[Rd] R CMD check not running examples under Windows
All,
I have a fresh build of R 2.8.0 from source on Windows XP using the latest
Rtools binary (Rtools29.exe). All appears to be well with the install and make
check-all exits cleanly. However, when running R CMD check mypkg the program
jumps from checking for non-ASCII to checking the PDF version of the manual:
* checking data for non-ASCII characters ... OK
* checking PDF version of manual ... OK
It skips the making the R-ex subdir and checking the examples. Here is the
complete log:
* using log directory 'C:/Data/research/dplR_dev/dplR.Rcheck'
* using R version 2.8.0 (2008-10-20)
* using session charset: ISO8859-1
* checking for file 'dplR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dplR' version '1.1.5'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for .dll and .exe files ... OK
* checking whether package 'dplR' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking PDF version of manual ... OK
I am running this with no flags yet it seems like I'm outside this line in the
check script:
if($opt_examples && (-d &file_path($library, $pkgname, "R-ex"))) {
Here is the version:
> version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 8.0
year 2008
month 10
day20
svn rev46754
language R
version.string R version 2.8.0 (2008-10-20)
>
And the PATH:
C:\Data\research\dplR_dev>PATH
PATH=c:\Rtools\bin;c:\Rtools\perl\bin;c:\Rtools\MinGW\bin;C:\R\R-2.8.0\bin\;C:\P
rogram Files\HTML Help Workshop\;C:\Program Files\MiKTeX 2.6\miktex\bin;C:\cygwi
n\bin;C:\FWTools2.2.6\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbe
m;C:\WINDOWS\system32\nls;C:\WINDOWS\system32\nls\ENGLISH;C:\Program Files\Novel
l\ZENworks\;C:\Program Files\QuickTime\QTSystem;C:\ArcGIS\arcexe9x\bin;C:\Progra
m Files\Common Files\GTK\2.0\bin;C:\Program Files\GPS Pathfinder Office 3.10;C:\
dpl;C:\Program Files\QuickTime\QTSystem\;C:\Program Files\SSH Communications Sec
urity\SSH Secure Shell;Z:.;
I expect some cygwin or perl issue but I'm not sure how to proceed in tracking
this down. Cygwin is a fresh install as well. Any suggestions on what to do
next greatly appreciated.
-A
~~~
Andy Bunn
Environmental Sciences, Huxley College
Western Washington University
Bellingham, WA 98225-9181
Skype: andy.bunn
Phone: 360-650-4252
Fax: 360-650-7284
http://myweb.facstaff.wwu.edu/bunna/
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD check not running examples under Windows
My suggestion is to submit the package to the win-builder service and
look whether that one checks your example, then you know if it is the
package or your setup that causes the problem.
Best,
Uwe Ligges
Andy Bunn wrote:
All,
I have a fresh build of R 2.8.0 from source on Windows XP using the latest
Rtools binary (Rtools29.exe). All appears to be well with the install and make
check-all exits cleanly. However, when running R CMD check mypkg the program
jumps from checking for non-ASCII to checking the PDF version of the manual:
* checking data for non-ASCII characters ... OK
* checking PDF version of manual ... OK
It skips the making the R-ex subdir and checking the examples. Here is the
complete log:
* using log directory 'C:/Data/research/dplR_dev/dplR.Rcheck'
* using R version 2.8.0 (2008-10-20)
* using session charset: ISO8859-1
* checking for file 'dplR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dplR' version '1.1.5'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for .dll and .exe files ... OK
* checking whether package 'dplR' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking PDF version of manual ... OK
I am running this with no flags yet it seems like I'm outside this line in the
check script:
if($opt_examples && (-d &file_path($library, $pkgname, "R-ex"))) {
Here is the version:
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 8.0
year 2008
month 10
day20
svn rev46754
language R
version.string R version 2.8.0 (2008-10-20)
And the PATH:
C:\Data\research\dplR_dev>PATH
PATH=c:\Rtools\bin;c:\Rtools\perl\bin;c:\Rtools\MinGW\bin;C:\R\R-2.8.0\bin\;C:\P
rogram Files\HTML Help Workshop\;C:\Program Files\MiKTeX 2.6\miktex\bin;C:\cygwi
n\bin;C:\FWTools2.2.6\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbe
m;C:\WINDOWS\system32\nls;C:\WINDOWS\system32\nls\ENGLISH;C:\Program Files\Novel
l\ZENworks\;C:\Program Files\QuickTime\QTSystem;C:\ArcGIS\arcexe9x\bin;C:\Progra
m Files\Common Files\GTK\2.0\bin;C:\Program Files\GPS Pathfinder Office 3.10;C:\
dpl;C:\Program Files\QuickTime\QTSystem\;C:\Program Files\SSH Communications Sec
urity\SSH Secure Shell;Z:.;
I expect some cygwin or perl issue but I'm not sure how to proceed in tracking
this down. Cygwin is a fresh install as well. Any suggestions on what to do
next greatly appreciated.
