gfortran: Command not found

[Spencer Graves]

Hi, All:

      How do I get information about the "R CMD check / build / install"
process, especially regarding what software to install and how to
configure it under Windows XP?

      I ask, because "R CMD check" complained, "gfortran: Command not
found".  I found 'gfortran-sjlj.exe' in 'C:\Program
Files\R\Rtools\MinGW\bin', which is in the path.

      This was on a package that I built successfully in January under R
2.6.2.  Now with R 2.7.0, I can't get it to work.

      Thanks for your help.
      Spencer Graves
######################

Contents of "00install.out":

installing R.css in
D:/spencerg/statmtds/splines/DierckxSpline/DierckxSpline.Rcheck

---------- Making package DierckxSpline ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
gfortran   -O3  -c bispev.f -o bispev.o
make[3]: gfortran: Command not found
make[3]: *** [bispev.o] Error 127
make[2]: *** [srcDynlib] Error 2
make[1]: *** [all] Error 2
make: *** [pkg-DierckxSpline] Error 2
*** Installation of DierckxSpline failed ***

Removing
'D:/spencerg/statmtds/splines/DierckxSpline/DierckxSpline.Rcheck/DierckxSpline'

#############################################

sessionInfo():

R version 2.7.0 (2008-04-22)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    
 
#############################################

PATH =

C:\Program Files\R\Rtools\bin;C:\Program
Files\R\Rtools\perl\bin;C:\Program
Files\R\Rtools\MinGW\bin;c:\perl\bin\;c:\program
files\thinkpad\utilities;c:\windows\system32;c:\windows;c:\windows\system32\wbem;c:\program
files\intel\wireless\bin\;c:\program
files\hummingbird\connectivity\11.00\accessories\;c:\program
files\intel\wireless\bin\;c:\program files\ati
technologies\ati.ace\;c:\program files\r\r-2.7.0\bin;c:\program
files\miktex 2.5\miktex\bin;c:\program files\html help
workshop;c:\mingw\bin;C:\Program Files\MATLAB\R2007a\bin;C:\Program
Files\MATLAB\R2007a\bin\win32;c:\program
files\matlab\r2006b\bin;c:\program
files\matlab\r2006b\bin\win32;C:\Program Files\MATLAB\MATLAB Component
Runtime\v76\runtime\win32;C:\Program Files\Common
Files\Lenovo;C:\Program Files\Intel\Wireless\Bin\;C:\Program
Files\Intel\Wireless\Bin\

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[Duncan Murdoch-2]

On 05/05/2008 8:37 PM, Spencer Graves wrote:
> Hi, All:
>
>       How do I get information about the "R CMD check / build / install"
> process, especially regarding what software to install and how to
> configure it under Windows XP?

You can check the R-admin manual, which has a complete description, or
get the latest info is at www.murdoch-sutherland.com/Rtools.

>
>       I ask, because "R CMD check" complained, "gfortran: Command not
> found".  I found 'gfortran-sjlj.exe' in 'C:\Program
> Files\R\Rtools\MinGW\bin', which is in the path.
>
>       This was on a package that I built successfully in January under R
> 2.6.2.  Now with R 2.7.0, I can't get it to work.

You need to update your Rtools.  Version 2.7 or 2.8 should work for you.
  (They are almost the same right now, but 2.7 is frozen, and 2.8 will
evolve until R 2.8.0 is released in the fall.)

Duncan Murdoch

>
>       Thanks for your help.
>       Spencer Graves
> ######################
>
> Contents of "00install.out":
>
> installing R.css in
> D:/spencerg/statmtds/splines/DierckxSpline/DierckxSpline.Rcheck
>
> ---------- Making package DierckxSpline ------------
>   adding build stamp to DESCRIPTION
>   installing NAMESPACE file and metadata
>   making DLL ...
> gfortran   -O3  -c bispev.f -o bispev.o
> make[3]: gfortran: Command not found
> make[3]: *** [bispev.o] Error 127
> make[2]: *** [srcDynlib] Error 2
> make[1]: *** [all] Error 2
> make: *** [pkg-DierckxSpline] Error 2
> *** Installation of DierckxSpline failed ***
>
> Removing
> 'D:/spencerg/statmtds/splines/DierckxSpline/DierckxSpline.Rcheck/DierckxSpline'
>
> #############################################
>
> sessionInfo():
>
> R version 2.7.0 (2008-04-22)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base    
>  
> #############################################
>
> PATH =
>
> C:\Program Files\R\Rtools\bin;C:\Program
> Files\R\Rtools\perl\bin;C:\Program
> Files\R\Rtools\MinGW\bin;c:\perl\bin\;c:\program
> files\thinkpad\utilities;c:\windows\system32;c:\windows;c:\windows\system32\wbem;c:\program
> files\intel\wireless\bin\;c:\program
> files\hummingbird\connectivity\11.00\accessories\;c:\program
> files\intel\wireless\bin\;c:\program files\ati
> technologies\ati.ace\;c:\program files\r\r-2.7.0\bin;c:\program
> files\miktex 2.5\miktex\bin;c:\program files\html help
> workshop;c:\mingw\bin;C:\Program Files\MATLAB\R2007a\bin;C:\Program
> Files\MATLAB\R2007a\bin\win32;c:\program
> files\matlab\r2006b\bin;c:\program
> files\matlab\r2006b\bin\win32;C:\Program Files\MATLAB\MATLAB Component
> Runtime\v76\runtime\win32;C:\Program Files\Common
> Files\Lenovo;C:\Program Files\Intel\Wireless\Bin\;C:\Program
> Files\Intel\Wireless\Bin\
>
> ______________________________________________
> R-devel@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

