build packages with vignettes in Windows

[Michael-240]

I've been trying to build a Windows binary of a package of mine without
success.  It seems that the files under inst/doc throw the script off.

I am using the command 'Rcmd INSTALL --build'.

---------- Making package genepi ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  installing inst files
FIND: Parameter format not correct
make[2]: *** [C:/Library/R/genepi/inst] Error 2
make[1]: *** [all] Error 2
make: *** [pkg-genepi] Error 2
*** Installation of genepi failed ***

I also tried a couple of packages downloaded from CRAN.  Those without
inst/doc directory worked fine and those who do have it didn't.

I'm using a fresh install of R-2.7.0 and Rtools-2.7.

Any clue of what was wrong with my setup?

Thanks,

Michael

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[Prof Brian Ripley]

On Tue, 29 Apr 2008, Michael wrote:

>
> I've been trying to build a Windows binary of a package of mine without
> success.  It seems that the files under inst/doc throw the script off.
>
> I am using the command 'Rcmd INSTALL --build'.
>
> ---------- Making package genepi ------------
>  adding build stamp to DESCRIPTION
>  installing NAMESPACE file and metadata
>  installing R files
>  installing inst files
> FIND: Parameter format not correct
> make[2]: *** [C:/Library/R/genepi/inst] Error 2
> make[1]: *** [all] Error 2
> make: *** [pkg-genepi] Error 2
> *** Installation of genepi failed ***
>
> I also tried a couple of packages downloaded from CRAN.  Those without
> inst/doc directory worked fine and those who do have it didn't.
>
> I'm using a fresh install of R-2.7.0 and Rtools-2.7.
>
> Any clue of what was wrong with my setup?

Your path is incorrect -- as 'R Installation and Administration' does warn
you.

>
> Thanks,
>
> Michael
>
> ______________________________________________
> 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)
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[Duncan Murdoch-2]

On 29/04/2008 12:54 PM, Michael wrote:

> I've been trying to build a Windows binary of a package of mine without
> success.  It seems that the files under inst/doc throw the script off.
>
> I am using the command 'Rcmd INSTALL --build'.
>
> ---------- Making package genepi ------------
>   adding build stamp to DESCRIPTION
>   installing NAMESPACE file and metadata
>   installing R files
>   installing inst files
> FIND: Parameter format not correct

That looks as though you don't have the tools installed correctly, you
have some other "find" earlier on your path.

Duncan Murdoch

> make[2]: *** [C:/Library/R/genepi/inst] Error 2
> make[1]: *** [all] Error 2
> make: *** [pkg-genepi] Error 2
> *** Installation of genepi failed ***
>
> I also tried a couple of packages downloaded from CRAN.  Those without
> inst/doc directory worked fine and those who do have it didn't.
>
> I'm using a fresh install of R-2.7.0 and Rtools-2.7.
>
> Any clue of what was wrong with my setup?
>
> Thanks,
>
> Michael
>
> ______________________________________________
> R-devel@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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[Gabor Grothendieck]

The use of the UNIX find command on Windows makes installation
very troublesome and fragile.   I wonder if you could include a
find2 or somesuch with the tools and change the scripts to use that
getting rid of find or use just use the Windows find command in the
scripts.  Or some other solution so that one does not have to have
a non-Windows find on the PATH.

If you don't have the find in Rtools first in your path then you have
problems like the one below and if you do have it first then it throws
off the scripts from other software.