-A
~~~
Andy Bunn
Environmental Sciences, Huxley College
Western Washington University
Bellingham, WA 98225-9181
Skype: andy.bunn
Phone: 360-650-4252
Fax: 360-650-7284
http://myweb.facstaff.wwu.edu/bunna/
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
__
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Re: [Rd] R CMD check not running examples under Windows
> -Original Message-
> From: Uwe Ligges [mailto:[EMAIL PROTECTED]
> Sent: Tuesday, December 09, 2008 2:03 AM
> To: Andy Bunn
> Cc: r-devel@r-project.org
> Subject: Re: [Rd] R CMD check not running examples under Windows
>
> My suggestion is to submit the package to the win-builder service and
> look whether that one checks your example, then you know if it is the
> package or your setup that causes the problem.
Uwe, thanks for the tip but the issue is definitely my system - not the
package. I've built a skeleton using package.skeleton() and the same phenomenon
occurs. Same with checking CRAN packages from source. If it is a problem with
my system - how do I go about trouble shooting?
>
> Best,
> Uwe Ligges
>
>
> Andy Bunn wrote:
> > All,
> >
> >
> > I have a fresh build of R 2.8.0 from source on Windows XP using the
> latest Rtools binary (Rtools29.exe). All appears to be well with the
> install and make check-all exits cleanly. However, when running R CMD
> check mypkg the program jumps from checking for non-ASCII to checking
> the PDF version of the manual:
> >
> > * checking data for non-ASCII characters ... OK
> > * checking PDF version of manual ... OK
> >
> > It skips the making the R-ex subdir and checking the examples. Here
> is the complete log:
> >
> >
> > * using log directory 'C:/Data/research/dplR_dev/dplR.Rcheck'
> > * using R version 2.8.0 (2008-10-20)
> > * using session charset: ISO8859-1
> > * checking for file 'dplR/DESCRIPTION' ... OK
> > * checking extension type ... Package
> > * this is package 'dplR' version '1.1.5'
> > * checking package name space information ... OK
> > * checking package dependencies ... OK
> > * checking if this is a source package ... OK
> > * checking for .dll and .exe files ... OK
> > * checking whether package 'dplR' can be installed ... OK
> > * checking package directory ... OK
> > * checking for portable file names ... OK
> > * checking DESCRIPTION meta-information ... OK
> > * checking top-level files ... OK
> > * checking index information ... OK
> > * checking package subdirectories ... OK
> > * checking R files for non-ASCII characters ... OK
> > * checking R files for syntax errors ... OK
> > * checking whether the package can be loaded ... OK
> > * checking whether the package can be loaded with stated dependencies
> ... OK
> > * checking whether the name space can be loaded with stated
> dependencies ... OK
> > * checking for unstated dependencies in R code ... OK
> > * checking S3 generic/method consistency ... OK
> > * checking replacement functions ... OK
> > * checking foreign function calls ... OK
> > * checking R code for possible problems ... OK
> > * checking Rd files ... OK
> > * checking Rd cross-references ... OK
> > * checking for missing documentation entries ... OK
> > * checking for code/documentation mismatches ... OK
> > * checking Rd \usage sections ... OK
> > * checking data for non-ASCII characters ... OK
> > * checking PDF version of manual ... OK
> >
> > I am running this with no flags yet it seems like I'm outside this
> line in the check script:
> > if($opt_examples && (-d &file_path($library, $pkgname, "R-ex"))) {
> >
> > Here is the version:
> >> version
> >_
> > platform i386-pc-mingw32
> > arch i386
> > os mingw32
> > system i386, mingw32
> > status
> > major 2
> > minor 8.0
> > year 2008
> > month 10
> > day20
> > svn rev46754
> > language R
> > version.string R version 2.8.0 (2008-10-20)
> >
> >
> > And the PATH:
> > C:\Data\research\dplR_dev>PATH
> > PATH=c:\Rtools\bin;c:\Rtools\perl\bin;c:\Rtools\MinGW\bin;C:\R\R-
> 2.8.0\bin\;C:\P
> > rogram Files\HTML Help Workshop\;C:\Program Files\MiKTeX
> 2.6\miktex\bin;C:\cygwi
> >
> n\bin;C:\FWTools2.2.6\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\Sys
> tem32\Wbe
> > m;C:\WINDOWS\system32\nls;C:\WINDOWS\system32\nls\ENGLISH;C:\Program
> Files\Novel
> > l\ZENworks\;C:\Program
> Files\QuickTime\QTSystem;C:\ArcGIS\arcexe9x\bin;C:\Progra
> > m Files\Common Files\GTK\2.0\bin;C:\Program Files\GPS Pathfinder
> Office 3.10;C:\
> > dpl;C:\Program Files\QuickTime\QTSystem\;C:\Program Files\SSH
> Communications Sec
> > urity\SSH Secure Shell;Z:.;
> >
> > I expect some cygwin or perl issue but I'm not sure how to proceed in
> tracking this down. Cygwin is a fresh install as well. Any suggestions
> on what to do next greatly appreciated.