______________________________________________
R-devel@... mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

[Prof Brian Ripley]

On Mon, 5 May 2008, Spencer Graves wrote:

> Hi, All:
>     How do I get information about the "R CMD check / build / install"
> process, especially regarding what software to install and how to configure
> it under Windows XP?

The 'R Installation and Adminstration' manual.

>     I ask, because "R CMD check" complained, "gfortran: Command not found".
> I found 'gfortran-sjlj.exe' in 'C:\Program Files\R\Rtools\MinGW\bin', which
> is in the path.

You need to update your Rtools.

>     This was on a package that I built successfully in January under R
> 2.6.2.  Now with R 2.7.0, I can't get it to work.
>     Thanks for your help.      Spencer Graves
> ######################
>
> Contents of "00install.out":
> installing R.css in
> D:/spencerg/statmtds/splines/DierckxSpline/DierckxSpline.Rcheck
>
> ---------- Making package DierckxSpline ------------
> adding build stamp to DESCRIPTION
> installing NAMESPACE file and metadata
> making DLL ...
> gfortran   -O3  -c bispev.f -o bispev.o
> make[3]: gfortran: Command not found
> make[3]: *** [bispev.o] Error 127
> make[2]: *** [srcDynlib] Error 2
> make[1]: *** [all] Error 2
> make: *** [pkg-DierckxSpline] Error 2
> *** Installation of DierckxSpline failed ***
>
> Removing
> 'D:/spencerg/statmtds/splines/DierckxSpline/DierckxSpline.Rcheck/DierckxSpline'
>
> #############################################
>
> sessionInfo():
> R version 2.7.0 (2008-04-22)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> #############################################
>
> PATH =
>
> C:\Program Files\R\Rtools\bin;C:\Program Files\R\Rtools\perl\bin;C:\Program
> Files\R\Rtools\MinGW\bin;c:\perl\bin\;c:\program
> files\thinkpad\utilities;c:\windows\system32;c:\windows;c:\windows\system32\wbem;c:\program
> files\intel\wireless\bin\;c:\program
> files\hummingbird\connectivity\11.00\accessories\;c:\program
> files\intel\wireless\bin\;c:\program files\ati
> technologies\ati.ace\;c:\program files\r\r-2.7.0\bin;c:\program files\miktex
> 2.5\miktex\bin;c:\program files\html help workshop;c:\mingw\bin;C:\Program
> Files\MATLAB\R2007a\bin;C:\Program Files\MATLAB\R2007a\bin\win32;c:\program
> files\matlab\r2006b\bin;c:\program files\matlab\r2006b\bin\win32;C:\Program
> Files\MATLAB\MATLAB Component Runtime\v76\runtime\win32;C:\Program
> Files\Common Files\Lenovo;C:\Program Files\Intel\Wireless\Bin\;C:\Program
> Files\Intel\Wireless\Bin\
>
> ______________________________________________
> R-devel@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

--
Brian D. Ripley,                  ripley@...
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  [phone] (self)
1 South Parks Road,                     [phone] (PA)
Oxford OX1 3TG, UK                Fax:  [phone]

______________________________________________
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[Spencer Graves]

Dear Professors Ripley and Murdoch:

      Thanks very much for the suggestion to upgrade my Rtools.  That
fixed the problem.

      Another question:  How do people typically debug problems linking
to legacy Fortran?  For example, is there a reasonable (open source)
debugger for gfortran?  In the DierckxSpline package, Sundar Dorai-Raj
and I link R to Fortran written by Paul Dierckx in 1979, last updated in
1987.  We've encountered segmentation errors killing R, which are
difficult to diagnose.

