date:20120508

Re: [Rd] file 2 is not in sorted order error building unsuffered consequences

2012-05-08 Thread Duncan Murdoch


On 12-05-08 1:46 AM, Joshua Wiley wrote:

Hi All,

I just downloaded the source tar ball (Revision: 59324 Last Changed
Date: 2012-05-07) and tried to compile on a Win x64 system.  I am
using Rtools version 2.15.0.1919.  The only change I make is changing
MkRules.dist ->  MkRules.local and setting Multi=64  I have previously
compiled unsuffered consquences without issue, but on the current
version, I get this error


windres -F pe-x86-64  -I../include -i dllversion.rc -o dllversion.o
comm: file 2 is not in sorted order
make[3]: *** [R.dll] Error 1
make[2]: *** [../../bin/x64/R.dll] Error 2
make[1]: *** [rbuild] Error 2
make: *** [all] Error 2

I did not note any other errors or warnings earlier on, though I may
have missed some.  I can provide the full log if requested.  Any
ideas?


I believe that message is about the file src/gnuwin32/Rdll.hide.  It is 
supposed to be sorted, using ASCII collation order.  I believe the 
version in the repository is sorted properly; can you check yours?


We've had some problems with recent versions of Cygwin not sorting 
properly.  The last instance had it put names in the order


 BZ2_bzWriteClose@20
 BZ2_bzWriteClose64@28

but ASCII order should put @ after 6.  Are you using the comm and Cygwin 
dlls from Rtools, or have you got newer ones?


Duncan Murdoch

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Re: [Rd] How to list package dependency on a Bioconductor package?

2012-05-08 Thread Steven Lund

I recently submit a package called QuasiSeq.  The package source and
Windows binary worked fine, but the MacOS X binary failed. The bottom of
the CRAN page for QuasiSeq shows

Downloads:
  Package source: QuasiSeq_1.0-1.tar.gz
  MacOS X binary: not available, see check log.
  Windows binary: QuasiSeq-1.0-1.zip
  Reference manual:  QuasiSeq.pdf


The log for the MacOS X binary shows
   - using R version 2.15.0 (2012-03-30)
   - using platform: i386-apple-darwin9.8.0 (32-bit)
   -  using session charset: ASCII
   -  checking for file 'QuasiSeq/DESCRIPTION' ... OK
   -  this is package 'QuasiSeq' version '1.0-1'
   -  checking package namespace information ... OK
   -  checking package dependencies ... ERROR
   Package required but not available: 'edgeR'

   See the information on DESCRIPTION files in the chapter
'Creating R
   packages' of the 'Writing R Extensions' manual.
   -  elapsed time (check, wall clock): 0:01

Is there a simple remedy to the problems caused by the dependency on edgeR,
or would you advise that I put a work-around into my source code using
'require' so I can list edgeR under Suggests instead of Depends or Includes?

Thank you for your time!

-Steve


On Tue, Jan 3, 2012 at 7:42 AM, Uwe Ligges
wrote:

>
>
> On 03.01.2012 00:16, Steven Lund wrote:
>
>> I know others have asked similar questions to the R developers, but I
>> could not find the solution to this question.  Please forgive me if I
>> have missed a crucial point in a previous post.
>>
>> I would like to submit a package to CRAN that depends on the
>> bioconductor package "edgeR".  Listing "edgeR" under the Depends or
>> Imports lines in the DESCRIPTION file for my package causes an error
>> when running the `R CMD check' command on my package's 'tar.gz' file:
>>
>> * checking package dependencies ... ERROR
>> Package required but not available: ÄedgeRÄ
>>
>>
>> Is there documentation or an example anywhere of how to handle
>> dependencies on Bioconductor packages when creating a package for
>> CRAN?
>>
>
>
> Same as for CRAN packages. The CRAN check farm will automatically install
> the dependency from BioConductor if available for the corresponding
> platform / R version.
>
> Uwe Ligges
>
>
>
>
>
>> Thank you!
>>
>> -Steve
>>
>> __**
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/**listinfo/r-devel
>>
>