> >
> > -A
> >
> > ~~~
> > Andy Bunn
> > Environmental Sciences, Huxley College
> > Western Washington University
> > Bellingham, WA 98225-9181
> > Skype: andy.bunn
> > Phone: 360-650-4252
> > Fax: 360-650-7284
> > http://myweb.facstaff.wwu.edu/bunna/
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
__
R-devel@r-project.org mailing list
https://stat.ethz.c
Re: [Rd] R CMD check not running examples under Windows
This is a shot in the dark, but I noticed your PATH contains spaces in
the paths to HTML Help and MiKTeX. The R Install & Admin manual
explicitly says not to paths with spaces. If anything, it won't hurt
to make this correction.
HTH,
Josh
--
http://quantemplation.blogspot.com
On Tue, Dec 9, 2008 at 11:32 AM, Andy Bunn <[EMAIL PROTECTED]> wrote:
>> -Original Message-
>> From: Uwe Ligges [mailto:[EMAIL PROTECTED]
>> Sent: Tuesday, December 09, 2008 2:03 AM
>> To: Andy Bunn
>> Cc: r-devel@r-project.org
>> Subject: Re: [Rd] R CMD check not running examples under Windows
>>
>> My suggestion is to submit the package to the win-builder service and
>> look whether that one checks your example, then you know if it is the
>> package or your setup that causes the problem.
>
> Uwe, thanks for the tip but the issue is definitely my system - not the
> package. I've built a skeleton using package.skeleton() and the same
> phenomenon occurs. Same with checking CRAN packages from source. If it is a
> problem with my system - how do I go about trouble shooting?
>
>
>
>>
>> Best,
>> Uwe Ligges
>>
>>
>> Andy Bunn wrote:
>> > All,
>> >
>> >
>> > I have a fresh build of R 2.8.0 from source on Windows XP using the
>> latest Rtools binary (Rtools29.exe). All appears to be well with the
>> install and make check-all exits cleanly. However, when running R CMD
>> check mypkg the program jumps from checking for non-ASCII to checking
>> the PDF version of the manual:
>> >
>> > * checking data for non-ASCII characters ... OK
>> > * checking PDF version of manual ... OK
>> >
>> > It skips the making the R-ex subdir and checking the examples. Here
>> is the complete log:
>> >
>> >
>> > * using log directory 'C:/Data/research/dplR_dev/dplR.Rcheck'
>> > * using R version 2.8.0 (2008-10-20)
>> > * using session charset: ISO8859-1
>> > * checking for file 'dplR/DESCRIPTION' ... OK
>> > * checking extension type ... Package
>> > * this is package 'dplR' version '1.1.5'
>> > * checking package name space information ... OK
>> > * checking package dependencies ... OK
>> > * checking if this is a source package ... OK
>> > * checking for .dll and .exe files ... OK
>> > * checking whether package 'dplR' can be installed ... OK
>> > * checking package directory ... OK
>> > * checking for portable file names ... OK
>> > * checking DESCRIPTION meta-information ... OK
>> > * checking top-level files ... OK
>> > * checking index information ... OK
>> > * checking package subdirectories ... OK
>> > * checking R files for non-ASCII characters ... OK
>> > * checking R files for syntax errors ... OK
>> > * checking whether the package can be loaded ... OK
>> > * checking whether the package can be loaded with stated dependencies
>> ... OK
>> > * checking whether the name space can be loaded with stated
>> dependencies ... OK
>> > * checking for unstated dependencies in R code ... OK
>> > * checking S3 generic/method consistency ... OK
>> > * checking replacement functions ... OK
>> > * checking foreign function calls ... OK
>> > * checking R code for possible problems ... OK
>> > * checking Rd files ... OK
>> > * checking Rd cross-references ... OK
>> > * checking for missing documentation entries ... OK
>> > * checking for code/documentation mismatches ... OK
>> > * checking Rd \usage sections ... OK
>> > * checking data for non-ASCII characters ... OK
>> > * checking PDF version of manual ... OK
>> >
>> > I am running this with no flags yet it seems like I'm outside this
>> line in the check script:
>> > if($opt_examples && (-d &file_path($library, $pkgname, "R-ex"))) {
>> >
>> > Here is the version:
>> >> version
>> >_
>> > platform i386-pc-mingw32
>> > arch i386
>> > os mingw32
>> > system i386, mingw32
>> > status
>> > major 2
>> > minor 8.0