      Thanks again.
      Spencer Graves

Prof Brian Ripley wrote:

> On Mon, 5 May 2008, Spencer Graves wrote:
>
>> Hi, All:
>>     How do I get information about the "R CMD check / build /
>> install" process, especially regarding what software to install and
>> how to configure it under Windows XP?
>
> The 'R Installation and Adminstration' manual.
>
>>     I ask, because "R CMD check" complained, "gfortran: Command not
>> found". I found 'gfortran-sjlj.exe' in 'C:\Program
>> Files\R\Rtools\MinGW\bin', which is in the path.
>
> You need to update your Rtools.
>
>>     This was on a package that I built successfully in January under
>> R 2.6.2.  Now with R 2.7.0, I can't get it to work.
>>     Thanks for your help.      Spencer Graves
>> ######################
>>
>> Contents of "00install.out": installing R.css in
>> D:/spencerg/statmtds/splines/DierckxSpline/DierckxSpline.Rcheck
>>
>> ---------- Making package DierckxSpline ------------
>> adding build stamp to DESCRIPTION
>> installing NAMESPACE file and metadata
>> making DLL ...
>> gfortran   -O3  -c bispev.f -o bispev.o
>> make[3]: gfortran: Command not found
>> make[3]: *** [bispev.o] Error 127
>> make[2]: *** [srcDynlib] Error 2
>> make[1]: *** [all] Error 2
>> make: *** [pkg-DierckxSpline] Error 2
>> *** Installation of DierckxSpline failed ***
>>
>> Removing
>> 'D:/spencerg/statmtds/splines/DierckxSpline/DierckxSpline.Rcheck/DierckxSpline'
>>
>>
>> #############################################
>>
>> sessionInfo(): R version 2.7.0 (2008-04-22)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>> #############################################
>>
>> PATH =
>>
>> C:\Program Files\R\Rtools\bin;C:\Program
>> Files\R\Rtools\perl\bin;C:\Program
>> Files\R\Rtools\MinGW\bin;c:\perl\bin\;c:\program
>> files\thinkpad\utilities;c:\windows\system32;c:\windows;c:\windows\system32\wbem;c:\program
>> files\intel\wireless\bin\;c:\program
>> files\hummingbird\connectivity\11.00\accessories\;c:\program
>> files\intel\wireless\bin\;c:\program files\ati
>> technologies\ati.ace\;c:\program files\r\r-2.7.0\bin;c:\program
>> files\miktex 2.5\miktex\bin;c:\program files\html help
>> workshop;c:\mingw\bin;C:\Program Files\MATLAB\R2007a\bin;C:\Program
>> Files\MATLAB\R2007a\bin\win32;c:\program
>> files\matlab\r2006b\bin;c:\program
>> files\matlab\r2006b\bin\win32;C:\Program Files\MATLAB\MATLAB
>> Component Runtime\v76\runtime\win32;C:\Program Files\Common
>> Files\Lenovo;C:\Program Files\Intel\Wireless\Bin\;C:\Program
>> Files\Intel\Wireless\Bin\
>>
>> ______________________________________________
>> R-devel@... mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>

______________________________________________
R-devel@... mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

[Dirk Eddelbuettel]

On Sat, May 17, 2008 at 01:04:03PM -0700, Spencer Graves wrote:

> Dear Professors Ripley and Murdoch:
>
>      Thanks very much for the suggestion to upgrade my Rtools.  That
> fixed the problem.
>
>      Another question:  How do people typically debug problems linking
> to legacy Fortran?  For example, is there a reasonable (open source)
> debugger for gfortran?  In the DierckxSpline package, Sundar Dorai-Raj
> and I link R to Fortran written by Paul Dierckx in 1979, last updated in
> 1987.  We've encountered segmentation errors killing R, which are
> difficult to diagnose.

Look at valgrind, which is also documented in the R Extensions manual.

Dirk
> >>making DLL ...

--
Three out of two people have difficulties with fractions.

______________________________________________
R-devel@... mailing list
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[Spencer Graves]

Dear Dirk:

      Thanks very much.  It helps to rtfm -- and it helps even more to
know which fm2r.

