R devel - Sep 2010 - Problem with WARNING...headers with CRLF line endings

Dear all,

When running R CMD check on Windows XP to test my package I get the 
following warning message:

"* checking line endings in C/C++/Fortran sources/headers ... WARNING
Found the following sources/headers with CR or CRLF line endings:
   src/xpsDict.h"

The problem is that this file is created by the compiler AUTOMATICALLY 
during the compilation process, and since the file is created by VC++ on 
WinXP, it will always have CRLF line endings.

Thus my question is:
- Is it really necessary to issues this warning message?
- If yes, could it be suppressed on Windows XP, since there it should 
obviously be no problem.

One more issue:
While I have always received this warning on my WinXP installation, for 
some lucky reason the warning did until now not appear on the 
Bioconductor Windows server, see BioC 2.6 with R-2.11.1:
http://bioconductor.org/checkResults/2.6/bioc-LATEST/xps/liverpool-checksrc.html

However, for some reason on BioC 2.7 running R-2.12.0 this warning does 
appear, see:
http://bioconductor.org/checkResults/2.7/bioc-LATEST/xps/liverpool-checksrc.html
For this reason I would  appreciate if there would be a possibility to 
suppress this warning message.

Thank you in advance.
Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at
_._._._._._._._._._._._._._._._._._

On 13 September 2010 at 23:07, cstrato wrote:
| Dear all,
| 
| When running R CMD check on Windows XP to test my package I get the 
| following warning message:
| 
| "* checking line endings in C/C++/Fortran sources/headers ... WARNING
| Found the following sources/headers with CR or CRLF line endings:
|    src/xpsDict.h"
| 
| The problem is that this file is created by the compiler AUTOMATICALLY 
| during the compilation process, and since the file is created by VC++ on 
| WinXP, it will always have CRLF line endings.
| 
| Thus my question is:
| - Is it really necessary to issues this warning message?
| - If yes, could it be suppressed on Windows XP, since there it should 
| obviously be no problem.
| 
| One more issue:
| While I have always received this warning on my WinXP installation, for 
| some lucky reason the warning did until now not appear on the 
| Bioconductor Windows server, see BioC 2.6 with R-2.11.1:
|
http://bioconductor.org/checkResults/2.6/bioc-LATEST/xps/liverpool-checksrc.html
| 
| However, for some reason on BioC 2.7 running R-2.12.0 this warning does 
| appear, see:
|
http://bioconductor.org/checkResults/2.7/bioc-LATEST/xps/liverpool-checksrc.html
| For this reason I would  appreciate if there would be a possibility to 
| suppress this warning message.

I once had the warning to in project and just added another filtering step
using this


## simple 0d 0a -> 0a converter to suppress a warning on Windows

filename <- commandArgs(trailingOnly=TRUE)[1]
if (!file.exists(filename)) q()

con <- file(filename, "rb")
bin <- readBin(con, raw(), 100000)
bin <- bin[ which(bin != "0d") ]
close(con)

Sys.sleep(1)

con <- file(filename, "wb")
writeBin(bin, con)
close(con)


Maybe you can use something like this and have the generated file transformed.

Dirk

-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com

> -----Original Message-----
> From: r-devel-bounces at r-project.org 
> [mailto:r-devel-bounces at r-project.org] On Behalf Of cstrato
> Sent: Monday, September 13, 2010 2:08 PM
> To: r-devel at r-project.org
> Subject: [Rd] Problem with WARNING...headers with CRLF line endings
> 
> Dear all,
> 
> When running R CMD check on Windows XP to test my package I get the 
> following warning message:
> 
> "* checking line endings in C/C++/Fortran sources/headers ... WARNING
> Found the following sources/headers with CR or CRLF line endings:
>    src/xpsDict.h"
> 
> The problem is that this file is created by the compiler 
> AUTOMATICALLY 
> during the compilation process, and since the file is created 
> by VC++ on 
> WinXP, it will always have CRLF line endings.
> 
> Thus my question is:
> - Is it really necessary to issues this warning message?
> - If yes, could it be suppressed on Windows XP, since there it should 
> obviously be no problem.
Older versions of Sun C compilers would refuse to
compile code with Windows-style line endings.  I don't
know if that is still the case.  One reason to run check
is to see if there are any platform-dependencies in
code on CRAN so the warning should not be suppressed.

(The S+ package system tries to avoid the problem by changing
line endings on text files when it compiles the package.
It is not trivial to reliably figure out which files are
meant to be text files.)

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com  
> 
> One more issue:
> While I have always received this warning on my WinXP 
> installation, for 
> some lucky reason the warning did until now not appear on the 
> Bioconductor Windows server, see BioC 2.6 with R-2.11.1:
> http://bioconductor.org/checkResults/2.6/bioc-LATEST/xps/liver
pool-checksrc.html
> 
> However, for some reason on BioC 2.7 running R-2.12.0 this 
> warning does 
> appear, see:
> http://bioconductor.org/checkResults/2.7/bioc-LATEST/xps/liver
pool-checksrc.html
> For this reason I would  appreciate if there would be a 
> possibility to 
> suppress this warning message.
> 
> Thank you in advance.
> Best regards
> Christian
> _._._._._._._._._._._._._._._._._._
> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
> V.i.e.n.n.a           A.u.s.t.r.i.a
> e.m.a.i.l:        cstrato at aon.at
> _._._._._._._._._._._._._._._._._._
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

Dear Dirk,

Thank you for this suggestion, however I have no idea where this code 
could be used.