>> > year 2008
>> > month 10
>> > day20
>> > svn rev46754
>> > language R
>> > version.string R version 2.8.0 (2008-10-20)
>> >
>> >
>> > And the PATH:
>> > C:\Data\research\dplR_dev>PATH
>> > PATH=c:\Rtools\bin;c:\Rtools\perl\bin;c:\Rtools\MinGW\bin;C:\R\R-
>> 2.8.0\bin\;C:\P
>> > rogram Files\HTML Help Workshop\;C:\Program Files\MiKTeX
>> 2.6\miktex\bin;C:\cygwi
>> >
>> n\bin;C:\FWTools2.2.6\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\Sys
>> tem32\Wbe
>> > m;C:\WINDOWS\system32\nls;C:\WINDOWS\system32\nls\ENGLISH;C:\Program
>> Files\Novel
>> > l\ZENworks\;C:\Program
>> Files\QuickTime\QTSystem;C:\ArcGIS\arcexe9x\bin;C:\Progra
>> > m Files\Common Files\GTK\2.0\bin;C:\Program Files\GPS Pathfinder
>> Office 3.10;C:\
>> > dpl;C:\Program Files\QuickTime\QTSystem\;C:\Program Files\SSH
>> Communications Sec
>> > urity\SSH Secure Shell;Z:.;
>> >
>> > I expect some cygwin or perl issue but I'm not sure how to proceed in
>> tracking this down. Cygwin is a fresh install as well. Any suggestions
>> on what to do next greatly appreciated.
>> >
>> > -A
>> >
>> > ~
Re: [Rd] R CMD check not running examples under Windows
No idea,
perhaps add some print statements in teh perl code that executes the
checks and see why it does not jump in.
uwe
Andy Bunn wrote:
-Original Message-
From: Uwe Ligges [mailto:[EMAIL PROTECTED]
Sent: Tuesday, December 09, 2008 2:03 AM
To: Andy Bunn
Cc: r-devel@r-project.org
Subject: Re: [Rd] R CMD check not running examples under Windows
My suggestion is to submit the package to the win-builder service and
look whether that one checks your example, then you know if it is the
package or your setup that causes the problem.
Uwe, thanks for the tip but the issue is definitely my system - not the
package. I've built a skeleton using package.skeleton() and the same phenomenon
occurs. Same with checking CRAN packages from source. If it is a problem with
my system - how do I go about trouble shooting?
Best,
Uwe Ligges
Andy Bunn wrote:
All,
I have a fresh build of R 2.8.0 from source on Windows XP using the
latest Rtools binary (Rtools29.exe). All appears to be well with the
install and make check-all exits cleanly. However, when running R CMD
check mypkg the program jumps from checking for non-ASCII to checking
the PDF version of the manual:
* checking data for non-ASCII characters ... OK
* checking PDF version of manual ... OK
It skips the making the R-ex subdir and checking the examples. Here
is the complete log:
* using log directory 'C:/Data/research/dplR_dev/dplR.Rcheck'
* using R version 2.8.0 (2008-10-20)
* using session charset: ISO8859-1
* checking for file 'dplR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dplR' version '1.1.5'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for .dll and .exe files ... OK
* checking whether package 'dplR' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies
... OK
* checking whether the name space can be loaded with stated
dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* checking PDF version of manual ... OK
I am running this with no flags yet it seems like I'm outside this
line in the check script:
if($opt_examples && (-d &file_path($library, $pkgname, "R-ex"))) {
Here is the version:
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 8.0
year 2008
month 10
day20
svn rev46754
language R
version.string R version 2.8.0 (2008-10-20)
And the PATH:
C:\Data\research\dplR_dev>PATH
PATH=c:\Rtools\bin;c:\Rtools\perl\bin;c:\Rtools\MinGW\bin;C:\R\R-
2.8.0\bin\;C:\P
rogram Files\HTML Help Workshop\;C:\Program Files\MiKTeX
2.6\miktex\bin;C:\cygwi
n\bin;C:\FWTools2.2.6\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\Sys
tem32\Wbe
m;C:\WINDOWS\system32\nls;C:\WINDOWS\system32\nls\ENGLISH;C:\Program
Files\Novel
l\ZENworks\;C:\Program
Files\QuickTime\QTSystem;C:\ArcGIS\arcexe9x\bin;C:\Progra
m Files\Common Files\GTK\2.0\bin;C:\Program Files\GPS Pathfinder
Office 3.10;C:\
dpl;C:\Program Files\QuickTime\QTSystem\;C:\Program Files\SSH
Communications Sec
urity\SSH Secure Shell;Z:.;
I expect some cygwin or perl issue but I'm not sure how to proceed in
tracking this down. Cygwin is a fresh install as well. Any suggestions
on what to do next greatly appreciated.
