[Rd] negative numerics in []
Hello, I'm a bit puzzled by what looks (to me) like a discrepancy between documentation and implementation. The documentation for [] says this about the indices: "Numeric values are coerced to integer as by as.integer (and hence truncated towards zero)." > as.integer(-3.1) [1] -3 Good. But: > x <- c(1,2,3) > x[-3.1] [1] 1 2 3 Given the documentation, I'd have expected a result of "[1] 1 2", because -3.1 should be coerced to -3 (by virtue of as.integer). What bit do I not get? (I'm using R 3.1.1, if that matters.) Best, Michael -- Dr. Michael Haupt Principal Member of Technical Staff Phone: +49 331 200 7277, Fax: +49 331 200 7561 Oracle Labs Oracle Deutschland B.V. & Co. KG, Schiffbauergasse 14, 14467 Potsdam, Germany __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R CMD check --as-cran does not show all error messages.
Hello, That is my first post here and I'd like to thanks everybody in
advance.
I am writing a package with some R functions and try to submit it to CRAN.
After build and check the package a number of times, I am struggling with
the fact that the CRAN people responsible for checking packages are
replying me with some mistakes that I just do NOT get when I do the check in
my computer. With the most recent R version, i.e. 3.1.1 and the command R
CMD check --as-cran on my package I get:
* using log directory ‘/home/thalles/Music/opentraj.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘opentraj/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘opentraj’ version ‘1.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Thalles Silva ’
New submission
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘opentraj’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ...
OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking 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 metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
Df2SpLinesDf 67.203 0.254 67.564
Df2SpLines 36.962 0.200 37.220
PlotTraj 6.802 0.048 6.860
hytraj07.lines5.641 0.049 5.699
hytraj07.linesDf 5.229 0.059 5.295
* checking PDF version of manual ... OK
NOTE: There was 1 note.
However, the people from CRAN claim that there is a error:
* checking R code for possible problems ... NOTE
PlotBgMap: no visible binding for global variable ‘canada.map’
This function 'PlotBgMap' loads this data set ‘canada.map’, that is part of
the package. And the *LazyData: yes* is set in the DESCRIPTION file. I know
that the cause of this error is because somehow, the package is not being
loaded in the NAMESPACE, but it should be there because I am using LazyData.
That is the code for the PlotBgMap function:
PlotBgMap <-function( traj, ... ) {
hySplitProj <- CRS(proj4string(traj))
canada <- spTransform(canada.map, hySplitProj)
plot(canada.map, border="white", col="lightgrey", ... )
}
I'd like to know if I am missing something in the Checking process, or if I
should do anything else to fix this error. Thanks.
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Re: [Rd] negative numerics in []
I can reproduce this. It seems to be happen when trying to drop the last element, e.g. > x <- 1:3 > x[-3.1] [1] 1 2 3 > x[-2.1] [1] 1 3 > x[-1.1] [1] 2 3 > x <- 1:2 > x[-2.1] [1] 1 2 > x[-1.1] [1] 2 > x <- 1:4 > x[-4.1] [1] 1 2 3 > x[-3.1] [1] 1 2 4 > x[-2.1] [1] 1 3 4 > x[-1.1] [1] 2 3 4 > x <- 1 > x[-1.1] [1] 1 My *guess* (all time I have) is that it's a bug where as.integer() is applied only *after* (silently) dropping negative indices out of range, e.g. > x <- 1:4 > x[-c(1:10+0.1)] [1] 4 Here -c(4:10+0.1) are dropped because they all > length(x). If someone wish to track this down further, the R source is available at https://svn.r-project.org/R/trunk/ (mirrored at https://github.com/wch/r-source). /Henrik On Thu, Sep 4, 2014 at 8:17 AM, Michael Haupt wrote: > Hello, > > I'm a bit puzzled by what looks (to me) like a discrepancy between > documentation