As I have said, this file is created automatically during the 
compilation by the compiler, and I have no idea at which point "R CMD 
check" does check for CRLF line endings, and how to interfere with this 
step. Do you have any ideas?

Best regards
Christian


On 9/13/10 11:31 PM, Dirk Eddelbuettel wrote:
>
> On 13 September 2010 at 23:07, cstrato wrote:
> | Dear all,
> |
> | When running R CMD check on Windows XP to test my package I get the
> | following warning message:
> |
> | "* checking line endings in C/C++/Fortran sources/headers ...
WARNING
> | Found the following sources/headers with CR or CRLF line endings:
> |    src/xpsDict.h"
> |
> | The problem is that this file is created by the compiler AUTOMATICALLY
> | during the compilation process, and since the file is created by VC++ on
> | WinXP, it will always have CRLF line endings.
> |
> | Thus my question is:
> | - Is it really necessary to issues this warning message?
> | - If yes, could it be suppressed on Windows XP, since there it should
> | obviously be no problem.
> |
> | One more issue:
> | While I have always received this warning on my WinXP installation, for
> | some lucky reason the warning did until now not appear on the
> | Bioconductor Windows server, see BioC 2.6 with R-2.11.1:
> |
http://bioconductor.org/checkResults/2.6/bioc-LATEST/xps/liverpool-checksrc.html
> |
> | However, for some reason on BioC 2.7 running R-2.12.0 this warning does
> | appear, see:
> |
http://bioconductor.org/checkResults/2.7/bioc-LATEST/xps/liverpool-checksrc.html
> | For this reason I would  appreciate if there would be a possibility to
> | suppress this warning message.
>
> I once had the warning to in project and just added another filtering step
> using this
>
>
> ## simple 0d 0a ->  0a converter to suppress a warning on Windows
>
> filename<- commandArgs(trailingOnly=TRUE)[1]
> if (!file.exists(filename)) q()
>
> con<- file(filename, "rb")
> bin<- readBin(con, raw(), 100000)
> bin<- bin[ which(bin != "0d") ]
> close(con)
>
> Sys.sleep(1)
>
> con<- file(filename, "wb")
> writeBin(bin, con)
> close(con)
>
>
> Maybe you can use something like this and have the generated file
transformed.
>
> Dirk
>

Dear Dirk,

Thank you for this suggestion, however since I am not very good in 
creating Makefiles I would appreciate if you could explain how to filter 
at the compile stage.

These are the lines which I think are essential:

xps.dll:  $(MYOBJ)
	$(LINK) /dll /def:xps.def /out:xps.dll fp10.obj $(SOFLAGS) $(LDFLAGS) 
$(GLIBS) *.obj
	
xpsDict.cxx: $(MYHDR) xpsLinkDef.h
	@echo "Generating dictionary $@..."
	@rootcint -f $@ -c $(MYHDR) xpsLinkDef.h
	
xpsDict.obj: xpsDict.cxx xpsDict.h
	$(CL) /I"${ROOTSYS}/include" /FIw32pragma.h /MT /EHsc /Ox /D
"MSVC" /D
"WIN32" /c xpsDict.cxx

clean:
	rm -f $(MYOBJ) *.a *.d *.rc

The line @rootcint creates the xpsLinkDef.h file.

Do I have to add something after the compilation step of xpsDict.obj?

Thank you in advance.
Best regards
Christian


On 9/15/10 10:51 PM, Dirk Eddelbuettel wrote:
>
> On 15 September 2010 at 22:39, cstrato wrote:
> | Dear Duncan, dear Herve,
> |
> | Thank you both for your help and suggestions. I think that you are both
> | right:
> |
> | In principle I do not want to put these files in the source tarball (and
> | I did not in the past), however because of the way R CMD check works
> | this seems to be the only possibility to get rid of the warning message.
> |
> | I agree that it is weird to get this warning message although these
> | files are not in the source tarball.
> |
> | Since I have a Makefile, as Herve mentions, I can try to remove these
>
> If you have a Makefile, then you have implicit rules as well as explicit
> ones.  That is how the file gets created.
>
> Now modify the rules and insert another layer which will do the filtering.
As
> the saying goes:  "there is no problem that cannot be solved by adding
> another layer of indirection".  Instead of requiring the generated
file,
> require the generated and filtered file.
>
> | files in the clean step, which currently is:
> |
> | clean:
> | 	rm -f $(MYOBJ) *.a *.d *.rc
> |
> | I will try to change this part but I am not sure if this will solve the
> | problem.
>
> I fear that the clean step runs too late.  You want the file filtered at
the
> compile stage.
>
> Dirk
>