-A
~~~
Andy Bunn
Environmental Sciences, Huxley College
Western Washington University
Bellingham, WA 98225-9181
Skype: andy.bunn
Phone: 360-650-4252
Fax: 360-650-7284
http://myweb.facstaff.wwu.edu/bunna/
__
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[Rd] any suggestions to deal with 'Argument list too long' for a R CMD check?
Since, gcc was using upwards of 2gb of ram to compile my package, I just split all the functions into individual files. I guess I'm too clever for myself, because now I get hit with the "Argument list too long" error. Is there a way to deal with this aside from writing my own configure script (which could possibly feed the gcc commands one by one). -Whit RHEL 5 [EMAIL PROTECTED] uname -a Linux linuxsvr.kls.corp 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST 2008 x86_64 x86_64 x86_64 GNU/Linux from 00install.out: * Installing *source* package 'RFincad' ... ** libs g++ -I/usr/local/lib64/R/include -I/usr/local/include -I./RAbstraction -I./R.tslib.backend -I./tslib -fpic -g -O2 -c aaAccrual_days_act252.cpp -o aaAccrual_days_act2\ 52.o make: execvp: g++: Argument list too long make: *** [aaAccrual_days_act252.o] Error 127 ERROR: compilation failed for package 'RFincad' ** Removing '/home/whit/dvl/fincad.utils/fincad.generate.R/RFincad.Rcheck/RFincad' __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] any suggestions to deal with 'Argument list too long' for a R CMD check?
Never used, but I seem to recall that this was good for that: http://en.wikipedia.org/wiki/Xargs Jeff On Tue, Dec 9, 2008 at 3:13 PM, Whit Armstrong <[EMAIL PROTECTED]> wrote: > Since, gcc was using upwards of 2gb of ram to compile my package, I > just split all the functions into individual files. > > I guess I'm too clever for myself, because now I get hit with the > "Argument list too long" error. > > Is there a way to deal with this aside from writing my own configure > script (which could possibly feed the gcc commands one by one). > > -Whit > > RHEL 5 > [EMAIL PROTECTED] uname -a > Linux linuxsvr.kls.corp 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 > EST 2008 x86_64 x86_64 x86_64 GNU/Linux > > from 00install.out: > > * Installing *source* package 'RFincad' ... > ** libs > g++ -I/usr/local/lib64/R/include -I/usr/local/include > -I./RAbstraction -I./R.tslib.backend -I./tslib -fpic -g -O2 -c > aaAccrual_days_act252.cpp -o aaAccrual_days_act2\ > 52.o > make: execvp: g++: Argument list too long > make: *** [aaAccrual_days_act252.o] Error 127 > ERROR: compilation failed for package 'RFincad' > ** Removing > '/home/whit/dvl/fincad.utils/fincad.generate.R/RFincad.Rcheck/RFincad' > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Jeffrey Ryan [EMAIL PROTECTED] ia: insight algorithmics www.insightalgo.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Warning from R CMD build
Hi,
I wonder about the reason for the following lines:
$ diff ~/local/lib64/R/bin/build /usr/lib64/R/bin/build
40c40
< my $revision = ' $Rev: 46832 $ ';
---
> my $revision = ' $Rev: 45803 $ ';
576,579d570
< if(-r "Makevars") {
< $makefiles .= " -f Makevars";
< R_system("${R::Vars::MAKE} $makefiles clean");
< }
it produces a warning like
$ R-devel CMD build Runuran
[...]
