Re: [Rd] question about assignment warnings for replacement methods

Hi Simon, On 11-04-08 01:05 PM, Simon Urbanek wrote: On Apr 8, 2011, at 2:55 PM, Hervé Pagès wrote: Hi Duncan, Marc, On 11-04-05 11:15 AM, Duncan Murdoch wrote: On 05/04/2011 1:51 PM, Marc Carlson wrote: Hi, I have seen several packages that with the most recent version of R are giving

Re: [Rd] R CMD build now removes empty dirs

-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, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org

[Rd] R CMD build --resave-data

CMD build --keep-empty-dirs --no-resave-data I hope the list of options/flags that we need to use to fix 'R CMD build' (and make it consistent with R CMD INSTALL) is not going to grow too much ;-) Thanks, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred

Re: [Rd] question about assignment warnings for replacement methods

, I'm not sure how literally to take it). Duncan Murdoch __ 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

[Rd] Typo in tools:::format.check_Rd_metadata()

with duplicated name '%s':, nm), .pretty_format(bad[[nm]])) })) Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100

Re: [Rd] two minor bugs in rowsum()

that the See Also section points to rowSums and not colSums, which adds to the confusion... Cheers, H. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100

[Rd] factor() on a double vector

-- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319

Re: [Rd] factor() on a double vector

the corresponding results. I see. Thanks Simon. I missed this: levels: an optional vector of the values that ‘x’ might have taken. The default is the unique set of values taken by ‘as.character(x)’, ... Cheers, H. Cheers, Simon On Feb 23, 2011, at 2:55 PM, Hervé Pagès wrote

[Rd] min/max of a vector with NAs and NaNs

the man page: By definition the min/max of a numeric vector containing an ‘NaN’ is ‘NaN’, except that the min/max of any vector containing an ‘NA’ is ‘NA’ even if it also contains an ‘NaN’. Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences

[Rd] Regression in error handling with R = 2.12

getting the full story: foo(bar()) Error in bar() : bar() is broken Error in foo(bar()) : error in evaluating the argument 'x' in selecting a method for function 'foo' Could this behavior be restored? Thanks, H. -- Hervé Pagès Program in Computational Biology Division of Public Health

Re: [Rd] faster base::sequence

/listinfo/r-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319

Re: [Rd] installed.packages Error: subscript out of bounds

(Value section). Thanks, H. On 11/10/2010 01:13 PM, Hervé Pagès wrote: Hi, Today we've seen the following problem with the R-2.12 that we use for our Windows builds: installed.packages() Error: subscript out of bounds After some investigation we discovered that the cause of this failure

[Rd] installing dependencies: binary vs source

packages: [1] stats graphics grDevices utils datasets methods base -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org

Re: [Rd] typo in ?eapply

On 11/10/2010 05:02 AM, Prof Brian Ripley wrote: On Tue, 9 Nov 2010, Hervé Pagès wrote: Hi, Found in ?eapply (in current R-devel): \value{ A named (unless \code{USE.NAMES = FALSE}) list. Note that the order of the components is arbitrary for hashed environments: currently

Re: [Rd] typo in ?eapply

On 11/10/2010 10:38 AM, Hervé Pagès wrote: On 11/10/2010 05:02 AM, Prof Brian Ripley wrote: On Tue, 9 Nov 2010, Hervé Pagès wrote: Hi, Found in ?eapply (in current R-devel): \value{ A named (unless \code{USE.NAMES = FALSE}) list. Note that the order of the components is arbitrary for hashed

[Rd] installed.packages Error: subscript out of bounds

(desc[Built], ;)[[1L]][1L], [ \t]+)[[1L]][2L] Thanks, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa

[Rd] typo in ?eapply

hashed? environments. } This looks like a typo. Thanks, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876

Re: [Rd] list2env() is broken

still worth reporting the problem, especially when it's a crash. Also AFAIK the posting guide says nothing about me having to use the debugging tools or come up with a solution before I report a problem. Thanks again for the fix, H. On Thu, 28 Oct 2010, Hervé Pagès wrote: Hi, The following

Re: [Rd] list2env() is broken

understanding the code. Yes, exactly and /Henrik /Henrik Thanks again for the fix, H. On Thu, 28 Oct 2010, Hervé Pagès wrote: Hi, The following code produces different kinds of problems depending on which platform you run it: x- as.list(1:20) names(x)- paste(A, 1:20, sep=) e- list2env(x