On Tue, Apr 29, 2008 at 2:29 PM, Duncan Murdoch <murdoch@...> wrote:

> On 29/04/2008 12:54 PM, Michael wrote:
> > I've been trying to build a Windows binary of a package of mine without
> > success.  It seems that the files under inst/doc throw the script off.
> >
> > I am using the command 'Rcmd INSTALL --build'.
> >
> > ---------- Making package genepi ------------
> >  adding build stamp to DESCRIPTION
> >  installing NAMESPACE file and metadata
> >  installing R files
> >  installing inst files
> > FIND: Parameter format not correct
> >
>
> That looks as though you don't have the tools installed correctly, you have
> some other "find" earlier on your path.
>
> Duncan Murdoch
>
>
>
> > make[2]: *** [C:/Library/R/genepi/inst] Error 2
> > make[1]: *** [all] Error 2
> > make: *** [pkg-genepi] Error 2
> > *** Installation of genepi failed ***
> >
> > I also tried a couple of packages downloaded from CRAN.  Those without
> > inst/doc directory worked fine and those who do have it didn't.
> >
> > I'm using a fresh install of R-2.7.0 and Rtools-2.7.
> > Any clue of what was wrong with my setup?
> >
> > Thanks,
> >
> > Michael
> >
> > ______________________________________________
> > R-devel@... mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
>
> ______________________________________________
> R-devel@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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[Duncan Murdoch-2]

On 29/04/2008 2:51 PM, Gabor Grothendieck wrote:
> The use of the UNIX find command on Windows makes installation
> very troublesome and fragile.   I wonder if you could include a
> find2 or somesuch with the tools and change the scripts to use that
> getting rid of find or use just use the Windows find command in the
> scripts.  Or some other solution so that one does not have to have
> a non-Windows find on the PATH.

Find isn't unique:  there are lots of versions of make, and grep, and
tar that don't work, either.  We've adopted a simple solution, and it
works:  when you're using the R tools, put them first on the path.

We've thought about including the R tools with R, which would increase
the size of the distribution quite a bit. Then Rcmd.exe could do the
path modifications, and you wouldn't need to worry about doing it
yourself.  That might still happen for 2.8.0.

Duncan Murdoch

>
> If you don't have the find in Rtools first in your path then you have
> problems like the one below and if you do have it first then it throws
> off the scripts from other software.
>
> On Tue, Apr 29, 2008 at 2:29 PM, Duncan Murdoch <murdoch@...> wrote:
>> On 29/04/2008 12:54 PM, Michael wrote:
>>> I've been trying to build a Windows binary of a package of mine without
>>> success.  It seems that the files under inst/doc throw the script off.
>>>
>>> I am using the command 'Rcmd INSTALL --build'.
>>>
>>> ---------- Making package genepi ------------
>>>  adding build stamp to DESCRIPTION
>>>  installing NAMESPACE file and metadata
>>>  installing R files
>>>  installing inst files
>>> FIND: Parameter format not correct
>>>
>> That looks as though you don't have the tools installed correctly, you have
>> some other "find" earlier on your path.
>>
>> Duncan Murdoch
>>
>>
>>
>>> make[2]: *** [C:/Library/R/genepi/inst] Error 2
>>> make[1]: *** [all] Error 2
>>> make: *** [pkg-genepi] Error 2
>>> *** Installation of genepi failed ***
>>>
>>> I also tried a couple of packages downloaded from CRAN.  Those without
>>> inst/doc directory worked fine and those who do have it didn't.
>>>
>>> I'm using a fresh install of R-2.7.0 and Rtools-2.7.
>>> Any clue of what was wrong with my setup?
>>>
>>> Thanks,
>>>
>>> Michael
>>>
>>> ______________________________________________
>>> R-devel@... mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>>
>> ______________________________________________
>> R-devel@... mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>
> ______________________________________________
> R-devel@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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[Michael-240]

On 29 Apr 2008, Duncan Murdoch wrote:

> On 29/04/2008 12:54 PM, Michael wrote:
> > I've been trying to build a Windows binary of a package of mine without
> > success.  It seems that the files under inst/doc throw the script off.
> >

> > I am using the command 'Rcmd INSTALL --build'.
> >
> > ---------- Making package genepi ------------
> >   adding build stamp to DESCRIPTION
> >   installing NAMESPACE file and metadata
> >   installing R files
> >   installing inst files
> > FIND: Parameter format not correct

> That looks as though you don't have the tools installed correctly, you have
> some other "find" earlier on your path.