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Re: [Rd] file 2 is not in sorted order error building unsuffered consequences

2012-05-08 Thread Joshua Wiley

On Tue, May 8, 2012 at 3:48 AM, Duncan Murdoch  wrote:
> On 12-05-08 1:46 AM, Joshua Wiley wrote:
>>
>> Hi All,
>>
>> I just downloaded the source tar ball (Revision: 59324 Last Changed
>> Date: 2012-05-07) and tried to compile on a Win x64 system.  I am
>> using Rtools version 2.15.0.1919.  The only change I make is changing
>> MkRules.dist ->  MkRules.local and setting Multi=64  I have previously
>> compiled unsuffered consquences without issue, but on the current
>> version, I get this error
>>
>>
>> windres -F pe-x86-64  -I../include -i dllversion.rc -o dllversion.o
>> comm: file 2 is not in sorted order
>> make[3]: *** [R.dll] Error 1
>> make[2]: *** [../../bin/x64/R.dll] Error 2
>> make[1]: *** [rbuild] Error 2
>> make: *** [all] Error 2
>>
>> I did not note any other errors or warnings earlier on, though I may
>> have missed some.  I can provide the full log if requested.  Any
>> ideas?
>
>
> I believe that message is about the file src/gnuwin32/Rdll.hide.  It is
> supposed to be sorted, using ASCII collation order.  I believe the version
> in the repository is sorted properly; can you check yours?

Thanks for your reply.  It looks sorted correctly and explicitly
sorting prior to running make does not change the error.  here is a
bit of output:

BZ2_bzBuffToBuffCompress@28
BZ2_bzBuffToBuffDecompress@24
BZ2_bzCompress@8
BZ2_bzCompressEnd@4
BZ2_bzCompressInit@16
BZ2_bzDecompress@4
BZ2_bzDecompressEnd@4
BZ2_bzDecompressInit@12
BZ2_bzRead@16
BZ2_bzReadClose@8
BZ2_bzReadGetUnused@16
BZ2_bzReadOpen@24
BZ2_bzWrite@16
BZ2_bzWriteClose64@28
BZ2_bzWriteClose@20

>
> We've had some problems with recent versions of Cygwin not sorting properly.
>  The last instance had it put names in the order
>
>  BZ2_bzWriteClose@20
>  BZ2_bzWriteClose64@28
>
> but ASCII order should put @ after 6.  Are you using the comm and Cygwin
> dlls from Rtools, or have you got newer ones?

As far as I know I should only be using the dlls from Rtools.  It is
the first thing on my path environment variable, and although cygwin
is installed, I do not even have it on my path.  Interestingly, there
are no problems if set MULTI=32 instead of 64 in MkRules.

Thanks again,

Josh

>
> Duncan Murdoch



-- 
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/

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Re: [Rd] How to list package dependency on a Bioconductor package?

2012-05-08 Thread Simon Urbanek

Steven,

On May 7, 2012, at 1:24 PM, Steven Lund wrote:

> I recently submit a package called QuasiSeq.  The package source and
> Windows binary worked fine, but the MacOS X binary failed. The bottom of
> the CRAN page for QuasiSeq shows
> 
> Downloads:
>  Package source: QuasiSeq_1.0-1.tar.gz
>  MacOS X binary: not available, see check log.
>  Windows binary: QuasiSeq-1.0-1.zip
>  Reference manual:  QuasiSeq.pdf
> 
> 
> The log for the MacOS X binary shows
>   - using R version 2.15.0 (2012-03-30)
>   - using platform: i386-apple-darwin9.8.0 (32-bit)
>   -  using session charset: ASCII
>   -  checking for file 'QuasiSeq/DESCRIPTION' ... OK
>   -  this is package 'QuasiSeq' version '1.0-1'
>   -  checking package namespace information ... OK
>   -  checking package dependencies ... ERROR
>   Package required but not available: 'edgeR'
> 
>   See the information on DESCRIPTION files in the chapter
> 'Creating R
>   packages' of the 'Writing R Extensions' manual.
>   -  elapsed time (check, wall clock): 0:01
> 
> Is there a simple remedy to the problems caused by the dependency on edgeR,
> or would you advise that I put a work-around into my source code using
> 'require' so I can list edgeR under Suggests instead of Depends or Includes?
> 