[Rd] list2env() is broken

the 'envir' arg is supplied) doesn't seem to have this problem. Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone

Re: [Rd] cannot connect to an FTP server with long HELLO message

(once every 20 attempts or so) I get a segfault when trying to open this url with url(). Cheers, H. On Thu, 21 Oct 2010, Hervé Pagès wrote: Hi, Trying to access files on the ftp server at ftp.ncbi.nih.gov will either give a time out or sometimes even a segfault on Linux. The 2 following

Re: [Rd] windows 64-bit package build on 32-bit machine

build a 32-bit library on a 64-bit windows machine. But it doesn't look possible to build a 64-bit library on a 32-bit windows machine? Thanks, --Michael __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Hervé Pagès

[Rd] cannot connect to an FTP server with long HELLO message

. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319

Re: [Rd] 'R CMD build' not cleaning the src/ folder on Windows

This problems seems to be solved in current R 2.12 RC. Thanks! H. On 10/10/2010 10:47 PM, Hervé Pagès wrote: Hi, 'R CMD build' (with R 2.12.0 RC) fails to clean the src/ folder on Windows: D:\biocbld\bbs-2.7-biocls meat/BUS/src BUS.cpp BUS.h D:\biocbld\bbs-2.7-biocR\bin\R CMD build meat\BUS

[Rd] 'R CMD build' not cleaning the src/ folder on Windows

ztvf BUS_1.5.0.tar.gz --wildcards '*.o' -rwxr--r-- biocbuild2/root 16503 2010-10-10 22:15 BUS/src/BUS.o Packages with a Makefile in src/ don't seem to be affected. This is with R 2.12.0 RC (2010-10-07 r53227). Thanks, H. -- Hervé Pagès Program in Computational Biology Division of Public Health

Re: [Rd] cleanup_pkg() in tools:::.build_packages() is broken

This has been fixed in R-beta. Thanks! H. On 10/01/2010 06:31 PM, Hervé Pagès wrote: Hi, The cleanup_pkg() function defined the big tools:::.build_packages() function in tools/R/build.R is currently broken. When Makefiles are used cleanup_pkg() doesn't clean anything because of the way

Re: [Rd] tar problem when using 'R CMD build' on Windows

Hi, On 09/30/2010 10:45 AM, Hervé Pagès wrote: [...] If that is not desirable, could the tools:::.build_packages() function not put quotes around the value of the TAR environment variable (the code does shQuote(TAR)), at least on Windows, so I can set this variable to tar --no-same-owner

[Rd] cleanup_pkg() in tools:::.build_packages() is broken

thru the 'args' argument. Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667

[Rd] tar problem when using 'R CMD build' on Windows

() (only the first doesn't put them) but that's another story. Thanks! H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone

Re: [Rd] More strange R CMD build/check errors on Windows

This has been addressed in current R-alpha, thanks! H. On 09/29/2010 02:11 PM, Hervé Pagès wrote: Hi, I can confirm that most of those strange R CMD build/check errors we observe on Windows are actually a consequence of the temp Rscript file collision I reported yesterday here: https

Re: [Rd] More strange R CMD build/check errors on Windows

temp file now), so I'm going to report them in a separate post. Can the patch above be applied? Thanks! H. On 09/11/2010 11:10 PM, Hervé Pagès wrote: Hi, This is a follow up to: https://stat.ethz.ch/pipermail/r-devel/2010-July/057921.html The Bioconductor daily builds have been reporting a lot

Re: [Rd] small inaccuracy in startup warning message

It looks like this has been fixed in current R-alpha. Thanks! H. On 09/28/2010 04:27 PM, Hervé Pagès wrote: Hi, Cosmetic. Starting R with e.g. --max-ppsize=-10 produces the following warning: WARNING: '-max-ppsize' value is negative: ignored The name of the option displayed in the warning

[Rd] small inaccuracy in startup warning message

the name of this option needs to be adjusted). This is with current R-alpha. Thanks! H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa

[Rd] temp Rscript file collision on Windows

Rterm process needs to create at most 1 temp Rscript file so maybe using rand() is not even needed. Note that Unix is safe because tmpfile() is used there (file src/unix/system.c). Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson

