r-devel@r-project.org discussions for January 2015

15	[Rd] RFC: getifexists() {was [Bug 16065] "exists" ...}

In November, we had a "bug repository conversation" with Peter Hagerty and myself: https://bugs.r-project.org/bugzilla/show_bug.cgi?id065 where the bug report title started with --- "exists" is a ...

Martin Maechler
Jan 8, 2015 at 9:16 am
Jan 9, 2015 at 7:56 pm

11	[Rd] New version of Rtools for Windows

I have just uploaded to CRAN a new version 3.2.0.1948 of Rtools for Windows. This will become visible there in a few hours, and be copied to mirrors thereafter. People who want to build packages that ...

Duncan Murdoch
Jan 7, 2015 at 4:00 pm
Jan 12, 2015 at 5:40 pm

7	[Rd] Request for help with UBSAN and total absense of CRAN response

CRAN has a package of mine in upload limbo because it failed UBSAN. I am not entirely ignorant on the topic of sanitizers and SAN / ASAN / UBSAN; we created not one but two Docker containers with ...

Dirk Eddelbuettel
Jan 13, 2015 at 3:30 pm
Jan 18, 2015 at 3:53 pm

7	[Rd] setequal: better readability, reduced memory footprint, and minor speedup

Hi, Current implementation: setequal <- function (x, y) { x <- as.vector(x) y <- as.vector(y) all(c(match(x, y, 0L) 0L, match(y, x, 0L) 0L)) } First what about replacing 'match(x, y, 0L) 0L' and ...

Hervé Pagès
Jan 6, 2015 at 9:02 pm
Jan 9, 2015 at 6:21 am

4	[Rd] Request to speed up save()

Hi, I am dealing with very large datasets and it takes a long time to save a workspace image. The options to save compressed data are: "gzip", "bzip2" or "xz", the default being gzip. I wonder if ...

Stewart Morris
Jan 15, 2015 at 12:45 pm
Jan 15, 2015 at 10:18 pm

4	[Rd] R CMD build looking for texi2dvi in the wrong place (R-devel)

R CMD build fails with recent R-devel because it is looking for texi2dvi in /usr/local/bin, but on this system, MacTex has installed it in /usr/bin. $ R CMD build IRanges * checking for file ...

Dan Tenenbaum
Jan 13, 2015 at 12:50 am
Jan 13, 2015 at 4:47 am

4	[Rd] unloadNamespace

In the documentation the closed thing I see to an explanation of this is that ?detach says "Unloading some namespaces has undesirable side effects" Can anyone explain why unloading tseries will load ...

Paul Gilbert
Jan 8, 2015 at 3:45 pm
Jan 9, 2015 at 9:41 pm

4	[Rd] latex warning

Dear all, I am getting an R CMD check warning about the PDF manual. I am having a hard time finding out what is wrong, here is the log of the Rd2pdf call. The full check (and other) log is at ...

Gábor Csárdi
Jan 8, 2015 at 10:18 pm
Jan 9, 2015 at 3:20 pm

4	[Rd] Potential cross-platform package building issue

I am using 32-bit R 3.1.2 on Windows 7. I recently conducted an `R CMD check --as-cran` on a recently-developed package and received only the 'New submission' note. Research on StackOverflow and on ...

Steven Ranney
Jan 3, 2015 at 8:49 pm
Jan 4, 2015 at 12:44 am

3	[Rd] Help finding source of warnings

I've been implementing a wrapper to the 2011 Fortran version of L-BFGS-B. In optim(), R uses a C translation of a Fortran version (the version number does not appear to be documented by the original ...

Prof J C Nash (U30A)
Jan 18, 2015 at 2:03 pm
Jan 18, 2015 at 2:56 pm

3	[Rd] Benchmark code, but avoid printing

Dear all, I am trying to benchmark code that occasionally prints on the screen and I want to suppress the printing. Is there an idiom for this? If I do sink(tempfile) microbenchmark(...) sink() then ...

Gábor Csárdi
Jan 2, 2015 at 5:02 pm
Jan 2, 2015 at 9:20 pm

2	[Rd] default min-v/nsize parameters

Just wanted to start a discussion on whether R could ship with more appropriate GC parameters. Right now, loading the recommended package Matrix leads to: used (Mb) gc trigger (Mb) max used (Mb) ...