Well, if your package doesn't depend on it, it should certainly not be in 
Depends. But that is a design decision (depending on packages outside CRAN is 
somewhat tricky because in general you cannot guarantee availability, but it is 
legal ;)).

If you need any additional non-CRAN dependencies on Mac OS X, they can be 
installed if there are working self-sufficient binaries, you just need to tell 
me.

Cheers,
Simon


> 
> On Tue, Jan 3, 2012 at 7:42 AM, Uwe Ligges
> wrote:
> 
>> 
>> 
>> On 03.01.2012 00:16, Steven Lund wrote:
>> 
>>> I know others have asked similar questions to the R developers, but I
>>> could not find the solution to this question.  Please forgive me if I
>>> have missed a crucial point in a previous post.
>>> 
>>> I would like to submit a package to CRAN that depends on the
>>> bioconductor package "edgeR".  Listing "edgeR" under the Depends or
>>> Imports lines in the DESCRIPTION file for my package causes an error
>>> when running the `R CMD check' command on my package's 'tar.gz' file:
>>> 
>>> * checking package dependencies ... ERROR
>>> Package required but not available: āedgeRā
>>> 
>>> 
>>> Is there documentation or an example anywhere of how to handle
>>> dependencies on Bioconductor packages when creating a package for
>>> CRAN?
>>> 
>> 
>> 
>> Same as for CRAN packages. The CRAN check farm will automatically install
>> the dependency from BioConductor if available for the corresponding
>> platform / R version.
>> 
>> Uwe Ligges
>> 
>> 
>> 
>> 
>> 
>>> Thank you!
>>> 
>>> -Steve
>>> 
>>> __**
>>> R-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/**listinfo/r-devel
>>> 
>> 
> 
>   [[alternative HTML version deleted]]
> 
> __
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> https://stat.ethz.ch/mailman/listinfo/r-devel

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Re: [Rd] How to list package dependency on a Bioconductor package?

2012-05-08 Thread Martin Morgan


On 5/8/2012 8:44 AM, Simon Urbanek wrote:

Steven,

On May 7, 2012, at 1:24 PM, Steven Lund wrote:


I recently submit a package called QuasiSeq.  The package source and
Windows binary worked fine, but the MacOS X binary failed. The bottom of
the CRAN page for QuasiSeq shows

Downloads:
  Package source: QuasiSeq_1.0-1.tar.gz
  MacOS X binary: not available, see check log.
  Windows binary: QuasiSeq-1.0-1.zip
  Reference manual:  QuasiSeq.pdf


The log for the MacOS X binary shows
   - using R version 2.15.0 (2012-03-30)
   - using platform: i386-apple-darwin9.8.0 (32-bit)
   -  using session charset: ASCII
   -  checking for file 'QuasiSeq/DESCRIPTION' ... OK
   -  this is package 'QuasiSeq' version '1.0-1'
   -  checking package namespace information ... OK
   -  checking package dependencies ... ERROR
   Package required but not available: 'edgeR'

   See the information on DESCRIPTION files in the chapter
'Creating R
   packages' of the 'Writing R Extensions' manual.
   -  elapsed time (check, wall clock): 0:01

Is there a simple remedy to the problems caused by the dependency on edgeR,
or would you advise that I put a work-around into my source code using
'require' so I can list edgeR under Suggests instead of Depends or Includes?