Thanks, I didn't let the Rtools Installer to update the PATH variable for me
because it says 'restart is required' which I didn't want to do, since I can
update the environment variable without rebooting Windows.

Michael

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[Duncan Murdoch-2]

On 29/04/2008 4:26 PM, Michael wrote:

> On 29 Apr 2008, Duncan Murdoch wrote:
>
>> On 29/04/2008 12:54 PM, Michael wrote:
>>> I've been trying to build a Windows binary of a package of mine without
>>> success.  It seems that the files under inst/doc throw the script off.
>>>
>
>>> I am using the command 'Rcmd INSTALL --build'.
>>>
>>> ---------- Making package genepi ------------
>>>   adding build stamp to DESCRIPTION
>>>   installing NAMESPACE file and metadata
>>>   installing R files
>>>   installing inst files
>>> FIND: Parameter format not correct
>
>> That looks as though you don't have the tools installed correctly, you have
>> some other "find" earlier on your path.
>
> Thanks, I didn't let the Rtools Installer to update the PATH variable for me
> because it says 'restart is required' which I didn't want to do, since I can
> update the environment variable without rebooting Windows.

Right, you don't need to set the system path for everything, but you do
need to set it in CMD (or other shell) before running Rcmd.

Duncan Murdoch

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[Gabor Grothendieck]

On Tue, Apr 29, 2008 at 4:00 PM, Duncan Murdoch <murdoch@...> wrote:

> On 29/04/2008 2:51 PM, Gabor Grothendieck wrote:
> > The use of the UNIX find command on Windows makes installation
> > very troublesome and fragile.   I wonder if you could include a
> > find2 or somesuch with the tools and change the scripts to use that
> > getting rid of find or use just use the Windows find command in the
> > scripts.  Or some other solution so that one does not have to have
> > a non-Windows find on the PATH.
> >
>
> Find isn't unique:  there are lots of versions of make, and grep, and tar
> that don't work, either.  We've adopted a simple solution, and it works:

It only works if you are very careful and actually it doesn't work because
it does not preserve Windows functionality for other programs.

> when you're using the R tools, put them first on the path.

That's not comparable because find comes with Windows whereas
those other programs you mention are addons.

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[Michael-240]

On 29 Apr 2008, Duncan Murdoch wrote:
 
> Right, you don't need to set the system path for everything, but you do
> need to set it in CMD (or other shell) before running Rcmd.

For Win 2K/XP/Vista, the system path can be set (through the GUI interface,
not sure how to do it with scripts) without restarting, for new CMD
processes started afterwards.

Michael

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[Gabor Grothendieck]

You can use the Windows batch PATH command.

On Wed, Apr 30, 2008 at 11:56 AM, Michael <wuolong@...> wrote:

> On 29 Apr 2008, Duncan Murdoch wrote:
>
> > Right, you don't need to set the system path for everything, but you do
> > need to set it in CMD (or other shell) before running Rcmd.
>
> For Win 2K/XP/Vista, the system path can be set (through the GUI interface,
> not sure how to do it with scripts) without restarting, for new CMD
> processes started afterwards.
>
> Michael
>
>
> ______________________________________________
> R-devel@... mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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[Duncan Murdoch-2]

On 4/30/2008 11:56 AM, Michael wrote:
> On 29 Apr 2008, Duncan Murdoch wrote:
>  
>> Right, you don't need to set the system path for everything, but you do
>> need to set it in CMD (or other shell) before running Rcmd.
>
> For Win 2K/XP/Vista, the system path can be set (through the GUI interface,
> not sure how to do it with scripts) without restarting, for new CMD
> processes started afterwards.

Sure, but the installer doesn't know how to do that.  It just sets the
path in the registry; it doesn't know how to give Explorer a kick to get
it to reload from there.  As far as I know there's no documented way to
do that.