Re: [Rd] More strange R CMD build/check errors on Windows

-24 r52991) on Windows Server 2003 R2 (32-bit). The tar command used is from current Rtools212. Cheers, H. On 09/15/2010 05:21 PM, Hervé Pagès wrote: On 09/14/2010 11:23 AM, Hervé Pagès wrote: Hi Uwe, On 09/14/2010 04:49 AM, Uwe Ligges wrote: ... Brian had some ideas that the problems

Re: [Rd] Lack of consistent cross-platform behaviour of tools:::buildVignettes()

interactively. Thanks! H. On 09/15/2010 09:54 PM, Hervé Pagès wrote: Hi, On both Unix and Windows there is a mechanism to add variables to the environment when R is started. I noticed that, on Unix, this mechanism is not used when R is started normally at the command line but only when it's started

Re: [Rd] running 'make' failed during vignette creation ('R CMD build') on Windows

This fixed in current R-alpha (r52991) too. Thanks! H. On 09/15/2010 11:33 PM, Hervé Pagès wrote: I think I found the problem. During the recent transition from Perl-based to R-based 'R CMD check/build', the rcmdfn() function in src/gnuwin32/front-ends/rcmdfn.c has been hacked quite a bit

Re: [Rd] running 'make' failed during vignette creation ('R CMD build') on Windows

variables that they used to see anymore. Only a normal 'R' command still gets them. Cheers, H. On 09/15/2010 04:55 PM, Hervé Pagès wrote: Hi, This is a follow-up to the problem reported here: https://stat.ethz.ch/pipermail/r-devel/2010-September/058460.html After I updated R-2.12 to 2010-09-13

[Rd] environment variable for tar()/untar()

= ., compressed = NA, extras = NULL, verbose = FALSE, tar = Sys.getenv(TAR)) Thanks! H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109

Re: [Rd] Suggestion: Add DESCRIPTION 'Date' to R CMD check log header

. Cheers, H. -k __ 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, M2-B876

Re: [Rd] Problem with WARNING...headers with CRLF line endings

that the clean step runs too late. But shouldn't 'R CMD check' run the clean step (if it runs it at all) right after the 'R CMD INSTALL' step? Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876

Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used

on a package for which the problem is gone so I went ahead and started to sing victory... not so fast! I'm gonna post with a new subject and give more details. H. On 09/14/2010 11:48 AM, Duncan Murdoch wrote: On 14/09/2010 2:46 PM, Hervé Pagès wrote: Duncan, On 09/13/2010 11:47 AM, Duncan Murdoch

[Rd] running 'make' failed during vignette creation ('R CMD build') on Windows

that is really puzzling is that if I cd to adSplit/inst/doc and run 'R CMD make' then it works. Any help/comment on this will be highly appreciated. Thanks, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview

Re: [Rd] More strange R CMD build/check errors on Windows

On 09/14/2010 11:23 AM, Hervé Pagès wrote: Hi Uwe, On 09/14/2010 04:49 AM, Uwe Ligges wrote: ... Brian had some ideas that the problems are related to the shell that is used. Is the problem still apparent in a very recent R-devel from few days ago? I am just back from vacations and have

[Rd] Lack of consistent cross-platform behaviour of tools:::buildVignettes()

Sys.getenv('TEXINPUTS') | R Fatal error: you must specify '--save', '--no-save' or '--vanilla' What about --slave? Thanks! -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle

Re: [Rd] More strange R CMD build/check errors on Windows

Hi Uwe, On 09/14/2010 04:49 AM, Uwe Ligges wrote: On 12.09.2010 12:10, Hervé Pagès wrote: Hi Peter, On 09/12/2010 01:51 AM, Peter Dalgaard wrote: On 09/12/2010 08:10 AM, Hervé Pagès wrote: ... AFAICT those problems were never seen before (i.e. with R 2.12). They show up randomly everyday

Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used

Duncan, On 09/13/2010 11:47 AM, Duncan Murdoch wrote: On 13/09/2010 2:38 PM, Hervé Pagès wrote: [...] Thanks for suggesting workarounds but don't you think there is a real problem? As I said, we don't use TEXINPUTS on Windows, we use the command line version. I didn't write the code, so I