Well, if your package doesn't depend on it, it should certainly not be in 
Depends. But that is a design decision (depending on packages outside CRAN is 
somewhat tricky because in general you cannot guarantee availability, but it is 
legal ;)).

If you need any additional non-CRAN dependencies on Mac OS X, they can be 
installed if there are working self-sufficient binaries, you just need to tell 
me.


We're talking about a Bioconductor package here; the Mac binaries are 
available for R-2-15 
http://bioconductor.org/packages/release/bioc/html/edgeR.html in the 
usual way; the Windows binaries are apparently discovered by the CRAN 
build system, so it sounds like CRAN's Mac builds are mis-configured, or 
Bioconductor's binary builds are inadequate?


Martin


Cheers,
Simon



On Tue, Jan 3, 2012 at 7:42 AM, Uwe Ligges
wrote:



On 03.01.2012 00:16, Steven Lund wrote:


I know others have asked similar questions to the R developers, but I
could not find the solution to this question.  Please forgive me if I
have missed a crucial point in a previous post.

I would like to submit a package to CRAN that depends on the
bioconductor package "edgeR".  Listing "edgeR" under the Depends or
Imports lines in the DESCRIPTION file for my package causes an error
when running the `R CMD check' command on my package's 'tar.gz' file:

* checking package dependencies ... ERROR
Package required but not available: āedgeRā


Is there documentation or an example anywhere of how to handle
dependencies on Bioconductor packages when creating a package for
CRAN?



Same as for CRAN packages. The CRAN check farm will automatically install
the dependency from BioConductor if available for the corresponding
platform / R version.

Uwe Ligges






Thank you!

-Steve

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--
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

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Re: [Rd] file 2 is not in sorted order error building unsuffered consequences

2012-05-08 Thread Duncan Murdoch


This time it was a similar error on a different file.  Now fixed.

Duncan Murdoch

On 08/05/2012 11:20 AM, Joshua Wiley wrote:

On Tue, May 8, 2012 at 3:48 AM, Duncan Murdoch  wrote:
>  On 12-05-08 1:46 AM, Joshua Wiley wrote:
>>
>>  Hi All,
>>
>>  I just downloaded the source tar ball (Revision: 59324 Last Changed
>>  Date: 2012-05-07) and tried to compile on a Win x64 system.  I am
>>  using Rtools version 2.15.0.1919.  The only change I make is changing
>>  MkRules.dist ->MkRules.local and setting Multi=64  I have previously
>>  compiled unsuffered consquences without issue, but on the current
>>  version, I get this error
>>
>>
>>  windres -F pe-x86-64  -I../include -i dllversion.rc -o dllversion.o
>>  comm: file 2 is not in sorted order
>>  make[3]: *** [R.dll] Error 1
>>  make[2]: *** [../../bin/x64/R.dll] Error 2
>>  make[1]: *** [rbuild] Error 2
>>  make: *** [all] Error 2
>>
>>  I did not note any other errors or warnings earlier on, though I may
>>  have missed some.  I can provide the full log if requested.  Any
>>  ideas?
>
>
>  I believe that message is about the file src/gnuwin32/Rdll.hide.  It is
>  supposed to be sorted, using ASCII collation order.  I believe the version
>  in the repository is sorted properly; can you check yours?

Thanks for your reply.  It looks sorted correctly and explicitly
sorting prior to running make does not change the error.  here is a
bit of output:

BZ2_bzBuffToBuffCompress@28
BZ2_bzBuffToBuffDecompress@24
BZ2_bzCompress@8
BZ2_bzCompressEnd@4
BZ2_bzCompressInit@16
BZ2_bzDecompress@4
BZ2_bzDecompressEnd@4
BZ2_bzDecompressInit@12
BZ2_bzRead@16
BZ2_bzReadClose@8
BZ2_bzReadGetUnused@16
BZ2_bzReadOpen@24
BZ2_bzWrite@16
BZ2_bzWriteClose64@28
BZ2_bzWriteClose@20

>
>  We've had some problems with recent versions of Cygwin not sorting properly.
>The last instance had it put names in the order
>
>BZ2_bzWriteClose@20
>BZ2_bzWriteClose64@28
>
>  but ASCII order should put @ after 6.  Are you using the comm and Cygwin
>  dlls from Rtools, or have you got newer ones?