Within a shell it's very easy to set the path, but it doesn't propagate
to processes started outside that shell.

Duncan Murdoch

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[Simon Urbanek]

On Apr 30, 2008, at 2:31 PM, Duncan Murdoch wrote:

> On 4/30/2008 11:56 AM, Michael wrote:
>> On 29 Apr 2008, Duncan Murdoch wrote:
>>
>>> Right, you don't need to set the system path for everything, but  
>>> you do
>>> need to set it in CMD (or other shell) before running Rcmd.
>> For Win 2K/XP/Vista, the system path can be set (through the GUI  
>> interface,
>> not sure how to do it with scripts) without restarting, for new CMD
>> processes started afterwards.
>
> Sure, but the installer doesn't know how to do that.  It just sets  
> the path in the registry; it doesn't know how to give Explorer a  
> kick to get it to reload from there.  As far as I know there's no  
> documented way to do that.
>

FWIW the PATH setting is effective immediately (at least on 2k/
XP ...). Any new shell you start (e.g. using Run..) will have the  
updated PATH already.

I was always very skeptical as editing PATH in the installer is  
concerned (and I have always declined any automated changes), but I  
really love the feature that allows me to edit the whole PATH  
interactively in an editor-like window.

Also note that the rebooting is optional, you can still safely decline  
it so I see no reason why that should deter anyone.

Cheers,
Simon

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[Duncan Murdoch-2]

On 4/30/2008 4:01 PM, Simon Urbanek wrote:

> On Apr 30, 2008, at 2:31 PM, Duncan Murdoch wrote:
>
>> On 4/30/2008 11:56 AM, Michael wrote:
>>> On 29 Apr 2008, Duncan Murdoch wrote:
>>>
>>>> Right, you don't need to set the system path for everything, but  
>>>> you do
>>>> need to set it in CMD (or other shell) before running Rcmd.
>>> For Win 2K/XP/Vista, the system path can be set (through the GUI  
>>> interface,
>>> not sure how to do it with scripts) without restarting, for new CMD
>>> processes started afterwards.
>>
>> Sure, but the installer doesn't know how to do that.  It just sets  
>> the path in the registry; it doesn't know how to give Explorer a  
>> kick to get it to reload from there.  As far as I know there's no  
>> documented way to do that.
>>
>
> FWIW the PATH setting is effective immediately (at least on 2k/
> XP ...). Any new shell you start (e.g. using Run..) will have the  
> updated PATH already.

Does that happen with the Rtools installer?  I didn't know that.  I
thought explorer only changes the PATH at startup, or when you edit it
from the control panel.

Duncan

> I was always very skeptical as editing PATH in the installer is  
> concerned (and I have always declined any automated changes), but I  
> really love the feature that allows me to edit the whole PATH  
> interactively in an editor-like window.
>
> Also note that the rebooting is optional, you can still safely decline  
> it so I see no reason why that should deter anyone.
>
> Cheers,
> Simon

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[Simon Urbanek]

On Apr 30, 2008, at 4:29 PM, Duncan Murdoch wrote:

> On 4/30/2008 4:01 PM, Simon Urbanek wrote:
>> On Apr 30, 2008, at 2:31 PM, Duncan Murdoch wrote:
>>> On 4/30/2008 11:56 AM, Michael wrote:
>>>> On 29 Apr 2008, Duncan Murdoch wrote:
>>>>
>>>>> Right, you don't need to set the system path for everything,  
>>>>> but  you do
>>>>> need to set it in CMD (or other shell) before running Rcmd.
>>>> For Win 2K/XP/Vista, the system path can be set (through the GUI  
>>>> interface,
>>>> not sure how to do it with scripts) without restarting, for new CMD
>>>> processes started afterwards.
>>>
>>> Sure, but the installer doesn't know how to do that.  It just  
>>> sets  the path in the registry; it doesn't know how to give  
>>> Explorer a  kick to get it to reload from there.  As far as I know  
>>> there's no  documented way to do that.
>>>
>> FWIW the PATH setting is effective immediately (at least on 2k/  
>> XP ...). Any new shell you start (e.g. using Run..) will have the  
>> updated PATH already.
>
> Does that happen with the Rtools installer?  I didn't know that.  I  
> thought explorer only changes the PATH at startup, or when you edit  
> it from the control panel.
>

