Re: [R-pkg-devel] R package with Java issue, out of mem heap error
Hello, This sounds like a problem you should discuss with/report to the maintainer of the particular package you are using, and you can get their email address from the DESCRIPTION file. Cheers, Max On 2017-11-10 07:23 AM, Cho, In-Ho [CCE E] wrote: Dear R developers: My group are facing a problem while using an R package of extream random trees. Using a slightly large data set (13000 rows×27 columns), the R package, specifically at the prediction task, aborts with error message like "Java outofmem .. heap...". I tested this on both Macpro and Window os. Any advice as to this issue will be really appreciated. Warm regards, In Ho ___ In Ho Cho, Ph.D. Assistant Professor Dept. Civil, Construction and Environmental Engineering Iowa State University 326 Town Engineering Ames, Iowa 50011-3232, USA office: 1-515-294-3241 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel -- - Maxime Turgeon, PhD candidate Department of Epidemiology, Biostatistics and Occupational Health McGill University __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] R Package Submission Problem
Hi Younathan,
You can ignore the first note: it simply says that this is a new package.
The second note highlights a few possible problems with your DESCRIPTION
file. It flags the word "Plasmode" as being possibly misspelled; if it
isn't, you can ignore the comment. Then it points out that the Title
field contains the name of the package; as per CRAN policy, you
shouldn't do that (cf. the manual,
https://cran.r-project.org/doc/manuals/r-release/R-exts.html#The-DESCRIPTION-file).
Finally, the third note says that there is a file in the tarball that
shouldn't be there, namely Plasmode.Rproj. You can control what is
omitted from the tarball using the .Rbuildignore file. In particular,
you could add the following line:
^Plasmode\.Rproj$
Max
On 2017-09-27 11:47 AM, Abdia, Younathan wrote:
Hi,
My name is Younathan and I am trying to submit it but every time it gives me
message that my package does not pass the incoming checks automatically and it
gives me 3 NOTES. I tried to fix them but I am unable to do so. If possible do
you know how to take care of the 3 Notes. The three notes are as following:
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Younathan Abdia '
New submission
Possibly mis-spelled words in DESCRIPTION:
Plasmode (3:8)
The Title field starts with the package name.
The build time stamp is missing.
* checking DESCRIPTION meta-information ... NOTE
Checking should be performed on sources prepared by 'R CMD build'.
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
'Plasmode.Rproj'
You can also see the NOTES by clicking on the link.
https://win-builder.r-project.org/incoming_pretest/170927_165838_Plasmode_010/00check.log
Please let me know if there is any question or concern. Thank you for help.
Regards,
Younathan
The information in this e-mail is intended only for th...{{dropped:14}}
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] \Sexpr{} expressions but no 'build/partial.rdb' file
Hi Phil,
As you said yourself, if you can't reproduce the message locally, it
will be difficult to fix. But maybe the following will help: I looked at
your Github repository, Tand it seems the only changes that were made to
your files in the man/ directory since your successful release of
mirtCAR 1.5 to CRAN is the doi's that you added. In particular, you're
using the macro \doi. As explained in WRE
(https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#User_002ddefined-macros),
since R 3.2.0 users can define their own Latex-like macros to be used in
the documentation files. I don't know how to fix your error, but I would
look into that first. Maybe it's a matter of a missing dependency (e.g.
one of the base packages), maybe you need to add an extra file to your
package when you use macros. But it still doesn't explain why the error
doesn't appear on all/most platforms...
Hope my comments help,
Max
On 2017-07-25 02:42 PM, Phil Chalmers wrote:
Hi all,
First time posting here, so hopefully I'm following the correct etiquette.
I recently received the error:
"Package has help file(s) containing build-stage \Sexpr{} expressions but
no 'build/partial.rdb' file."
when submitting a package to CRAN (source code: https://github.com/
philchalmers/mirtCAT). However, I'm having difficulty reproducing the exact
problem on my Windows and Linux computers with the latest R dev version
(2017-07-25 r72968). Moreover, I don't really understand the issue, as I do
not use \Sexpr{} anywhere in the package.
After a quick search, I found a link on SO (https://stackoverflow.com/
questions/32357637/two-note-messages-from-r-cmd-check-as-cran), but it does
not appear too helpful as far as I can tell (I don't explicitly use
\package_() commands anywhere). Can anyone shed some light on this
warning and my difficulty in reproducing the message? Thank you in advance.
