Re: [Rd] Submitting packages with weak circular dependencies to CRAN.
Hi Pavel, On 03/08/2013 04:42 PM, Pavel N. Krivitsky wrote: Hello, R-devel, I am planning to submit two packages, A and B, to CRAN. Package B uses an API exported by package A, while package A uses package B to test the API in question. Thus, package B Depends on, and Enhances, A, and A Suggests B. Could I get some guidance on submitting them to CRAN? A cannot be checked without B, but B cannot be installed without A. The CRAN people will probably have a better solution to offer but the following 3-step procedure should work, at least in theory: - First submit a degraded version of A i.e. a version that doesn't suggest B and where all the tests using B are turned off. - Then submit B. - Then submit the full version of A with a higher version. Or, merge A and B in a single package... Cheers, H. Thanks in advance, Pavel Krivitsky __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Submitting packages with weak circular dependencies to CRAN.
On 09.03.2013 10:02, Hervé Pagès wrote: Hi Pavel, On 03/08/2013 04:42 PM, Pavel N. Krivitsky wrote: Hello, R-devel, I am planning to submit two packages, A and B, to CRAN. Package B uses an API exported by package A, while package A uses package B to test the API in question. Thus, package B Depends on, and Enhances, A, and A Suggests B. Could I get some guidance on submitting them to CRAN? A cannot be checked without B, but B cannot be installed without A. The CRAN people will probably have a better solution to offer but the following 3-step procedure should work, at least in theory: - First submit a degraded version of A i.e. a version that doesn't suggest B and where all the tests using B are turned off. - Then submit B. - Then submit the full version of A with a higher version. Or, merge A and B in a single package... ... or ask the CRAN people directly. They will tell you to go ahead, submit A and mention in the submission mail that the Suggested B which Depends on A will be uploaded once A has been accepted. Best, Uwe Ligges Cheers, H. Thanks in advance, Pavel Krivitsky __ 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
[Rd] question on why Rigroup package moved to Archive on CRAN
Hi, Who should I ask about my package Rigroup_0.83 being moved to Archive status on CRAN and no longer available via install.package? I have no problems with the move if this was simply because of low demand. However, if there was a build issue with the newest releases that caused problems, I would be happy to address it. I'll just ask my students to install it from my own locally hosted source archive. Thanks, Kevin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] question on why Rigroup package moved to Archive on CRAN
On Sat, Mar 9, 2013 at 12:25 PM, Kevin Hendricks wrote: > Hi, > > Who should I ask about my package Rigroup_0.83 being moved to Archive status > on CRAN and no longer available via install.package? I have no problems with > the move if this was simply because of low demand. However, if there was a > build issue with the newest releases that caused problems, I would be happy > to address it. I'll just ask my students to install it from my own locally > hosted source archive. Most likely yourself; from the 'CRAN Repository Policy' [http://cran.r-project.org/web/packages/policies.html]: "Packages will not normally be removed from CRAN: however, they may be archived, including at the maintainer's request. Packages for which R CMD check gives an ‘ERROR’ when a new R x.y.0 version is released will be archived (or in exceptional circumstances updated by the CRAN team) unless the maintainer has set a firm deadline for an upcoming update (and keeps to it). Maintainers will be asked to update packages which show any warnings or significant notes, especially at around the time of a new x.y.0 release. Packages which are not updated are liable to be archived." /Henrik > > Thanks, > > Kevin > __ > 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
[Rd] Why cannot `Rscript -e` accept an empty line?
