[Rd] Rprof(..., memory.profiling=TRUE) to profile C memory allocation?
Could someone please confirm/refute that Rprof(..., memory.profiling=TRUE) can also be used to profile memory allocation done in a C function (src/*.c) that uses, e.g. allocVector(INTSXP, n) but also allocations such as R_alloc(n, sizeof(int)) ? Modulo how R was built, does the answer depend on OS? I'm interested in all the major ones (Linux, OS X and Windows). Thanks, Henrik __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R string comparisons may vary with platform (plain text)
On Sat, Nov 22, 2014 at 12:42 PM, Duncan Murdoch wrote: > On 22/11/2014, 2:59 PM, Stuart Ambler wrote: >> A colleague¹s R program behaved differently when I ran it, and we thought >> we traced it probably to different results from string comparisons as >> below, with different R versions. However the platforms also differed. A >> friend ran it on a few machines and found that the comparison behavior >> didn¹t correlate with R version, but rather with platform. >> >> I wonder if you¹ve seen this. If it¹s not some setting I¹m unaware of, >> maybe someone should look into it. Sorry I haven¹t taken the time to read >> the source code myself. > > Looks like a collation order issue. See ?Comparison. With the oddity that both platforms use what look like similar locales: LC_COLLATE=en_US.UTF-8 LC_COLLATE=en_US.utf8 /Henrik > > Duncan Murdoch > >> Thanks, >> Stuart >> >> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" >> Platform: x86_64-unknown-linux-gnu (64-bit) >> Sys.getlocale() >> [1] >> "LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF >> -8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_ >> NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICA >> TION=C" >> >> "-1" > "1" >> [1] TRUE >> >> "-1" <"1" >> [1] FALSE >> >> "1" < "-1" >> [1] TRUE >> >> "1" < "-" >> [1] FALSE >> >> Vs. >> >> R version 3.1.1 (2014-07-10) ‹ ³Sock it to Me" >> Platform: x86_64-redhat-linux-gnu (64-bit) >> Sys.getlocale() >> [1] >> "LC_CTYPE=en_US.utf8;LC_NUMERIC=C;LC_TIME=en_US.utf8;LC_COLLATE=en_US.utf8 >> ;LC_MONETARY=en_US.utf8;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAME >> =C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.utf8;LC_IDENTIFICATION >> =C" >> >> "-1" > "1" >> [1] FALSE >> >> "-1" <"1" >> [1] TRUE >> >> "1" < "-1" >> [1] FALSE >> >> "1" < "-" >> [1] FALSE >> >> __ >> 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] R string comparisons may vary with platform (plain text)
You mean where it says that some platforms may not respect the locale (I assume, though don’t know, that en_US.UTF-8 and en_US.utf8 would be the same)? But I gather that the general problem has been looked into and is difficult to solve; thanks. On 11/22/14, 12:42 PM, "Duncan Murdoch" wrote: >On 22/11/2014, 2:59 PM, Stuart Ambler wrote: >> A colleague¹s R program behaved differently when I ran it, and we >>thought >> we traced it probably to different results from string comparisons as >> below, with different R versions. However the platforms also differed. >> A >> friend ran it on a few machines and found that the comparison behavior >> didn¹t correlate with R version, but rather with platform. >> >> I wonder if you¹ve seen this. If it¹s not some setting I¹m unaware of, >> maybe someone should look into it. Sorry I haven¹t taken the time to >>read >> the source code myself. > >Looks like a collation order issue. See ?Comparison. > >Duncan Murdoch > >> Thanks, >> Stuart >> >> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" >> Platform: x86_64-unknown-linux-gnu (64-bit) >> Sys.getlocale() >> [1] >> >>"LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.U >>TF >> >>-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;L >>C_ >> >>NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFI >>CA >> TION=C" >> >> "-1" > "1" >> [1] TRUE >> >> "-1" <"1" >> [1] FALSE >> >> "1" < "-1" >> [1] TRUE >> >> "1" < "-" >> [1] FALSE >> >> Vs. >> >> R version 3.1.1 (2014-07-10) ‹ ³Sock it to Me" >> Platform: x86_64-redhat-linux-gnu (64-bit) >> Sys.getlocale() >> [1] >> >>"LC_CTYPE=en_US.utf8;LC_NUMERIC=C;LC_TIME=en_US.utf8;LC_COLLATE=en_US.utf >>8 >> >>;LC_MONETARY=en_US.utf8;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAM >>E >> >>=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.utf8;LC_IDENTIFICATIO >>N >> =C" >> >> "-1" > "1" >> [1] FALSE >> >> "-1" <"1" >> [1] TRUE >> >> "1" < "-1" >> [1] FALSE >> >> "1" < "-" >> [1] FALSE >> >> __ >> 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] R string comparisons may vary with platform (plain text)