* DONE (Runuran)
* creating vignettes ... OK
* cleaning src
make: *** No rule to make target `clean'. Stop.
* running cleanup
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'Runuran_0.8.900.tar.gz'
"Writing R Extensions" however says:
Note that @file{Makevars} should not normally contain targets, as it is
(except on Windows) included before the default makefile and
@command{make}
is called without an explicit target.
Josef
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Re: [Rd] any suggestions to deal with 'Argument list too long' for a R CMD check?
I love xargs for all kinds of stuff, but I really don't want to write my own configure script. looks like simple solution is to recombine into one big source file rather than splitting each function out. pita... -Whit On Tue, Dec 9, 2008 at 4:23 PM, Jeff Ryan <[EMAIL PROTECTED]> wrote: > Never used, but I seem to recall that this was good for that: > > http://en.wikipedia.org/wiki/Xargs > > Jeff > > On Tue, Dec 9, 2008 at 3:13 PM, Whit Armstrong <[EMAIL PROTECTED]> wrote: >> Since, gcc was using upwards of 2gb of ram to compile my package, I >> just split all the functions into individual files. >> >> I guess I'm too clever for myself, because now I get hit with the >> "Argument list too long" error. >> >> Is there a way to deal with this aside from writing my own configure >> script (which could possibly feed the gcc commands one by one). >> >> -Whit >> >> RHEL 5 >> [EMAIL PROTECTED] uname -a >> Linux linuxsvr.kls.corp 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 >> EST 2008 x86_64 x86_64 x86_64 GNU/Linux >> >> from 00install.out: >> >> * Installing *source* package 'RFincad' ... >> ** libs >> g++ -I/usr/local/lib64/R/include -I/usr/local/include >> -I./RAbstraction -I./R.tslib.backend -I./tslib -fpic -g -O2 -c >> aaAccrual_days_act252.cpp -o aaAccrual_days_act2\ >> 52.o >> make: execvp: g++: Argument list too long >> make: *** [aaAccrual_days_act252.o] Error 127 >> ERROR: compilation failed for package 'RFincad' >> ** Removing >> '/home/whit/dvl/fincad.utils/fincad.generate.R/RFincad.Rcheck/RFincad' >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > > > -- > Jeffrey Ryan > [EMAIL PROTECTED] > > ia: insight algorithmics > www.insightalgo.com > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Warning from R CMD build
The message (it is not even a warning) is harmless. The change is
documented in the NEWS file, and is useful for some packages (Matrix as I
recall).
On Tue, 9 Dec 2008, Josef Leydold wrote:
Hi,
I wonder about the reason for the following lines:
$ diff ~/local/lib64/R/bin/build /usr/lib64/R/bin/build
40c40
< my $revision = ' $Rev: 46832 $ ';
---
my $revision = ' $Rev: 45803 $ ';
576,579d570
< if(-r "Makevars") {
< $makefiles .= " -f Makevars";
< R_system("${R::Vars::MAKE} $makefiles clean");
< }
it produces a warning like
$ R-devel CMD build Runuran
[...]
* DONE (Runuran)
* creating vignettes ... OK
* cleaning src
make: *** No rule to make target `clean'. Stop.
* running cleanup
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'Runuran_0.8.900.tar.gz'
"Writing R Extensions" however says:
Note that @file{Makevars} should not normally contain targets, as it is
(except on Windows) included before the default makefile and
@command{make}
is called without an explicit target.
Note 'normally'.
Josef
__
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https://stat.ethz.ch/mailman/listinfo/r-devel
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
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Re: [Rd] any suggestions to deal with 'Argument list too long' for a R CMD check?