See the example below (under Ubuntu): $ Rscript -e '1' -e '2' [1] 1 [1] 2 $ Rscript -e '1' -e '' -e '2' ERROR: option '-e' requires an argument $ uname -a Linux xie 3.5.0-25-generic #39-Ubuntu SMP Mon Feb 25 18:26:58 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Similar problem under Windows: Rscript -e "1" -e "" -e "2" [1] 1 Error: object 'e' not found Execution halted I can certainly save the code in a script and run Rscript foo.R, but I'm curious why Rscript stops when the -e argument is an empty string. Regards, Yihui -- Yihui Xie Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] question on why Rigroup package moved to Archive on CRAN
Hi, Thanks for that info. It works/builds without error or warnings on my RedHat Enterprise 6 with R 2.15.2 version which I use but must be broken somehow on later versions. I will see if I can find the autobuild warnings error report someplace. Kevin Sent from my iPad On 2013-03-09, at 4:00 PM, Henrik Bengtsson wrote: > On Sat, Mar 9, 2013 at 12:25 PM, Kevin Hendricks > wrote: >> Hi, >> >> Who should I ask about my package Rigroup_0.83 being moved to Archive status >> on CRAN and no longer available via install.package? I have no problems >> with the move if this was simply because of low demand. However, if there >> was a build issue with the newest releases that caused problems, I would be >> happy to address it. I'll just ask my students to install it from my own >> locally hosted source archive. > > Most likely yourself; from the 'CRAN Repository Policy' > [http://cran.r-project.org/web/packages/policies.html]: > > "Packages will not normally be removed from CRAN: however, they may be > archived, including at the maintainer's request. > > Packages for which R CMD check gives an ‘ERROR’ when a new R x.y.0 > version is released will be archived (or in exceptional circumstances > updated by the CRAN team) unless the maintainer has set a firm > deadline for an upcoming update (and keeps to it). > > Maintainers will be asked to update packages which show any warnings > or significant notes, especially at around the time of a new x.y.0 > release. Packages which are not updated are liable to be archived." > > /Henrik > >> >> Thanks, >> >> Kevin >> __ >> 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
Re: [Rd] question on why Rigroup package moved to Archive on CRAN
Hi, One last quick question ... does anyone archive older CRAN package check summaries? I searched the web but could not find any. My package was archived in February of this year so any package check summary from earlier than that should help me figure out what is broken on MacOSX or Windows. Thanks, Kevin Sent from my iPad On 2013-03-09, at 4:38 PM, Kevin Hendricks wrote: > Hi, > Thanks for that info. It works/builds without error or warnings on my RedHat > Enterprise 6 with R 2.15.2 version which I use but must be broken somehow on > later versions. I will see if I can find the autobuild warnings error report > someplace. > > Kevin > > > Sent from my iPad > > On 2013-03-09, at 4:00 PM, Henrik Bengtsson wrote: > >> On Sat, Mar 9, 2013 at 12:25 PM, Kevin Hendricks >> wrote: >>> Hi, >>> >>> Who should I ask about my package Rigroup_0.83 being moved to Archive >>> status on CRAN and no longer available via install.package? I have no >>> problems with the move if this was simply because of low demand. However, >>> if there was a build issue with the newest releases that caused problems, I >>> would be happy to address it. I'll just ask my students to install it from >>> my own locally hosted source archive. >> >> Most likely yourself; from the 'CRAN Repository Policy' >> [http://cran.r-project.org/web/packages/policies.html]: >> >> "Packages will not normally be removed from CRAN: however, they may be >> archived, including at the maintainer's request. >> >> Packages for which R CMD check gives an ‘ERROR’ when a new R x.y.0 >> version is released will be archived (or in exceptional circumstances >> updated by the CRAN team) unless the maintainer has set a firm >> deadline for an upcoming update (and keeps to it). >> >> Maintainers will be asked to update packages which show any warnings >> or significant notes, especially at around the time of a new x.y.0 >> release. Packages which are not updated are liable to be archived." >> >> /Henrik >> >>> >>> Thanks, >>> >>> Kevin >>> __ >>> 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] question on why Rigroup package moved to Archive on CRAN
On Sat, Mar 9, 2013 at 2:17 PM, Kevin Hendricks
wrote:
> Hi,
> One last quick question ... does anyone archive older CRAN package check
> summaries? I searched the web but could not find any. My package was
> archived in February of this year so any package check summary from earlier
> than that should help me figure out what is broken on MacOSX or Windows.