Re: [Rd] Problem with WARNING...headers with CRLF line endings

/mailman/listinfo/r-devel __ 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

Re: [Rd] Problem with WARNING...headers with CRLF line endings

only from 4MB to 4.3MB. Thus in principle I could upload both files to SVN for BioC 2.7, and this should eliminate the warning message. What is your opinion? I still don't understand why you want to have them in the source tarball. H. Best regards Christian On 9/14/10 11:32 PM, Hervé Pagès

Re: [Rd] Problem with WARNING...headers with CRLF line endings

On 09/14/2010 03:30 PM, Duncan Murdoch wrote: On 14/09/2010 6:08 PM, Hervé Pagès wrote: On 09/14/2010 02:58 PM, cstrato wrote: Dear Herve, Thank you for your reply, however maybe I was not quite clear. The files xpsDict.h and xpsDict.cxx are automatically created by the ROOT framework during

Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used

On 09/13/2010 03:34 AM, Duncan Murdoch wrote: Hervé Pagès wrote: Hi Duncan, On 09/12/2010 05:07 AM, Duncan Murdoch wrote: On 12/09/2010 12:49 AM, Hervé Pagès wrote: Hi Duncan, On 09/11/2010 03:56 AM, Duncan Murdoch wrote: On 11/09/2010 12:52 AM, Hervé Pagès wrote: Hi, I found

[Rd] More strange R CMD build/check errors on Windows

everyday and any package seems to be a potential victim (I've not been able to observe any obvious pattern so far). Does anyone have any idea what could make 'R CMD build' and 'R CMD check' so confused/unreliable on Windows? Thanks, H. -- Hervé Pagès Program in Computational Biology Division of Public

Re: [Rd] More strange R CMD build/check errors on Windows

Hi Peter, On 09/12/2010 01:51 AM, Peter Dalgaard wrote: On 09/12/2010 08:10 AM, Hervé Pagès wrote: ... AFAICT those problems were never seen before (i.e. with R 2.12). They show up randomly everyday for a small number of packages (between 10 and 20 out of 400). The set of victims changes

Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used

Hi Duncan, On 09/12/2010 05:07 AM, Duncan Murdoch wrote: On 12/09/2010 12:49 AM, Hervé Pagès wrote: Hi Duncan, On 09/11/2010 03:56 AM, Duncan Murdoch wrote: On 11/09/2010 12:52 AM, Hervé Pagès wrote: Hi, I found the following problem with recent R-devel (2010-08-26 r52817) on Windows (32

Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used

Hi Duncan, On 09/11/2010 03:56 AM, Duncan Murdoch wrote: On 11/09/2010 12:52 AM, Hervé Pagès wrote: Hi, I found the following problem with recent R-devel (2010-08-26 r52817) on Windows (32-bit and 64-bit): 'R CMD build pkg' gets stalled during vignett creation for packages that have

[Rd] R CMD build cannot create vignettes on Windows if Makefile is used

that be related to the problem? I don't see that problem on platforms other than Windows or with R 2.12 Thanks, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024

Re: [Rd] Speeding up transpose

not_matrix; } __ 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, M2

[Rd] new bug in install.packages()

(and not attached): [1] tools_2.12.0 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319

[Rd] Very slow subsetting by name

and R-2.12.0. Thanks, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319

[Rd] Strange issues with new R-based 'R CMD build' and 'R CMD check' scripts on Windows

r52464). Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319

Re: [Rd] No output/no source tarball produced by 'R CMD build' on Windows (but ret code is 0)

-buildsrc.html Cheers, H. On 06/21/2010 12:20 PM, Hervé Pagès wrote: Hi, After updating R-2.12 on the Bioconductor build system about 1 week ago (we update R every 4-6 weeks for our devel builds), we've started to see something never seen before on Windows: for some BioC packages, 'R CMD build

Re: [Rd] R-based version of R CMD build broken on Windows

Uwe Ligges wrote: On 10.06.2010 23:16, Hervé Pagès wrote: Hi, The R-based version of R CMD build doesn't work for me on Windows: E:\biocbld\bbs-2.7-biocR\bin\R CMD build meat\Biobase * checking for file 'meat\Biobase/DESCRIPTION' ... OK * preparing 'Biobase': * checking DESCRIPTION meta

