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] Logical Error? (PR#13516)
This is not a bug. Please do read the FAQ before posting and creating work for others. http://cran.r-project.org/doc/FAQ/R-FAQ.html#R-Bugs http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f Joshua Ulrich -- http://quantemplation.blogspot.com On Tue, Feb 10, 2009 at 8:55 AM, wrote: > Full_Name: Suzi Alves Camey > Version: 2.7.2 > OS: > Submission from: (NULL) (143.54.37.254) > > > Using the commands bellow I expected that the answer is TRUE, but it is FALSE! > > P_exposicao=.9 > (1-P_exposicao)==.1 > > __ > 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] bug of *switch* function
Because "<-" assigs a value. It does not name the alternatives. Again, please read ?switch. These two examples are the same: > organism <- 'foo' > (species <- switch(organism, human <- "HS", fly <- "DM", yeast <- "SC")) [1] "HS" > (species <- switch(organism, "HS", "DM", "SC")) [1] "HS" Josh -- http://quantemplation.blogspot.com On Mon, Mar 9, 2009 at 9:35 AM, guangchuang yu wrote: > But Why ? > > Why can not use "<-" ? > > On Mon, Mar 9, 2009 at 10:31 PM, Jeff Ryan wrote: > >> This isn't a bug in R. >> >> You are assigning within the switch statement, and it is returning the >> first TRUE value (human). >> >> Use "=" not "<-" >> >> species <- switch(organism, human="HS", fly="DM", yeast="SC") >> > species >> [1] "SC" >> >> >> HTH >> Jeff >> >> On Mon, Mar 9, 2009 at 8:55 AM, guangchuang yu >> wrote: >> > Hi, >> > >> > When I call the *switch* function first time, it works. but when I call >> it >> > at the second time, it does nothing. The version I use is R version 2.9.0 >> > Under development (unstable) (2009-02-21 r47969) >> > >> > >> > here is the output: >> > >> >> organism="human" >> >> species <- switch(organism, >> > human <- "Hs", >> > fly <- "Dm", >> > mouse <- "Mm", >> > rat <- "Rn", >> > yeast <- "Sc" >> > ) >> > species <- switch(organism, >> > + human <- "Hs", >> > + fly <- "Dm", >> > + mouse <- "Mm", >> > + rat <- "Rn", >> > + yeast <- "Sc" >> > + ) >> >> species >> > [1] "Hs" >> >> organism="yeast" >> >> species <- switch(organism, >> > human <- "Hs", >> > fly <- "Dm", >> > mouse <- "Mm", >> > rat <- "Rn", >> > yeast <- "Sc" >> > ) >> > species <- switch(organism, >> > + human <- "Hs", >> > + fly <- "Dm", >> > + mouse <- "Mm", >> > + rat <- "Rn", >> > + yeast <- "Sc" >> > + ) >> >> species >> > [1] "Hs" >> > >> > >> > when I change *organism* to "yeast", and call *switch* function again, >> > *species* suppose to be changed to "Sc", but it remain it's original >> value. >> > >> > You can see my screenshot at >> > http://ygc.azpala.com/2009/03/09/bug-of-r-29-dev >> > >> > -- >> > Bests, >> > Guangchuang Yu >> > >> > --~--~-~--~~~---~--~~ >> > Rm 848 Dept 9 >> > Institute of Radiation Medicine >> > 27 Taiping Rd. Haidian Dist. >> > Beijing, 100850, China >> > Telephone: (86)-010-66931422 >> > Mobile: +86-13439009806 >> > Email: guangchuan...@gmail.com >> > -~--~~~~--~~--~--~--- >> > >> > [[alternative HTML version deleted]] >> > >> > __ >> > R-devel@r-project.org mailing list >> > https://stat.ethz.ch/mailman/listinfo/r-devel >> > >> >> >> >> -- >> Jeffrey Ryan >> jeffrey.r...@insightalgo.com >> >> ia: insight algorithmics >> www.insightalgo.com >> > > > > -- > Bests, > Guangchuang Yu > > --~--~-~--~~~---~--~~ > Rm 848 Dept 9 > Institute of Radiation Medicine > 27 Taiping Rd. Haidian Dist. > Beijing, 100850, China > Telephone: (86)-010-66931422 > Mobile: +86-13439009806 > Email: guangchuan...@gmail.com > -~--~~~~--~~--~--~--- > > [[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
Re: [Rd] surprising behaviour of names<-