FWIW, it fails check on my Mac as follows:
* checking examples ... ERROR
Running examples in 'Rigroup-Ex.R' failed
The error most likely occurred in:
> ### Name: igroupAlls
> ### Title: calculates logical All for small integer groups of logical
> ### vectors
> ### Aliases: igroupAlls
> ### Keywords: utilities
>
> ### ** Examples
>
> y <- rnorm(100)
> i <- rep(1:25,4)
> x <- (y > 1.0)
> alls <- igroupAlls(x,i)
Error in .External("igroupFuns", x, i, R_IGFMINS, na.rm, PACKAGE = "Rigroup") :
Incorrect number of arguments (4), expecting 1 for 'igroupFuns'
Calls: igroupAlls -> .External
Execution halted
Dan
> Thanks,
> Kevin
>
>
> Sent from my iPad
>
> On 2013-03-09, at 4:38 PM, Kevin Hendricks
> wrote:
>
>> Hi,
>> Thanks for that info. It works/builds without error or warnings on my
>> RedHat Enterprise 6 with R 2.15.2 version which I use but must be broken
>> somehow on later versions. I will see if I can find the autobuild warnings
>> error report someplace.
>>
>> Kevin
>>
>>
>> Sent from my iPad
>>
>> On 2013-03-09, at 4:00 PM, Henrik Bengtsson wrote:
>>
>>> On Sat, Mar 9, 2013 at 12:25 PM, Kevin Hendricks
>>> wrote:
Hi,
Who should I ask about my package Rigroup_0.83 being moved to Archive
status on CRAN and no longer available via install.package? I have no
problems with the move if this was simply because of low demand. However,
if there was a build issue with the newest releases that caused problems,
I would be happy to address it. I'll just ask my students to install it
from my own locally hosted source archive.
>>>
>>> Most likely yourself; from the 'CRAN Repository Policy'
>>> [http://cran.r-project.org/web/packages/policies.html]:
>>>
>>> "Packages will not normally be removed from CRAN: however, they may be
>>> archived, including at the maintainer's request.
>>>
>>> Packages for which R CMD check gives an ‘ERROR’ when a new R x.y.0
>>> version is released will be archived (or in exceptional circumstances
>>> updated by the CRAN team) unless the maintainer has set a firm
>>> deadline for an upcoming update (and keeps to it).
>>>
>>> Maintainers will be asked to update packages which show any warnings
>>> or significant notes, especially at around the time of a new x.y.0
>>> release. Packages which are not updated are liable to be archived."
>>>
>>> /Henrik
>>>
Thanks,
Kevin
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>>
>> __
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>
> __
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Re: [Rd] Why cannot `Rscript -e` accept an empty line?
On Sat, Mar 9, 2013 at 9:32 PM, Yihui Xie wrote:
> See the example below (under Ubuntu):
>
> $ Rscript -e '1' -e '2'
> [1] 1
> [1] 2
> $ Rscript -e '1' -e '' -e '2'
> ERROR: option '-e' requires an argument
> $ uname -a
> Linux xie 3.5.0-25-generic #39-Ubuntu SMP Mon Feb 25 18:26:58 UTC 2013
> x86_64 x86_64 x86_64 GNU/Linux
>
> Similar problem under Windows:
>
> Rscript -e "1" -e "" -e "2"
> [1] 1
> Error: object 'e' not found
> Execution halted
>
> I can certainly save the code in a script and run Rscript foo.R, but
> I'm curious why Rscript stops when the -e argument is an empty string.
There's some over-zealous argument parsing in the main R startup
shell script. You didn't try negative numbers, did you?
$ Rscript -e "-1"
ERROR: option '-e' requires an argument
$ Rscript -e "+1"
[1] 1
The R script strips anything starting with a - from the arg after -e
and throws that error if there's nothing left. The relevant lines are:
-e)
if test -n "`echo ${2} | ${SED} 's/^-.*//'`"; then
a=`echo "${2}" | ${SED} -e 's/ /~+~/g'`; shift
else
error "option '${1}' requires an argument"
fi
- now at least that's on Unix. The Windows problem looks like its
doing something else, and mashing some quotes up and passing 'e' as an
expression to one of the other -e options.
Not sure what the fix might be, except maybe for the user to always
wrap their expressions in curly brackets...
Barry
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Re: [Rd] question on why Rigroup package moved to Archive on CRAN
Hi Dan,
Thank you! I dig up a Mac at work and recreate this.