[Rd] R-based version of R CMD build broken on Windows

see anything like that on the check summaries for CRAN packages: http://cran.r-project.org/web/checks/check_summary.html Maybe because CRAN only runs R CMD check which is still Perl-based? Thanks, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred

[Rd] Broken link in HTML version of R Installation and Administration manual

/a but latter in the file, the referred section is tagged with: a name=g_t64_002dbit-Windows-builds/a Thanks, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109

Re: [Rd] named empty list

Thanks Martin. H. Martin Maechler wrote: HP == Hervé Pagès hpa...@fhcrc.org on Thu, 03 Jun 2010 13:25:10 -0700 writes: HP Hi, HP I just realized that a named empty list is displayed the same HP way as an empty list: list(aa=2:5)[0] HP list() list() HP list

[Rd] named empty list

=en_CA.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- Hervé Pagès Program in Computational Biology Division of Public Health

[Rd] Argument recycling in substring()

. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319

Re: [Rd] suggestion how to use memcpy in duplicate.c

__ 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 -- Hervé Pagès Program in Computational Biology Division of Public Health

Re: [Rd] suggestion how to use memcpy in duplicate.c

Follow up... Hervé Pagès wrote: Hi Matthew, Matthew Dowle wrote: Just to add some clarification, the suggestion wasn't motivated by speeding up a length 3 vector being recycled 3.3 million times. But its a good point that any change should not make that case slower. I don't know how much

Re: [Rd] suggestion how to use memcpy in duplicate.c

Hervé Pagès wrote: [...] Code: === #include stdio.h #include string.h #include stdlib.h void memcpy_with_recycling_of_src(char *dest, size_t dest_nblocks, const char *src, size_t src_nblocks

Re: [Rd] as(1:4, numeric) versus as.numeric(1:4, numeric)

has a use for it other than in as()? If you look at the code, you'll see that would simplify it significantly, and even speed up selection somewhat. There's a change I would be happy about! That sounds all good to me. Thanks, H. John On 4/1/10 2:59 PM, Hervé Pagès wrote: John Chambers

Re: [Rd] as(1:4, numeric) versus as.numeric(1:4, numeric)

. Cheers, H. Regards, John On 3/31/10 3:52 PM, Hervé Pagès wrote: Hi, class(as(1:4, numeric)) [1] integer Surprising but an explanation could be that an integer vector being a particular case of numeric vector, this coercion has nothing to do because 1:4 is already numeric. And indeed

Re: [Rd] as(1:4, numeric) versus as.numeric(1:4, numeric)

names, so the user doesn't have to switch between select*/show* tools depending on whether f=coerce or not. H. John On 4/1/10 12:31 AM, Hervé Pagès wrote: Hi John, John Chambers wrote: The example is confusing and debatable, but not an obvious bug. And your presentation of it is the cause

[Rd] as(1:4, numeric) versus as.numeric(1:4, numeric)

] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8 [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- Hervé

[Rd] Missing arg default values in Docs are not triggering an 'R CMD check' warning

Hi, Having foo - function(x, y, z) {TRUE} in my code and foo(x, y=NULL, z=0) in the \usage section of my man page will trigger the following warning during R CMD check: * checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'foo': foo Code:

[Rd] unname() returns a named vector when the input vector has length 0

Hi, x - c(aa=22, bb=555) unname(x[FALSE]) named numeric(0) Cheers, H. sessionInfo() R version 2.10.0 (2009-10-26) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_CA.UTF-8LC_COLLATE=en_CA.UTF-8 [5] LC_MONETARY=C

[Rd] inaccurate integer conversion in coercion

Hi, as.integer(100) # 10 billions [1] NA Warning message: NAs introduced by coercion as.integer(-100) # minus 10 billions [1] NA Warning message: NAs introduced by coercion as.integer(100) # 10 billions as a string [1] 2147483647 Warning message: inaccurate

Re: [Rd] crash with NAs in subscripted assignment of a raw vector

Seth Falcon wrote: 2009/9/24 Hervé Pagès hpa...@fhcrc.org: x - charToRaw(ABCDEFGx) x[c(1:3, NA, 6)] - x[8] *** caught segfault *** address 0x8402423f, cause 'memory not mapped' Thanks for the report. I have a fix which I will commit after some testing. Thanks Seth! H