On Thu, Mar 12, 2009 at 3:24 PM, G. Jay Kerns wrote: > Wacek Kusnierczyk wrote: > > [snip] > >> as i explained a few months ago, i study r to find examples of bad >> design. if anyone in the r core is interested in having the problems i >> report fixed, i'm happy to get involved in a discussion about the design >> and implementation. if not, i'm happy with just pointing out the issues. > > :-) > > I am prompted to imagine someone pointing out to the volunteers of the > International Red Cross - on the field of a natural disaster, no less > - that their uniforms are not an acceptably consistent shade of > pink... or that the screws on their tourniquets do not have the > appropriate pitch as to minimize the friction for the turner... Your analogy may overstate the case a bit, since R volunteers - while providing a valuable service to the community - are not dealing with matters of life and death. Habitat for Humanity (an organization that provides free housing to the under-privileged) would be a better comparison. I'm sure those volunteers would appreciate a critique of their work, provided the critique was not condescending and focused on serving the community better, not to showcase the acumen of the one giving the critique. > > As a practicing statistician I am simply thankful that the bleeding is > stopped. :-) > > Cheers to R-Core (and the hundreds of other volunteers). > Jay > I second that. Thanks to R-Core et al for all their generous efforts. > > > *** > G. Jay Kerns, Ph.D. > Associate Professor > Department of Mathematics & Statistics > Youngstown State University > Youngstown, OH 44555-0002 USA > Office: 1035 Cushwa Hall > Phone: (330) 941-3310 Office (voice mail) > -3302 Department > -3170 FAX > E-mail: gke...@ysu.edu > http://www.cc.ysu.edu/~gjkerns/ > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > Best, Josh -- http://quantemplation.blogspot.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] 'is.integer' (PR#13671)
> typeof(1) [1] "double" 1 is obviously *not* an integer value. Best, Josh -- http://quantemplation.blogspot.com http://www.fosstrading.com On Wed, Apr 22, 2009 at 12:45 PM, wrote: > Full_Name: Mauricio > Version: 2.9.0 (2009-04-17) > OS: i486-pc-linux-gnu > Submission from: (NULL) (193.205.203.3) > > > This is a very simple function that seems not to be working, according to the > definition given by '?is.integer'. > > I checked in the Bug Tracking page at http://bugs.R-project.org/, but I didn't > find any related message. > > The possible problem is: > > >> is.integer(1) > [1] FALSE > > and 1 is obviously an integer value. > > > I would really appreciate if you could clarify if this is really a bug or not. > > Thanks in advance, > > Mauricio > >> version > _ > platform i486-pc-linux-gnu > arch i486 > os linux-gnu > system i486, linux-gnu > status > major 2 > minor 9.0 > year 2009 > month 04 > day 17 > svn rev 48333 > language R > version.string R version 2.9.0 (2009-04-17) > > __ > 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] dir.create does not return a value (PR#13686)
Robert,
The function always returns a value, but it doesn't print the value.
Look at the source code for dir.create(), then read ?invisible.
Best,
Josh
--
http://www.fosstrading.com
On Sat, May 2, 2009 at 7:41 AM, Robert Hijmans wrote:
> Thanks, I am not sure if this is desirable (a function returning a
> value only when 'asked' to do so), but I am intrigued. How can one put
> such behaviour in an R function?
>
> Robert
>
>
> On Sat, May 2, 2009 at 8:27 PM, Sundar Dorai-Raj wrote:
>> Not a bug. Try:
>>
>> print(dir.create("foo"))
>>
>> or
>>
>> foo <- dir.create("foo")
>> foo
>>
>> HTH,
>>
>> --sundar
>>
>> On Sat, May 2, 2009 at 5:10 AM, wrote:
>>> ?dir.create (part of the base package) says that:
>>> "dir.create and Sys.chmod return a logical vector indicating which
>>> operation succeeded for each of the files attempted"
>>>
>>> However, on my system it returns nothing (whether successful or not):
>>>
dir.create(":::@!#!::")
dir.create('b')
>>>
>>>
sessionInfo()
>>> R version 2.9.0 (2009-04-17)
>>> i386-pc-mingw32
>>>
>>> locale:
>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>>> States.1252;LC_MONETARY=English_United
>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> HTH, Robert
>>>
>>> __
>>> 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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