Phil
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
--
-
Maxime Turgeon, PhD candidate
Department of Epidemiology, Biostatistics and Occupational Health
McGill University
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Help
Hi Larisa, This has been covered before; see https://mailman.stat.ethz.ch/pipermail/r-devel/2014-March/068497.html Essentially, it is reminder to check that this information is correct. As such, you can ignore it if it is indeed correct. Max On 2017-04-28 09:15 AM, LARISA ZAMORA MATAMOROS wrote: Dear sir. I intended to upload a R package to the CRAN, but I received an e-mail with an attached file “00check.log”. The text of this file ends with two notes, I made modifications to resolve the last note: -- * checking Rd line widths ... NOTE Rd file 'ExpRep-package.Rd': \examples lines wider than 100 characters: S_Integral_Theorem(n=100, p=0.5, linf = 0, lsup = 50, Compare = TRUE, Table = TRUE, Graph = TRUE, GraphE = TRUE) Rd file 'S_Integral_Theorem.Rd': \usage lines wider than 90 characters: S_Integral_Theorem(n = 200, p = 0.5, linf = 0, lsup = 100, Compare = TRUE, Table = TRUE, Graph = TRUE, GraphE = TRUE) \examples lines wider than 100 characters: S_Integral_Theorem (n = 200, p = 0.5, linf = 0, lsup = 100, Compare = TRUE, Table = TRUE, Graph = TRUE, GraphE = TRUE) Rd file 'S_Local_Limit_Theorem.Rd': \usage lines wider than 90 characters: S_Local_Limit_Theorem(n = 170, p = 0.5, Compare = TRUE, Table = TRUE, Graph = TRUE, GraphE = TRUE) Rd file 'S_Poisson_Theorem.Rd': \usage lines wider than 90 characters: S_Poisson_Theorem(n = 2000, p = 0.002, Compare = TRUE, Table = TRUE, Graph = TRUE, GraphE = FALSE) These lines will be truncated in the PDF manual. -- But I don’t know how to resolve the first note. I am sending the first 9 lines of the 00check.log file, where this note appears: * using log directory 'd:/RCompile/CRANincoming/R-devel/ExpRep.Rcheck' * using R version 3.4.0 beta (2017-04-10 r72503) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'ExpRep/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'ExpRep' version '1.0' * checking CRAN incoming feasibility ... NOTE Maintainer: 'Larisa Zamora-Matamoros ' Therefore I am asking for help to resolve the note "* checking CRAN incoming feasibility..." I thank very much for the help. Sincerely yours. Larisa Zamora -- En su setenta cumpleaños la Universidad de Oriente festeja el saber. Del 16 al 19 mayo, II Convención Internacional de Ciencias Sociales y Ambientales. (http://www.convenciones.uo.edu.cu/index.php/2CICSA) Del 1 al 3 junio, IV Convención Internacional de Educación Física y Alto Rendimiento Deportivo. (http://www.convenciones.uo.edu.cu/index.php/4CIEF) Del 29 de nov al 1ro de diciembre de este año. (http://www.convenciones.uo.edu.cu/index.php/22CQ/22CQ2017) -- [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel -- - Maxime Turgeon, PhD candidate Department of Epidemiology, Biostatistics and Occupational Health McGill University __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] R package with external C++ library
Hi Ege, For writing to standard output/error, you can use Rcout or Rcerr (defined by Rcpp; they even have a vignette showing how to use it in the Rcpp gallery). Alternatively, if you're using C code, you can replace printf by Rprintf (this is explained in Writing R extensions, section 6.5). For abort, you can use error() instead (this is documented in WRE, section 6.2). Hope this helps, Max On 2016-08-03 03:36 PM, Ege Rubak wrote: Hi, I would like to port Google's s2-library for spherical geometry (see e.g. https://github.com/micolous/s2-geometry-library for a fork on GitHub). It is not a standard library that can easily be installed on various systems, so I would like to include the source code in the R package. The catch is that I would like to modify the source code as little as possible :-) I have package everything and added configure scripts and a tiny R-function that calls one of the C++-functions (using the antiquated .C interface for now -- that will of course be changed) in this repo: https://github.com/spatstat/s2 It compiles into a working package on Ubuntu (travis-ci + my laptop), OSX (travis-ci), and Windows (appveyor + my surface pro), but R CMD check produces some warnings (and a note about the size of the shared object, but I assume that is less important). The main things seem to be related to (travis log is at https://travis-ci.org/spatstat/s2/jobs/149578339): 1. Deprecated C++ headers and . 2. Compiled code that calls entry points which might terminate R or write to stdout/stderr. Is it hopeless to get on CRAN with warnings like these? I'm not very used to writing C/C++ code, but I guess 1. can be fixed by a few sed commands with the replacement headers and corresponding new function names. Point 2. can probably also be fixed with a reasonable effort, but I haven't investigated yet, and I would like an opinion from the list before spending more time on this. In more generality the question could be phrased something like: "When including C++ code from an upstream library which you do not control should R CMD check be completely spotless or is some flexibility to be expected in these circumstances?" Cheers, Ege PS: Extra question (prehaps particularly aimed at Dirk): When I will actually start to use the C++ library I expect it could be beneficial to use Rcpp. I have seen RcppModules mentioned somewhere, and I wonder if such an external C++ library would make sense to interface via RcppModules (again aiming at changing upstream sources as little as possible)? -- - Maxime Turgeon, PhD candidate Department of Epidemiology, Biostatistics and Occupational Health McGill University __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Regarding Fortran 77/95 Codes for building R package