Michael Lawrence
Jan 15, 2015 at 11:55 pm
Jan 18, 2015 at 7:40 am

2	[Rd] Is the tcltk failure in affylmGUI related to R bug 15957

I maintain the package affylmGUI. It works when installed on many previous versions of R. I have today tested exactly the same code under R-2.15.3, R-3.0.2, R-3.1.0, R-3.1.1, R-3.1.2 and R-devel. I ...

Keith Satterley
Jan 14, 2015 at 5:50 am
Jan 18, 2015 at 4:17 am

2	[Rd] R CMD check: "..." used in a situation where it does not exist

Dear R developers, when running R CMD check, the R Under development (unstable) (2015-01-13 r67453) gives me the following NOTE: cbind.fsets: possible error in list(...): ... used in a situation ...

Michal Burda
Jan 14, 2015 at 7:42 am
Jan 14, 2015 at 1:30 pm

2	[Rd] gsub with perl=TRUE results in 'this version of PCRE is not compiled with Unicode property support' in R-devel

The following code: res <- gsub("(*UCP)\\b(i)\\b", "", "nhgrimelanomaclass", perl = TRUE) results in: Error in gsub(sprintf("(*UCP)\\b(%s)\\b", "i"), "", "nhgrimelanomaclass", : invalid regular ...

Dan Tenenbaum
Jan 7, 2015 at 11:25 pm
Jan 8, 2015 at 2:57 pm

2	[Rd] On base::rank

Have a look at the following, taken from base::rank: ... if (!is.na(na.last) && any(nas)) { yy <- integer(length(x)) # <~~~~~~~~~ storage.mode(yy) <- storage.mode(y) # <~~~~~~~~ yy <- NA NAkeep <- ...

Arunkumar Srinivasan
Jan 8, 2015 at 12:46 pm
Jan 8, 2015 at 2:37 pm

2	[Rd] Failing lm-tests due to extra 0 in scientific notation?

Hello. I've compiled R on Windows many times, and this is the first time I've seen this error. While running make check-all (and using testInstalledBasic("both")), the lm-tests routines fail, and, as ...

Avraham Adler
Jan 7, 2015 at 6:24 am
Jan 7, 2015 at 4:35 pm

1	[Rd] S3 generic method dispatch on promises

Dear R friends I wanted a function to make a simple percent table that would be easy for students to use. The goal originally was to have a simple thing people would call like this pctable(rowvar, ...

Paul Johnson
Jan 16, 2015 at 11:02 pm
Jan 16, 2015 at 11:21 pm

1	[Rd] Closing over Garbage

Given a large data.frame, a function trains a series of models by looping over two steps: 1. Create a model-specific subset of the complete training data 2. Train a model on the subset data The ...

Christian Sigg
Jan 15, 2015 at 5:37 pm
Jan 15, 2015 at 7:43 pm

1	[Rd] R under deveoplment CMD check note " ... used in a situation where it does not exist"

Hi all, just installed the current version of R-devel (2015-01-13 r67453) from CRAN. Package checking via CMD check suddenly prints a lot of notes that complain of ... used in a situation where it ...

Peter Langfelder
Jan 15, 2015 at 2:15 am
Jan 15, 2015 at 6:40 am

1	[Rd] Cost of garbage collection seems excessive

When doing repeated regressions on large data sets, I'm finding that the time spent on garbage collection often exceeds the time spent on the regression itself. Consider this test program which I'm ...

Nathan Kurz
Jan 9, 2015 at 9:31 am
Jan 11, 2015 at 7:25 pm

1	[Rd] Rtools install on new Windows 8.1 desktop stalls with "Not responding"

Hello, When I try to install Rtools in the usual way into C:\Rtools on a new Windows 8.1 desktop it stalls near the beginning of the "Extracting files..." step. The Task Manager Status for the Setup ...

Dominick Samperi
Jan 6, 2015 at 5:59 am
Jan 6, 2015 at 7:38 am

1	[Rd] Help in building R with minGW

Dear R users, I would need some help in building R using minGW in windows 8.1. After using the command *configure *(./configure --enable-R-shlib --with-readline=no --with-x=no), I use the command ...

Edoardo Baldoni
Jan 2, 2015 at 5:33 pm
Jan 2, 2015 at 8:47 pm

1	[Rd] Reimplement stats:::plotNode as iterative to avoid recursion limits?

Hi All, I've gotten a number of reports from users about gplots::heatmap.2 generating 'node stack overflow' errors. As it turns out, these errors originate in stats:::plotNode, and are triggered when ...