On 22/11/2014, 2:59 PM, Stuart Ambler wrote: > A colleague¹s R program behaved differently when I ran it, and we thought > we traced it probably to different results from string comparisons as > below, with different R versions. However the platforms also differed. A > friend ran it on a few machines and found that the comparison behavior > didn¹t correlate with R version, but rather with platform. > > I wonder if you¹ve seen this. If it¹s not some setting I¹m unaware of, > maybe someone should look into it. Sorry I haven¹t taken the time to read > the source code myself. Looks like a collation order issue. See ?Comparison. Duncan Murdoch > Thanks, > Stuart > > R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" > Platform: x86_64-unknown-linux-gnu (64-bit) > Sys.getlocale() > [1] > "LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF > -8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_ > NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICA > TION=C" > > "-1" > "1" > [1] TRUE > > "-1" <"1" > [1] FALSE > > "1" < "-1" > [1] TRUE > > "1" < "-" > [1] FALSE > > Vs. > > R version 3.1.1 (2014-07-10) ‹ ³Sock it to Me" > Platform: x86_64-redhat-linux-gnu (64-bit) > Sys.getlocale() > [1] > "LC_CTYPE=en_US.utf8;LC_NUMERIC=C;LC_TIME=en_US.utf8;LC_COLLATE=en_US.utf8 > ;LC_MONETARY=en_US.utf8;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAME > =C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.utf8;LC_IDENTIFICATION > =C" > > "-1" > "1" > [1] FALSE > > "-1" <"1" > [1] TRUE > > "1" < "-1" > [1] FALSE > > "1" < "-" > [1] FALSE > > __ > 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] R string comparisons may vary with platform (plain text)
A colleague¹s R program behaved differently when I ran it, and we thought we traced it probably to different results from string comparisons as below, with different R versions. However the platforms also differed. A friend ran it on a few machines and found that the comparison behavior didn¹t correlate with R version, but rather with platform. I wonder if you¹ve seen this. If it¹s not some setting I¹m unaware of, maybe someone should look into it. Sorry I haven¹t taken the time to read the source code myself. Thanks, Stuart R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" Platform: x86_64-unknown-linux-gnu (64-bit) Sys.getlocale() [1] "LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF -8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_ NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICA TION=C" "-1" > "1" [1] TRUE "-1" <"1" [1] FALSE "1" < "-1" [1] TRUE "1" < "-" [1] FALSE Vs. R version 3.1.1 (2014-07-10) ‹ ³Sock it to Me" Platform: x86_64-redhat-linux-gnu (64-bit) Sys.getlocale() [1] "LC_CTYPE=en_US.utf8;LC_NUMERIC=C;LC_TIME=en_US.utf8;LC_COLLATE=en_US.utf8 ;LC_MONETARY=en_US.utf8;LC_MESSAGES=en_US.utf8;LC_PAPER=en_US.utf8;LC_NAME =C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.utf8;LC_IDENTIFICATION =C" "-1" > "1" [1] FALSE "-1" <"1" [1] TRUE "1" < "-1" [1] FALSE "1" < "-" [1] FALSE __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Large size shared library
On 22/11/2014 08:34, Chen, Han wrote:
Dear all,
I have an R package that I plan to submit to CRAN in the near
future,
but it gave me a note when I ran "R CMD check --as-cran" saying that my
libs directory is 7.0Mb. I wrote some functions in C++ and my source
code included several low-level C++ libraries as header files. When I
compiled manually using g++ without the -g flag, my shared library (.so)
was about 400Kb; but when I compiled with the -g flag, it was about
7.0Mb... I am assuming there was a lot of debugging information created
when I turned on -g, possibly because the compiler had to look for a lot
of classes and functions in low-level C++ libraries, but I am worried
that the package would fail CRAN check due to the large size .so file
created (it seems R has -g flag on by default when compiling C/C++ code
according to ${R_HOME}/etc/Makeconf). Does anyone have any suggestions
on how I could possibly make my shared library file smaller? Even though
I can compile it manually without the -g flag, general users will !
use R default to install the package and it could take a lot of
space.
Thanks in advance!
7MB is not 'a lot of space'. There are CRAN packages which compiled
with -g take ca 80MB.
Best,
Han
-
Han Chen, Ph.D.
Postdoctoral Research Fellow
Department of Biostatistics
Harvard School of Public Health
http://www.hsph.harvard.edu/han-chen/
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Brian D. Ripley, rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK
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[Rd] Large size shared library
Dear all,
I have an R package that I plan to submit to CRAN in the near future, but it
gave me a note when I ran "R CMD check --as-cran" saying that my libs directory
is 7.0Mb. I wrote some functions in C++ and my source code included several
low-level C++ libraries as header files. When I compiled manually using g++
without the -g flag, my shared library (.so) was about 400Kb; but when I
compiled with the -g flag, it was about 7.0Mb... I am assuming there was a lot
of debugging information created when I turned on -g, possibly because the
compiler had to look for a lot of classes and functions in low-level C++
libraries, but I am worried that the package would fail CRAN check due to the
large size .so file created (it seems R has -g flag on by default when
compiling C/C++ code according to ${R_HOME}/etc/Makeconf). Does anyone have any
suggestions on how I could possibly make my shared library file smaller? Even
though I can compile it manually without the -g flag, general users will !
use R default to install the package and it could take a lot of space. Thanks
in advance!
Best,
Han
-
Han Chen, Ph.D.
Postdoctoral Research Fellow
Department of Biostatistics
Harvard School of Public Health
http://www.hsph.harvard.edu/han-chen/
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