[Rd] crash with NAs in subscripted assignment of a raw vector

LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred

Re: [Rd] R devel repository tarball naming issue

Thanks Martin! The latest snapshot (R-devel_2009-09-03.tar.gz) looks OK. FYI the tarballs with a broken name are still here (ftp://ftp.stat.math.ethz.ch/Software/R/): R-devel_.tar.bz2 R-devel_.tar.gz Cheers, H. Martin Maechler wrote: HP == Hervé Pagès hpa...@fhcrc.org on Wed, 02 Sep

Re: [Rd] Resizing a named vector crashes R with gctorture(TRUE) (PR#13837)

Duncan Murdoch wrote: On 15/07/2009 10:15 PM, Hervé Pagès wrote: I have to confess that I'm a little bit puzzled by how the PROTECT/UNPROTECT mechanism is used in the C code of R. Duncan, you say the problem you just fixed was an easy one. I looked at the C code too and was able to recognize

Re: [Rd] Resizing a named vector crashes R with gctorture(TRUE) (PR#13837)

Duncan Murdoch wrote: On 7/16/2009 2:34 PM, Hervé Pagès wrote: Duncan Murdoch wrote: On 15/07/2009 10:15 PM, Hervé Pagès wrote: I have to confess that I'm a little bit puzzled by how the PROTECT/UNPROTECT mechanism is used in the C code of R. Duncan, you say the problem you just fixed

Re: [Rd] Resizing a named vector crashes R with gctorture(TRUE) (PR#13837)

Duncan Murdoch wrote: On 16/07/2009 5:06 PM, Hervé Pagès wrote: Duncan Murdoch wrote: On 7/16/2009 2:34 PM, Hervé Pagès wrote: Duncan Murdoch wrote: On 15/07/2009 10:15 PM, Hervé Pagès wrote: I have to confess that I'm a little bit puzzled by how the PROTECT/UNPROTECT mechanism is used

[Rd] Resizing a named vector crashes R with gctorture(TRUE)

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, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206

Re: [Rd] Resizing a named vector crashes R with gctorture(TRUE) (PR#13837)

murd...@stats.uwo.ca wrote: On 15/07/2009 8:30 PM, murd...@stats.uwo.ca wrote: On 15/07/2009 8:08 PM, Hervé Pagès wrote: Hi, x - c(a=10, b=20) length(x) - 1 x a 10 But with gctorture turned on, I get: gctorture(TRUE) x - c(a=10, b=20) length(x) - 1 x

Re: [Rd] Resizing a named vector crashes R with gctorture(TRUE) (PR#13837)

trigger garbage collection (e.g. PROTECT(allocVector()) is close to the return statement). Because making exceptions like this can make your code really hard to maintain in the long term. Cheers, H. Hervé Pagès wrote: murd...@stats.uwo.ca wrote: On 15/07/2009 8:30 PM, murd...@stats.uwo.ca wrote

Re: [Rd] bug in seq_along

/mailman/listinfo/r-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319

[Rd] Protection stack overflow when calling setGeneric()/setMethod() from within .onLoad()

/053607.html Also note that if I make foo() a function of one argument only, I don't get the protection stack overflow anymore. Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box

Re: [Rd] formal argument envir matched by multiple actual arguments

-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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred

[Rd] formal argument envir matched by multiple actual arguments

attached base packages: [1] stats graphics grDevices utils datasets methods base -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa

[Rd] png() error in recent R-devel on Windows

datasets methods base Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667

Re: [Rd] bug in classesToAM()

, H. __ 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, M2-B876 P.O. Box

Re: [Rd] Recent snapshot tarballs of R-devel don't compile

symbolic links into src/library/Recommended/ as they used to. I don't know what OS this procedure is running on but maybe 'tar' started to do some strange strings with symlinks after an OS update/upgrade... Thanks, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences

Re: [Rd] Recent snapshot tarballs of R-devel don't compile

to be reported to the site which makes them. Perhaps you mean ftp://ftp.stat.math.ethz.ch/Software/R/R-devel_2008-12-03.tar.bz2 ? In which case see the README in that directory for how to report a problem. Will do. Thanks! H. -- Hervé Pagès Program in Computational Biology Division of Public Health

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