Gregory R. Warnes
Jan 1, 2015 at 11:35 pm
Jan 2, 2015 at 6:26 pm

1	[Rd] Unexpected behavior of debug() in step-wise mode

41;309;0c Why does debug() enter Browse[3] here at all, and why does it happen the I think this is the result of debugging being implemented by setting a flag in the environment of the function being ...

Radford Neal
Jan 1, 2015 at 2:49 pm
Jan 1, 2015 at 4:00 pm

0	[Rd] [PATCH] Makefile: add support for git svn clones

git has an interface for cloning SVN repositories into git which some users might decide to use. For those users' surprise, the repository will always fail to build on svnonly target and it will exit ...

Felipe Balbi
Jan 13, 2015 at 5:00 am
Jan 13, 2015 at 5:00 am

0	[Rd] Bug in URLencode and patch

I believe the implementation of utils::URLencode is non-compliant with RFC 3986, which it claims to implement (http://tools.ietf.org/html/rfc3986). Specifically, its percent encoding uses lowercase ...

Thomas J. Leeper
Jan 11, 2015 at 1:34 pm
Jan 11, 2015 at 1:34 pm

0	[Rd] Shouldn't grDevices::quartz() give an error instead of a warning when not available?

Warning message: In quartz() : Quartz device is not available on this platform Should this have generated an error instead? to: Error in .External2(C_X11, d$display, d$width, d$height, ...

Henrik Bengtsson
Jan 11, 2015 at 1:04 am
Jan 11, 2015 at 1:04 am

0	[Rd] as.hexmode(big number) fails in R-3.1.2

There was recently a discussion here on how to tell if a number was integral. Did that prod someone into change as.hexmode in R-3.1.2 so that it aborts if given a number to big to fit into a 32-bit ...

William Dunlap
Jan 9, 2015 at 10:50 pm
Jan 9, 2015 at 10:50 pm

0	[Rd] Testing R packages on Solaris Studio

I have setup a Solaris server to test packages before submitting to CRAN, in order to catch problems that might not reveal themselves on Fedora, Debian, OSX or Windows. The machine runs a Solaris ...

Jeroen Ooms
Jan 8, 2015 at 8:52 pm
Jan 8, 2015 at 8:52 pm

0	[Rd] UCBAdmissions help link update request

Currently the help for UCBAdmissions has a link to Michael Friendly's old faculty page, <http://www.math.yorku.ca/SCS/friendly.html This goes to a redirect page. The new address is datavis.ca. As it ...

John Christie
Jan 1, 2015 at 4:56 pm
Jan 1, 2015 at 4:56 pm

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R > r-devel > January 2015

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31 discussions - 117 posts

[Rd] RFC: getifexists() {was [Bug 16065] "exists" ...}

[Rd] New version of Rtools for Windows

[Rd] Request for help with UBSAN and total absense of CRAN response

[Rd] setequal: better readability, reduced memory footprint, and minor speedup

[Rd] Request to speed up save()

[Rd] R CMD build looking for texi2dvi in the wrong place (R-devel)

[Rd] unloadNamespace

[Rd] latex warning

[Rd] Potential cross-platform package building issue

[Rd] Help finding source of warnings

[Rd] Benchmark code, but avoid printing

[Rd] default min-v/nsize parameters

[Rd] Is the tcltk failure in affylmGUI related to R bug 15957

[Rd] R CMD check: "..." used in a situation where it does not exist

[Rd] gsub with perl=TRUE results in 'this version of PCRE is not compiled with Unicode property support' in R-devel

[Rd] On base::rank

[Rd] Failing lm-tests due to extra 0 in scientific notation?

[Rd] S3 generic method dispatch on promises

[Rd] Closing over Garbage

[Rd] R under deveoplment CMD check note " ... used in a situation where it does not exist"

[Rd] Cost of garbage collection seems excessive

[Rd] Rtools install on new Windows 8.1 desktop stalls with "Not responding"

[Rd] Help in building R with minGW

[Rd] Reimplement stats:::plotNode as iterative to avoid recursion limits?

[Rd] Unexpected behavior of debug() in step-wise mode

[Rd] [PATCH] Makefile: add support for git svn clones

[Rd] Bug in URLencode and patch

[Rd] Shouldn't grDevices::quartz() give an error instead of a warning when not available?

[Rd] as.hexmode(big number) fails in R-3.1.2

[Rd] Testing R packages on Solaris Studio

[Rd] UCBAdmissions help link update request

46 users for January 2015

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