths of the form
>>>>> /cydrive/c/PROG..., but this would require more extensive changes
>>>>> to build scripts, etc.
>>>>> There is another change that causes Rtools tar to choke in some
>>>>> circumstances under Windows because it tries to change ownership
>>>>> of the files extracted when it shouldn't. These error
>>>>> messags can be suppressed by using the Control Panel to set
>>>>> TAR_OPTIONS=--no-same-owner.
>>>> I am still wondering what to do about this?  I have created a
>>>> directory called C:\PROGRA~1\R\R-212~1.X\etci386 and have copied
>>>> Makeconf into it.  That lets me use Rcmd SHLIB but its quite an ugly
>>>> workaround and there must be some better resolution than that.  Also I
>>>> am wondering if this same problem will crop up elsewhere.
>>> You could try running within Cygwin, as I do, on the theory that what
>>> works
>>> for me might work for you.  I do use the "nodosfilewarning" setting as
>>> Dominick mentioned.
>>> However, I will say that my Windows build system is much less reliable
>>> than
>>> it used to be.  I don't know the cause:  I started 64 bit builds on
>>> Windows
>>> 7 at around the same time as I upgraded Cygwin, so it could be any of
>>> those
>>> causes.  I'm tending to believe it's a Cygwin problem or a Cygwin-Win7
>>> incompatibility, but I haven't had time to work out a reliable system.
>>>  (Symptoms I see are that very few overnight builds are succeeding;
>>> almost
>>> all the ones you see on CRAN/bin/windows/base have required manual
>>> restarts
>>> after they've failed partway through.)
>>> Unfortunately, I am not going to have the time to diagnose or fix this in
>>> the next couple of months.  If you have spare time, you might want to try
>>> older versions of the Rtools (perhaps mixing new compilers with old
>>> Rtools/bin and Cygwin DLLs).
>>> Duncan Murdoch
>> Where in the sources is the C:\PROGRA~1\R\R-212~1.X\etci386 [sic] path
>> set?
> I don't know.  Possibilities include src/gnuwin32/fixed/Makefile line 31
> (where a bad R_ARCH would do it).  Do you have R_ARCH set as an environment
> variable or on the command line when you call make? I think the latter would
> override the setting in MkRules, I'm not sure about the former.

Thanks.  I now have a better workaround.  The batch file shown below
works but if /i386 is changed to i386 then it fails because it looks
for a directory called etci386:

  set R_ARCH=/i386
  "C:\Program Files\R\R-2.12.x\bin\i386\Rcmd.exe" SHLIB myprog.c

1. It seems the / is missing between etc and $(R_ARCH) on lines 31 and
38 of that Makefile (or if etci386 is intended then the actual
structure of R that is installed is wrong).
2. page 8 of R-admin manual says that there is an --arch argument with
values i386, 32, x64, 64 but neither "Rcmd --help" nor "Rcmd SHLIB
--help" document an argument for setting the architecture.
3. on page 12 of the R-ext manual it refers to
R_HOME/etcR_ARCH/Makeconf so the documentation and how the Makefile
works seems inconsistent with the actual R directory structure which
is etc/i386 and not etci386.

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email: ggrothendieck at gmail.com

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