As far as I know I should only be using the dlls from Rtools.  It is
the first thing on my path environment variable, and although cygwin
is installed, I do not even have it on my path.  Interestingly, there
are no problems if set MULTI=32 instead of 64 in MkRules.

Thanks again,

Josh

>
>  Duncan Murdoch





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Re: [Rd] How to list package dependency on a Bioconductor package?

2012-05-08 Thread Simon Urbanek


On May 8, 2012, at 11:56 AM, Martin Morgan wrote:

> On 5/8/2012 8:44 AM, Simon Urbanek wrote:
>> Steven,
>> 
>> On May 7, 2012, at 1:24 PM, Steven Lund wrote:
>> 
>>> I recently submit a package called QuasiSeq.  The package source and
>>> Windows binary worked fine, but the MacOS X binary failed. The bottom of
>>> the CRAN page for QuasiSeq shows
>>> 
>>> Downloads:
>>>  Package source: QuasiSeq_1.0-1.tar.gz
>>>  MacOS X binary: not available, see check log.
>>>  Windows binary: QuasiSeq-1.0-1.zip
>>>  Reference manual:  QuasiSeq.pdf
>>> 
>>> 
>>> The log for the MacOS X binary shows
>>>   - using R version 2.15.0 (2012-03-30)
>>>   - using platform: i386-apple-darwin9.8.0 (32-bit)
>>>   -  using session charset: ASCII
>>>   -  checking for file 'QuasiSeq/DESCRIPTION' ... OK
>>>   -  this is package 'QuasiSeq' version '1.0-1'
>>>   -  checking package namespace information ... OK
>>>   -  checking package dependencies ... ERROR
>>>   Package required but not available: 'edgeR'
>>> 
>>>   See the information on DESCRIPTION files in the chapter
>>> 'Creating R
>>>   packages' of the 'Writing R Extensions' manual.
>>>   -  elapsed time (check, wall clock): 0:01
>>> 
>>> Is there a simple remedy to the problems caused by the dependency on edgeR,
>>> or would you advise that I put a work-around into my source code using
>>> 'require' so I can list edgeR under Suggests instead of Depends or Includes?
>>> 
>> Well, if your package doesn't depend on it, it should certainly not be in 
>> Depends. But that is a design decision (depending on packages outside CRAN 
>> is somewhat tricky because in general you cannot guarantee availability, but 
>> it is legal ;)).
>> 
>> If you need any additional non-CRAN dependencies on Mac OS X, they can be 
>> installed if there are working self-sufficient binaries, you just need to 
>> tell me.
> 
> We're talking about a Bioconductor package here; the Mac binaries are 
> available for R-2-15 
> http://bioconductor.org/packages/release/bioc/html/edgeR.html in the usual 
> way; the Windows binaries are apparently discovered by the CRAN build system, 
> so it sounds like CRAN's Mac builds are mis-configured, or Bioconductor's 
> binary builds are inadequate?
> 

Neither, nor. 