Hi Vineetha, The key part of Writing R extensions is section 1.2.3., especially the following sentence: "Packages making use of Fortran 90/95 features should use file extension.f90or.f95for the source files". Incidentally, your question has already been asked on this mailing list: https://stat.ethz.ch/pipermail/r-devel/2007-December/047695.html. Best, Max On 16-07-28 01:30 PM, Vineetha Warriyar Kodalore Vijayan wrote: > Hi, > > > I'm new to programming and now trying to build a R package which uses > Fortran 95 codes ( gfortran 6.1 compiler) with a view to submit to CRAN at > some point of time. I did go through the "Writing R extension" manual and got > an impression that the codes must be in FORTRAN 77. > > I would like to know if I can proceed with my fortran 95 codes or do I have > to change everything into FORTRAN 77. I would really appreciate if you can > provide a right direction how to proceed. > > > Thank you, > > Vineetha > > > > [[alternative HTML version deleted]] > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel -- - Maxime Turgeon, PhD candidate Department of Epidemiology, Biostatistics and Occupational Health McGill University [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Warning that are Unintentionally OS-Specific (Maybe Bug in warning?)
Hi Bill,
This is just a hypothesis, but it could have something to do with the
fact that you're using parallel::mclapply inside your function pk.nca?
This would certainly explain why you have different behaviours on
Windows and Unix systems. It would also explain why you get a different
behaviour between options(warn=0) and options(warn=1), since the master
receives the exceptions at different times in both cases.
Max
On 16-07-20 01:13 PM, Bill Denney wrote:
Hi François,
I thought that was the issue, too, but I confirmed it wasn't that by
adding a print statement right above the warning in my code. The print
statement displays the message even when the warning (one line below
with no conditionals between) doesn't show anything.
Also, why would it behave differently when options(warn=1) is set
rather than the default of options(warn=0)?
Thanks,
Bill
On 7/20/2016 3:06 PM, François Michonneau wrote:
Hi Bill,
The problem is not with the warning() function but with your if()
test that triggers the warning. It probably has something to do with
slight differences in rounding. I suggest you use debug() or browser()
on each platform to see why your condition is TRUE or FALSE.
Cheers,
-- François
On Wed, Jul 20, 2016 at 2:42 PM, Bill Denney wrote:
Hi,
I'm developing the PKNCA package, and I've got an odd difference
between
warning behavior on different operating systems that I can't figure
out.
When I run the following code on Windows 10 (with R 3.3.0), I get the
following warning:
library(PKNCA)
source("https://raw.githubusercontent.com/billdenney/pknca/master/tests/testthat/generate.data.R";)
tmpconc <- generate.conc(2, 1, 0:24)
tmpconc$conc <- 0
tmpdose <- generate.dose(tmpconc)
myconc <- PKNCAconc(tmpconc, conc~time|treatment+ID)
mydose <- PKNCAdose(tmpdose, dose~time|treatment+ID)
mydata <- PKNCAdata(myconc, mydose)
myresult <- pk.nca(mydata)
Warning messages:
1: In pk.calc.half.life(conc = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, :
Too few points for half-life calculation (min.hl.points=3 with
only 0
points)
2: In pk.calc.half.life(conc = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, :
Too few points for half-life calculation (min.hl.points=3 with
only 0
points)
When I run the code on Linux (Ubuntu 16.04 with R 3.3.1), I do not
get a
warning. When I run the code on Linux after "options(warn=1)", I
get the
warning. I have confirmed that the same code path is taken in both
Windows
and Linux by simply inserting a print statement next to the
warning. The
actual warning code is:
warning(sprintf(
"Too few points for half-life calculation (min.hl.points=%g
with only
%g points)",
min.hl.points, nrow(dfK)))
This platform inconsistency is causing issues with my package
because the
package expects the warnings, and the user should know about the
warnings.
I've got test cases expecting the warnings, and they fail everywhere
but
Windows
(https://cran.r-project.org/web/checks/check_results_PKNCA.html).
Does anyone have an idea why warnings may behave differently on Windows
compared to non-Windows platforms? Is this a bug in R somewhere?
(I've not
been able to make a simpler example that triggers the issue,
unfortunately.)
Thanks,
Bill
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
--
-
Maxime Turgeon, PhD candidate
Department of Epidemiology, Biostatistics and Occupational Health
McGill University
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