Kevin
On 2013-03-09, at 5:52 PM, Dan Tenenbaum wrote:
> On Sat, Mar 9, 2013 at 2:17 PM, Kevin Hendricks
> wrote:
>> Hi,
>> One last quick question ... does anyone archive older CRAN package check
>> summaries? I searched the web but could not find any. My package was
>> archived in February of this year so any package check summary from earlier
>> than that should help me figure out what is broken on MacOSX or Windows.
>
> FWIW, it fails check on my Mac as follows:
>
> * checking examples ... ERROR
> Running examples in 'Rigroup-Ex.R' failed
> The error most likely occurred in:
>
>> ### Name: igroupAlls
>> ### Title: calculates logical All for small integer groups of logical
>> ### vectors
>> ### Aliases: igroupAlls
>> ### Keywords: utilities
>>
>> ### ** Examples
>>
>> y <- rnorm(100)
>> i <- rep(1:25,4)
>> x <- (y > 1.0)
>> alls <- igroupAlls(x,i)
> Error in .External("igroupFuns", x, i, R_IGFMINS, na.rm, PACKAGE = "Rigroup")
> :
> Incorrect number of arguments (4), expecting 1 for 'igroupFuns'
> Calls: igroupAlls -> .External
> Execution halted
>
>
> Dan
>
>
>> Thanks,
>> Kevin
>>
>>
>> Sent from my iPad
>>
>> On 2013-03-09, at 4:38 PM, Kevin Hendricks
>> wrote:
>>
>>> Hi,
>>> Thanks for that info. It works/builds without error or warnings on my
>>> RedHat Enterprise 6 with R 2.15.2 version which I use but must be broken
>>> somehow on later versions. I will see if I can find the autobuild warnings
>>> error report someplace.
>>>
>>> Kevin
>>>
>>>
>>> Sent from my iPad
>>>
>>> On 2013-03-09, at 4:00 PM, Henrik Bengtsson wrote:
>>>
On Sat, Mar 9, 2013 at 12:25 PM, Kevin Hendricks
wrote:
> Hi,
>
> Who should I ask about my package Rigroup_0.83 being moved to Archive
> status on CRAN and no longer available via install.package? I have no
> problems with the move if this was simply because of low demand.
> However, if there was a build issue with the newest releases that caused
> problems, I would be happy to address it. I'll just ask my students to
> install it from my own locally hosted source archive.
Most likely yourself; from the 'CRAN Repository Policy'
[http://cran.r-project.org/web/packages/policies.html]:
"Packages will not normally be removed from CRAN: however, they may be
archived, including at the maintainer's request.
Packages for which R CMD check gives an ‘ERROR’ when a new R x.y.0
version is released will be archived (or in exceptional circumstances
updated by the CRAN team) unless the maintainer has set a firm
deadline for an upcoming update (and keeps to it).
Maintainers will be asked to update packages which show any warnings
or significant notes, especially at around the time of a new x.y.0
release. Packages which are not updated are liable to be archived."
/Henrik
>
> Thanks,
>
> Kevin
> __
> 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
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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Re: [Rd] question on why Rigroup package moved to Archive on CRAN
Hi Dan,
In case this catches anyone else ...
FWIW, I found the issue ... in my Rinit.c, my package uses the .External call
which actually takes one SEXP which points to a "varargs-like" list.
Under 2.15.X and earlier, I thought the proper entry for an .External call was
as below since it only does take one pointer as an argument:
#include "Rigroup.h"
/* Automate using sed or something. */
#if _MSC_VER >= 1000
__declspec(dllexport)
#endif
static const R_ExternalMethodDef R_ExtDef[] = {
{"igroupFuns", (DL_FUNC)&igroupFuns, 1},
{NULL, NULL, 0},
};
void R_init_Rigroup(DllInfo *info)
{
R_registerRoutines(info,NULL,NULL,NULL,R_ExtDef);
}
But now according to the latest online docs on building your own package it
says:
"For routines with a variable number of arguments invoked viathe .External
interface, one specifies -1 for the number of arguments which tells R not to
check the actual number passed. Note that the number of arguments passed to
.External are not currently checked but they will be in R 3.0.0."
So I need to change my Rinit.c to change the "1" to a "-1" and that error
should go away.
Thanks again for all your help with this. I will update my package and
resubmit it once version 3.0 gets released and I get a chance to verify that
this does in fact fix the problem.
Kevin
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