Just a suggestion. I googled for your error message you got e.g. "make ... error 127" and I got Yeah, error 127 indicates that make can't find a program that it needs to run a command. My guess would be that she doesn't have g++ installed (some distributions package it separately from gcc so it is possible to have the c compiler installed but not the c++ compiler) Maybe it will be worthwhile to check if you have installed every required header files or needed compilers/libraries. But as I mentioned, this is just a suggestion. Cheers, Mathieu Whit Armstrong a écrit : I love xargs for all kinds of stuff, but I really don't want to write my own configure script. looks like simple solution is to recombine into one big source file rather than splitting each function out. pita... -Whit On Tue, Dec 9, 2008 at 4:23 PM, Jeff Ryan <[EMAIL PROTECTED]> wrote: Never used, but I seem to recall that this was good for that: http://en.wikipedia.org/wiki/Xargs Jeff On Tue, Dec 9, 2008 at 3:13 PM, Whit Armstrong <[EMAIL PROTECTED]> wrote: Since, gcc was using upwards of 2gb of ram to compile my package, I just split all the functions into individual files. I guess I'm too clever for myself, because now I get hit with the "Argument list too long" error. Is there a way to deal with this aside from writing my own configure script (which could possibly feed the gcc commands one by one). -Whit RHEL 5 [EMAIL PROTECTED] uname -a Linux linuxsvr.kls.corp 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST 2008 x86_64 x86_64 x86_64 GNU/Linux from 00install.out: * Installing *source* package 'RFincad' ... ** libs g++ -I/usr/local/lib64/R/include -I/usr/local/include -I./RAbstraction -I./R.tslib.backend -I./tslib -fpic -g -O2 -c aaAccrual_days_act252.cpp -o aaAccrual_days_act2\ 52.o make: execvp: g++: Argument list too long make: *** [aaAccrual_days_act252.o] Error 127 ERROR: compilation failed for package 'RFincad' ** Removing '/home/whit/dvl/fincad.utils/fincad.generate.R/RFincad.Rcheck/RFincad' __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Jeffrey Ryan [EMAIL PROTECTED] ia: insight algorithmics www.insightalgo.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Institute of Mathematics Ecole Polytechnique Fédérale de Lausanne STAT-IMA-FSB-EPFL, Station 8 CH-1015 Lausanne Switzerland http://stat.epfl.ch/ Tel: + 41 (0)21 693 7907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] any suggestions to deal with 'Argument list too long' for a R CMD check?
Thanks for the suggestion. this package was building successfully until I split it up into smaller files. (there are 4489 files in the src directory) I suspect it's a hard limit in the linux kernel. http://www.linuxjournal.com/article/6060 since R CMD check is generating the actual commands that are passed to bash, it's a little out of my control (unless I write my own config script, which I do not want to do). -Whit On Tue, Dec 9, 2008 at 5:07 PM, Mathieu Ribatet <[EMAIL PROTECTED]> wrote: > Just a suggestion. I googled for your error message you got e.g. "make ... > error 127" and I got > > Yeah, error 127 indicates that make can't find a program that it needs to > run a command. My guess would be that she doesn't have g++ installed > (some distributions package it separately from gcc so it is possible to > have the c compiler installed but not the c++ compiler) > > > > Maybe it will be worthwhile to check if you have installed every required > header files or needed compilers/libraries. > But as I mentioned, this is just a suggestion. > Cheers, > Mathieu > > Whit Armstrong a écrit : >> >> I love xargs for all kinds of stuff, but I really don't want to write >> my own configure script. >> >> looks like simple solution is to recombine into one big source file >> rather than splitting each function out. pita... >> >> -Whit >> >> >> On Tue, Dec 9, 2008 at 4:23 PM, Jeff Ryan <[EMAIL PROTECTED]> wrote: >> >>> >>> Never used, but I seem to recall that this was good for that: >>> >>> http://en.wikipedia.org/wiki/Xargs >>> >>> Jeff >>> >>> On Tue, Dec 9, 2008 at 3:13 PM, Whit Armstrong <[EMAIL PROTECTED]> >>> wrote: >>> Since, gcc was using upwards of 2gb of ram to compile my package, I just split all the functions into individual files. I guess I'm too clever for myself, because now I get hit with the "Argument list too long" error. Is there a way to deal with this aside from writing my own configure script (which could possibly feed the gcc commands one by one). -Whit RHEL 5 [EMAIL PROTECTED] uname -a Linux linuxsvr.kls.corp 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST 2008 x86_64 x86_64 x86_64 GNU/Linux from 00install.out: * Installing *source* package 'RFincad' ... ** libs g++ -I/usr/local/lib64/R/include -I/usr/local/include -I./RAbstraction -I./R.tslib.backend -I./tslib -fpic -g -O2 -c aaAccrual_days_act252.cpp -o aaAccrual_days_act2\ 52.o make: execvp: g++: Argument list too long make: *** [aaAccrual_days_act252.o] Error 127 ERROR: compilation failed for package 'RFincad' ** Removing '/home/whit/dvl/fincad.utils/fincad.generate.R/RFincad.Rcheck/RFincad' __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel >>> >>> -- >>> Jeffrey Ryan >>> [EMAIL PROTECTED] >>> >>> ia: insight algorithmics >>> www.insightalgo.com >>> >>> >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > -- > Institute of Mathematics > Ecole Polytechnique Fédérale de Lausanne > STAT-IMA-FSB-EPFL, Station 8 > CH-1015 Lausanne Switzerland > http://stat.epfl.ch/ > Tel: + 41 (0)21 693 7907 > > > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] any suggestions to deal with 'Argument list too long' for a R CMD check?