Hmm I thought it did, but a subsequent test shows it doesn't.  
Apparently I must have triggered a change in the Control Panel so PATH  
was updated even before reboot.

Anyway, there are free tools with source that show how to send a  
broadcast message to make that change active immediately, e.g.:
http://www.codeproject.com/KB/applications/SetEnv.aspx?fid=230498&df=90&mpp=25&noise=3&sort=Position&view=Quick&select=1531752&fr=48

BTW: By testing this I found out that the Rtools installer is not as  
smart as it could be - when you run it a second time it will duplicate  
the paths.

Cheers,
Simon

>
>> I was always very skeptical as editing PATH in the installer is  
>> concerned (and I have always declined any automated changes), but  
>> I  really love the feature that allows me to edit the whole PATH  
>> interactively in an editor-like window.
>> Also note that the rebooting is optional, you can still safely  
>> decline  it so I see no reason why that should deter anyone.
>> Cheers,
>> Simon
>
>

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[Duncan Murdoch-2]

On 4/30/2008 5:02 PM, Simon Urbanek wrote:

> On Apr 30, 2008, at 4:29 PM, Duncan Murdoch wrote:
>> On 4/30/2008 4:01 PM, Simon Urbanek wrote:
>>> On Apr 30, 2008, at 2:31 PM, Duncan Murdoch wrote:
>>>> On 4/30/2008 11:56 AM, Michael wrote:
>>>>> On 29 Apr 2008, Duncan Murdoch wrote:
>>>>>
>>>>>> Right, you don't need to set the system path for everything,  
>>>>>> but  you do
>>>>>> need to set it in CMD (or other shell) before running Rcmd.
>>>>> For Win 2K/XP/Vista, the system path can be set (through the GUI  
>>>>> interface,
>>>>> not sure how to do it with scripts) without restarting, for new CMD
>>>>> processes started afterwards.
>>>>
>>>> Sure, but the installer doesn't know how to do that.  It just  
>>>> sets  the path in the registry; it doesn't know how to give  
>>>> Explorer a  kick to get it to reload from there.  As far as I know  
>>>> there's no  documented way to do that.
>>>>
>>> FWIW the PATH setting is effective immediately (at least on 2k/  
>>> XP ...). Any new shell you start (e.g. using Run..) will have the  
>>> updated PATH already.
>>
>> Does that happen with the Rtools installer?  I didn't know that.  I  
>> thought explorer only changes the PATH at startup, or when you edit  
>> it from the control panel.
>>
>
>
> Hmm I thought it did, but a subsequent test shows it doesn't.  
> Apparently I must have triggered a change in the Control Panel so PATH  
> was updated even before reboot.
>
> Anyway, there are free tools with source that show how to send a  
> broadcast message to make that change active immediately, e.g.:
> http://www.codeproject.com/KB/applications/SetEnv.aspx?fid=230498&df=90&mpp=25&noise=3&sort=Position&view=Quick&select=1531752&fr=48
>
> BTW: By testing this I found out that the Rtools installer is not as  
> smart as it could be - when you run it a second time it will duplicate  
> the paths.

Inno Setup supports no-reboot for PATH changes, and Rtools 2.8 now uses
that.  So no more reboots necessary.

And the installer is a little bit smarter now than it was:  it is now
idempotent in its PATH mods.  It's not as smart as it could be, still
allowing lots of duplication there, but it won't add the same head twice
in a row.

Duncan Murdoch

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