Re: [R-pkg-devel] [External] Re: try() in R CMD check --as-cran

2019-06-14 Thread Tomas Kalibera
The advantage of "abort" (R_Suicide) over the default (R error) is that it cannot be caught accidentally, so that one can detect more errors, and it may be easier to find where the error happened. To make the default behavior less surprising/more user friendly, and to allow intentional

Re: [R-pkg-devel] access is denied

2019-06-20 Thread Tomas Kalibera
If you have not already done so, I'd check the package directory (and its parent) is not opened in any application, including Windows Explorer, including current working directory in any command prompt. I'd also make sure the package is not loaded in any R session. The error message may be

Re: [R-pkg-devel] Warning about "serialize/load".

2019-07-15 Thread Tomas Kalibera
On 7/15/19 2:06 AM, Travers Ching wrote: I think the major change was saving of alt-rep objects efficiently. Example save(1:1e8, file=...) is very efficient. I'm not sure if that is all that changed it, but I couldn't find documentation on the differences. Yes, format version 3 provides

Re: [R-pkg-devel] Single character in Fortran function and FCONE and FCLEN macros

2019-09-03 Thread Tomas Kalibera
On 9/3/19 3:07 PM, Benjamin Christoffersen wrote: > Dear Sirs, > > I have tried to update my 'dynamichazard' package on CRAN but I have > had some issues with the '-Wlto-type-mismatch' checks. In particular, > I have tried to follow "Writing R Extensions" section "Fortran > character strings" and

Re: [R-pkg-devel] My test passes in OSx on Travis, but not in OSx on CRAN

2019-09-13 Thread Tomas Kalibera
The error seems to be because you are trying to write to the user's home directory. This is not allowed. Probably by accident your test creates "~/testcsv4.csv" (the same problem is present for other test files). Best Tomas On 9/13/19 1:21 PM, Vincent van Hees wrote: Dear all, I have a test

Re: [R-pkg-devel] Linking with OpenBLAS complains lapacke not found

2019-09-09 Thread Tomas Kalibera
Please refer to BLAS_LIBS, LAPACK_LIBS in Writing R Extensions. For an example package that uses BLAS/LAPACK, see e.g. "stats" or "Matrix". The package will then use the BLAS/LAPACK implementation as chosen by the user/system administrator at dynamic linking time (see R Installation and

Re: [R-pkg-devel] R, BLAS, and FCLEN (solved)

2019-09-13 Thread Tomas Kalibera
Dear Göran, I can reproduce the problem with eha version 2.6.0. The reason for the type mismatch, and hence the LTO warning, is _not_ the calls to dgemv from Fortran code, but the calls to dgemv from the C code from the other source files in your package. There is no need to go through

Re: [R-pkg-devel] Fwd: Reproducing CRAN pre-tests

2019-09-21 Thread Tomas Kalibera
On 9/20/19 2:43 AM, Aravind J. wrote: Hi, I was able to fix the issue and submit my package successfully to CRAN. However, the question remains, is there any way to replicate the CRAN pre-tests locally for future debugging, particularly in a windows environment? I had tried rhub platforms

Re: [R-pkg-devel] Warning in system2(..., stdout = FALSE, stderr = FALSE) :, '"pdflatex"' not found

2019-09-19 Thread Tomas Kalibera
On 9/19/19 6:29 AM, Spencer Graves wrote: Update: A web search for 'installing pdflatex for "R CMD" on Windows 10?' suggested I install MiKTeX.  I did that from miktex.org, and it got me past that error.  Spencer Please note these things are documented in R Installation and Administration

Re: [R-pkg-devel] unicode WARNING on solaris?