>> 
>> Cheers,
>> Simon
>> 
>> 
>>> On Tue, Jan 3, 2012 at 7:42 AM, Uwe Ligges
>>> wrote:
>>> 
 
 On 03.01.2012 00:16, Steven Lund wrote:
 
> I know others have asked similar questions to the R developers, but I
> could not find the solution to this question.  Please forgive me if I
> have missed a crucial point in a previous post.
> 
> I would like to submit a package to CRAN that depends on the
> bioconductor package "edgeR".  Listing "edgeR" under the Depends or
> Imports lines in the DESCRIPTION file for my package causes an error
> when running the `R CMD check' command on my package's 'tar.gz' file:
> 
> * checking package dependencies ... ERROR
> Package required but not available: āedgeRā
> 
> 
> Is there documentation or an example anywhere of how to handle
> dependencies on Bioconductor packages when creating a package for
> CRAN?
> 
 
 Same as for CRAN packages. The CRAN check farm will automatically install
 the dependency from BioConductor if available for the corresponding
 platform / R version.
 
 Uwe Ligges
 
 
 
 
 
> Thank you!
> 
> -Steve
> 
> __**
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/**listinfo/r-devel
> 
>>> [[alternative HTML version deleted]]
>>> 
>>> __
>>> 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.ch/mailman/listinfo/r-devel
> 
> 
> -- 
> Dr. Martin Morgan, PhD
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
> 
> 

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Re: [Rd] f951.exe: sorry, unimplemented: 64-bit mode not compiled

2012-05-08 Thread Balasubramanian Narasimhan

The original post below refers to an issue that arose with glmnet. It 
has since been fixed but the underlying problem (I believe) is a bug in 
gcc/gfortran 2.6.3 toolchain.  Here is a reproducible example, test.f90.


program dblbug
  real :: x, y
  x=2
  y=exp(dble(x))
end program dblbug

Compile with gfortran -fdefault-real-8 -o test test.f90.

The program will crash on Windows but not on i386 or x86_64 linux (same 
version of toolchain) but I think that says nothing.


Note: The glmnet code was originally written for single precision and 
hence the flag -fdefault-real-8. The fix was to just to remove the "dble."


-Naras



On 5/4/12 6:58 PM, Simon Urbanek wrote:

On May 4, 2012, at 8:48 PM, Spencer Graves wrote:


Hello:


  Under my Windows 7 system, "R CMD check DiercxkSpline_1.1-5.tar.gz" fails 
because:


f951.exe: sorry, unimplemented: 64-bit mode not compiled in


This typically means that you're using the wrong (old) compiler. The new MinGW 
compilers support both -m32 and -m64. You have to set the PATH to the new 
compilers (in the gcc-4.6.3 subdirectory of Rtools) *before* any old compilers 
in Rtools.

Cheers,
Simon



make: *** [bispev.o] Error 1
gfortran -m64 -O2  -mtune=core2 -c bispev.f -o bispev.o
f951.exe: sorry, unimplemented: 64-bit mode not compiled in

make: *** [bispev.o] Error 1
ERROR: compilation failed for package 'DierckxSpline'


  A similar problem was reported for package "glmnet" 
(http://stackoverflow.com/questions/10291189/compiling-glmnet-failed-in-windows) plus one with R 
2.14.2 
(http://r.789695.n4.nabble.com/Problems-when-building-a-package-for-Windows-64-td4464488.html).  
However, I get this with R 2.15.0 and the latest R tools (reinstalled earlier today).  On R-Forge, 
DierckxSpline has "Build status:  Current", which suggests that R-Forge does NOT have 
this problem.  I read through the two replies to these two earlier questions without seeing how to 
fix my problem.





  Thanks in advance for any suggestions.


  Spencer Graves

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Re: [Rd] file 2 is not in sorted order error building unsuffered consequences

Re: [Rd] How to list package dependency on a Bioconductor package?

Re: [Rd] file 2 is not in sorted order error building unsuffered consequences

Re: [Rd] How to list package dependency on a Bioconductor package?

Re: [Rd] How to list package dependency on a Bioconductor package?

Re: [Rd] file 2 is not in sorted order error building unsuffered consequences

Re: [Rd] How to list package dependency on a Bioconductor package?

Re: [Rd] f951.exe: sorry, unimplemented: 64-bit mode not compiled

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