and implementation. > > The documentation for [] says this about the indices: "Numeric values are > coerced to integer as by as.integer (and hence truncated towards zero)." > >> as.integer(-3.1) > [1] -3 > > Good. But: > >> x <- c(1,2,3) >> x[-3.1] > [1] 1 2 3 > > Given the documentation, I'd have expected a result of "[1] 1 2", because > -3.1 should be coerced to -3 (by virtue of as.integer). > > What bit do I not get? (I'm using R 3.1.1, if that matters.) > > Best, > > Michael > > -- > Dr. Michael Haupt > Principal Member of Technical Staff > Phone: +49 331 200 7277, Fax: +49 331 200 7561 > Oracle Labs > Oracle Deutschland B.V. & Co. KG, Schiffbauergasse 14, 14467 Potsdam, Germany > > __ > 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] negative numerics in []
On 04/09/2014 12:52 PM, Henrik Bengtsson wrote: I can reproduce this. It seems to be happen when trying to drop the last element, e.g. > x <- 1:3 > x[-3.1] [1] 1 2 3 > x[-2.1] [1] 1 3 > x[-1.1] [1] 2 3 > x <- 1:2 > x[-2.1] [1] 1 2 > x[-1.1] [1] 2 > x <- 1:4 > x[-4.1] [1] 1 2 3 > x[-3.1] [1] 1 2 4 > x[-2.1] [1] 1 3 4 > x[-1.1] [1] 2 3 4 > x <- 1 > x[-1.1] [1] 1 My *guess* (all time I have) is that it's a bug where as.integer() is applied only *after* (silently) dropping negative indices out of range, e.g. > x <- 1:4 > x[-c(1:10+0.1)] [1] 4 Here -c(4:10+0.1) are dropped because they all > length(x). If someone wish to track this down further, the R source is available at https://svn.r-project.org/R/trunk/ (mirrored at https://github.com/wch/r-source). The documentation in the R Language Definition states quite clearly that the truncation happens first, so this definitely looks like a bug. It also states "A negative out of bounds value for |i| [the index] causes an error", which is also not true, but it seems possible that a documentation change would be less disruptive than a code change. Duncan Murdoch /Henrik On Thu, Sep 4, 2014 at 8:17 AM, Michael Haupt wrote: > Hello, > > I'm a bit puzzled by what looks (to me) like a discrepancy between documentation and implementation. > > The documentation for [] says this about the indices: "Numeric values are coerced to integer as by as.integer (and hence truncated towards zero)." > >> as.integer(-3.1) > [1] -3 > > Good. But: > >> x <- c(1,2,3) >> x[-3.1] > [1] 1 2 3 > > Given the documentation, I'd have expected a result of "[1] 1 2", because -3.1 should be coerced to -3 (by virtue of as.integer). > > What bit do I not get? (I'm using R 3.1.1, if that matters.) > > Best, > > Michael > > -- > Dr. Michael Haupt > Principal Member of Technical Staff > Phone: +49 331 200 7277, Fax: +49 331 200 7561 > Oracle Labs > Oracle Deutschland B.V. & Co. KG, Schiffbauergasse 14, 14467 Potsdam, Germany > > __ > 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] negative numerics in []
Just for the sake of completeness, I raised a closely related issue back in 2010 which my students discovered. https://stat.ethz.ch/pipermail/r-help/2010-March/231788.html Bryan On Sep 4, 2014, at 11:17 AM, Michael Haupt wrote: > Hello, > > I'm a bit puzzled by what looks (to me) like a discrepancy between > documentation and implementation. > > The documentation for [] says this about the indices: "Numeric values are > coerced to integer as by as.integer (and hence truncated towards zero)." > >> as.integer(-3.1) > [1] -3 > > Good. But: > >> x <- c(1,2,3) >> x[-3.1] > [1] 1 2 3 > > Given the documentation, I'd have expected a result of "[1] 1 2", because > -3.1 should be coerced to -3 (by virtue of as.integer). > > What bit do I not get? (I'm using R 3.1.1, if that matters.) > > Best, > > Michael > > -- > Dr. Michael Haupt > Principal Member of Technical Staff > Phone: +49 331 200 7277, Fax: +49 331 200 7561 > Oracle Labs > Oracle Deutschland B.V. & Co. KG, Schiffbauergasse 14, 14467 Potsdam, Germany > > __ > 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