On Tue, 9 Dec 2008, Whit Armstrong wrote: Thanks for the suggestion. this package was building successfully until I split it up into smaller files. (there are 4489 files in the src directory) I suspect it's a hard limit in the linux kernel. http://www.linuxjournal.com/article/6060 since R CMD check is generating the actual commands that are passed to bash, it's a little out of my control (unless I write my own config script, which I do not want to do). Well 'R CMD check' is not doing so: perhaps SHLIB called by INSTALL is. What I suspect is happening is that there is a link command starting with 'g++' that is too long. POSIX requires at least 4096 arguments (which you will exceed), but Linux 2.6 seems to have a limit of much more (unlimited in the current kernel, which yours is not, 32767 in 2.16.14). It is more likely that you are hititng the length limit for the command line, and one way out is to use short file names. One useful ref: http://www.in-ulm.de/~mascheck/various/argmax Note that having all the functions in one file can help the optimizer, but there is another possibility, to have several files of closely related functions. -Whit On Tue, Dec 9, 2008 at 5:07 PM, Mathieu Ribatet <[EMAIL PROTECTED]> wrote: Just a suggestion. I googled for your error message you got e.g. "make ... error 127" and I got Yeah, error 127 indicates that make can't find a program that it needs to run a command. My guess would be that she doesn't have g++ installed (some distributions package it separately from gcc so it is possible to have the c compiler installed but not the c++ compiler) Maybe it will be worthwhile to check if you have installed every required header files or needed compilers/libraries. But as I mentioned, this is just a suggestion. Cheers, Mathieu Whit Armstrong a écrit : I love xargs for all kinds of stuff, but I really don't want to write my own configure script. looks like simple solution is to recombine into one big source file rather than splitting each function out. pita... -Whit On Tue, Dec 9, 2008 at 4:23 PM, Jeff Ryan <[EMAIL PROTECTED]> wrote: Never used, but I seem to recall that this was good for that: http://en.wikipedia.org/wiki/Xargs Jeff On Tue, Dec 9, 2008 at 3:13 PM, Whit Armstrong <[EMAIL PROTECTED]> wrote: Since, gcc was using upwards of 2gb of ram to compile my package, I just split all the functions into individual files. I guess I'm too clever for myself, because now I get hit with the "Argument list too long" error. Is there a way to deal with this aside from writing my own configure script (which could possibly feed the gcc commands one by one). -Whit RHEL 5 [EMAIL PROTECTED] uname -a Linux linuxsvr.kls.corp 2.6.18-92.1.18.el5 #1 SMP Wed Nov 5 09:00:19 EST 2008 x86_64 x86_64 x86_64 GNU/Linux from 00install.out: * Installing *source* package 'RFincad' ... ** libs g++ -I/usr/local/lib64/R/include -I/usr/local/include -I./RAbstraction -I./R.tslib.backend -I./tslib -fpic -g -O2 -c aaAccrual_days_act252.cpp -o aaAccrual_days_act2\ 52.o make: execvp: g++: Argument list too long make: *** [aaAccrual_days_act252.o] Error 127 ERROR: compilation failed for package 'RFincad' ** Removing '/home/whit/dvl/fincad.utils/fincad.generate.R/RFincad.Rcheck/RFincad' __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Jeffrey Ryan [EMAIL PROTECTED] ia: insight algorithmics www.insightalgo.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Institute of Mathematics Ecole Polytechnique Fédérale de Lausanne STAT-IMA-FSB-EPFL, Station 8 CH-1015 Lausanne Switzerland http://stat.epfl.ch/ Tel: + 41 (0)21 693 7907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] any suggestions to deal with 'Argument list too long' for a R CMD check?
Thanks for the link, Prof. Ripley. > What I suspect is happening is that there is a link command starting with > 'g++' that is too long. > One useful ref: http://www.in-ulm.de/~mascheck/various/argmax interesting... on my system: [EMAIL PROTECTED] src]$ getconf ARG_MAX 131072 [EMAIL PROTECTED] src]$ Let me try on another machine w/ a more recent kernel before I take up more of everyone's time. -Whit __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