      Best Wishes,
      Spencer

Dirk Eddelbuettel wrote:

> On Sat, May 17, 2008 at 01:04:03PM -0700, Spencer Graves wrote:
>  
>> Dear Professors Ripley and Murdoch:
>>
>>      Thanks very much for the suggestion to upgrade my Rtools.  That
>> fixed the problem.
>>
>>      Another question:  How do people typically debug problems linking
>> to legacy Fortran?  For example, is there a reasonable (open source)
>> debugger for gfortran?  In the DierckxSpline package, Sundar Dorai-Raj
>> and I link R to Fortran written by Paul Dierckx in 1979, last updated in
>> 1987.  We've encountered segmentation errors killing R, which are
>> difficult to diagnose.
>>    
>
> Look at valgrind, which is also documented in the R Extensions manual.
>
> Dirk
>  
>>>> making DLL ...
>>>>        
>
>

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R-devel@... mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

[Prof Brian Ripley]

On Sat, 17 May 2008, Spencer Graves wrote:

> Dear Professors Ripley and Murdoch:
>     Thanks very much for the suggestion to upgrade my Rtools.  That fixed
> the problem.
>     Another question:  How do people typically debug problems linking to
> legacy Fortran?  For example, is there a reasonable (open source) debugger
> for gfortran?

gdb, just as for C.

If you mean under Windows, then for a while gdb for MinGW was problematic
but latest builds seem to work with the current compilers.

> In the DierckxSpline package, Sundar Dorai-Raj and I link R to
> Fortran written by Paul Dierckx in 1979, last updated in 1987.  We've
> encountered segmentation errors killing R, which are difficult to diagnose.
>     Thanks again.
>     Spencer Graves
> Prof Brian Ripley wrote:
>> On Mon, 5 May 2008, Spencer Graves wrote:
>>
>>> Hi, All:
>>>     How do I get information about the "R CMD check / build / install"
>>> process, especially regarding what software to install and how to
>>> configure it under Windows XP?
>>
>> The 'R Installation and Adminstration' manual.
>>
>>>     I ask, because "R CMD check" complained, "gfortran: Command not
>>> found". I found 'gfortran-sjlj.exe' in 'C:\Program
>>> Files\R\Rtools\MinGW\bin', which is in the path.
>>
>> You need to update your Rtools.
>>
>>>     This was on a package that I built successfully in January under R
>>> 2.6.2.  Now with R 2.7.0, I can't get it to work.
>>>     Thanks for your help.      Spencer Graves
>>> ######################
>>>
>>> Contents of "00install.out": installing R.css in
>>> D:/spencerg/statmtds/splines/DierckxSpline/DierckxSpline.Rcheck
>>>
>>> ---------- Making package DierckxSpline ------------
>>> adding build stamp to DESCRIPTION
>>> installing NAMESPACE file and metadata
>>> making DLL ...
>>> gfortran   -O3  -c bispev.f -o bispev.o
>>> make[3]: gfortran: Command not found
>>> make[3]: *** [bispev.o] Error 127
>>> make[2]: *** [srcDynlib] Error 2
>>> make[1]: *** [all] Error 2
>>> make: *** [pkg-DierckxSpline] Error 2
>>> *** Installation of DierckxSpline failed ***
>>>
>>> Removing
>>> 'D:/spencerg/statmtds/splines/DierckxSpline/DierckxSpline.Rcheck/DierckxSpline'
>>>
>>> #############################################
>>>
>>> sessionInfo(): R version 2.7.0 (2008-04-22)
>>> i386-pc-mingw32
>>>
>>> locale:
>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>>> States.1252;LC_MONETARY=English_United
>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>> #############################################
>>>
>>> PATH =
>>>
>>> C:\Program Files\R\Rtools\bin;C:\Program
>>> Files\R\Rtools\perl\bin;C:\Program
>>> Files\R\Rtools\MinGW\bin;c:\perl\bin\;c:\program
>>> files\thinkpad\utilities;c:\windows\system32;c:\windows;c:\windows\system32\wbem;c:\program
>>> files\intel\wireless\bin\;c:\program
>>> files\hummingbird\connectivity\11.00\accessories\;c:\program
>>> files\intel\wireless\bin\;c:\program files\ati
>>> technologies\ati.ace\;c:\program files\r\r-2.7.0\bin;c:\program
>>> files\miktex 2.5\miktex\bin;c:\program files\html help
>>> workshop;c:\mingw\bin;C:\Program Files\MATLAB\R2007a\bin;C:\Program
>>> Files\MATLAB\R2007a\bin\win32;c:\program
>>> files\matlab\r2006b\bin;c:\program
>>> files\matlab\r2006b\bin\win32;C:\Program Files\MATLAB\MATLAB Component
>>> Runtime\v76\runtime\win32;C:\Program Files\Common Files\Lenovo;C:\Program
>>> Files\Intel\Wireless\Bin\;C:\Program Files\Intel\Wireless\Bin\
>>>
>>> ______________________________________________
>>> R-devel@... mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>>
>

--
Brian D. Ripley,                  ripley@...
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  [phone] (self)
1 South Parks Road,                     [phone] (PA)
Oxford OX1 3TG, UK                Fax:  [phone]

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