2019-09-24 Thread Tomas Kalibera
On 9/24/19 1:57 AM, Toby Hocking wrote: Hi all, is there a known fix for this WARNING which I am getting on solaris for my newly submitted nc package? https://www.r-project.org/nosvn/R.check/r-patched-solaris-x86/nc-00check.html It seems that deparse() came across some non-printable

Re: [R-pkg-devel] implications of staged install for data processing packages

2019-06-28 Thread Tomas Kalibera
On 6/28/19 5:16 PM, Florian Oswald wrote: oh ok i see: so i will always be able to do clean(path = "~/data.csv") for example? in that case I completely misunderstood this and there must indeed be some system.file call buried somewhere. will check. thanks! In case it is hard to find manually,

Re: [R-pkg-devel] netcdf question

2019-11-04 Thread Tomas Kalibera
On 11/4/19 8:40 PM, Roy Mendelssohn - NOAA Federal via R-package-devel wrote: Hi All: I am wondering if it is possible to find out when packages that use the netcdf libraries are built on the CRAN machines (such as ncdf4) what versions of the netcdf library are being used on at least Mac and

Re: [R-pkg-devel] invalid multibyte string on solaris?

2019-11-01 Thread Tomas Kalibera
On 10/31/19 12:58 AM, Toby Hocking wrote: Hi all, I am getting an "invalid multibyte string" error from one of my examples when it is run on solaris, which results in check FAILURE: https://www.r-project.org/nosvn/R.check/r-patched-solaris-x86/nc-00check.html To fix this I guess I could just

Re: [R-pkg-devel] Updating package with a dependency (rJava) that doesn't build on all flavours

2019-11-13 Thread Tomas Kalibera
On 11/13/19 10:19 AM, Tomáš Kliegr wrote: Hello, This question has not stirred much discussion ... If this is the wrong place to ask, I was wondering if some one point me to where I should ask, or who to approach? If I understand this issue correctly, it does not affect only my package,

Re: [R-pkg-devel] Compiler warning using C versions of base R integrate function

2019-11-28 Thread Tomas Kalibera
On 11/21/19 7:25 PM, Devin Incerti wrote: Hi, I'm attempting to submit a very minor update to my package where I replaced a deprecated C++ function with an alternative. However, I'm receiving an unrelated warning "*array subscript -1 is outside array bounds of ‘double [52]’ [-Warray-bounds] *"

Re: [R-pkg-devel] install.R running out of memory

2019-11-04 Thread Tomas Kalibera
On 11/3/19 1:05 PM, Viktor Gal wrote: ah yeah i forgot to mention. it’s the same, i.e. it’s not the byte code compilation that causes this behaviour but the preparation for lazy loading. R is not optimized for these cases (generated code, source file with >100,000 lines of code), but R has

Re: [R-pkg-devel] Package or namespace load failed: undefined symbol

2019-09-25 Thread Tomas Kalibera
On 9/25/19 1:00 PM, Ralf Stubner wrote: On Wed, Sep 25, 2019 at 10:29 AM Sameh M. Abdulah wrote: I am installing OpenBLAS because I need LAPACKE libraries which I cannot find on the current version of OpenBLAS on CRAN. I add the libraries directory in my package to the PKG_CONFIG_PATH. Is

Re: [R-pkg-devel] unicode WARNING on solaris?

2019-09-25 Thread Tomas Kalibera
es. I see \u4e8c \u4e09 \U0001F60E. Tomas > > On Tue, Sep 24, 2019 at 1:38 AM Tomas Kalibera > mailto:tomas.kalib...@gmail.com>> wrote: > > On 9/24/19 1:57 AM, Toby Hocking wrote: > > Hi all, > > > > is there a known fix for this WARNING which I

Re: [R-pkg-devel] How reproduce CRAN check

2019-09-25 Thread Tomas Kalibera
On 9/17/19 6:17 PM, Cristiane Hayumi Taniguti wrote: Hello, thanks for all the answers. I did the new tests with all suggestions. I included the Rprintf in my script, however it did not show any NaN when running with my examples (the same that CRAN check pointed the error) The approach of

Re: [R-pkg-devel] Help on Windows CRAN Check

2020-03-05 Thread Tomas Kalibera
On 3/5/20 4:26 AM, John Lawson wrote: > I see this error on the CRAN Check report > >> ### ** Examples >> >> #Definitive Screening Design >> library(daewr) >> set.seed(1234) >> x <- DefScreen(m=5,c=0) >> colnames(x) <- paste("x",1:5,sep="") >> x$y <- 3*x$x1 + 2*x$x2 + 2*x$x4*x$x5 + x$x3^2 +

Re: [R-pkg-devel] [FORGED] Re: Help on Windows CRAN Check

2020-03-05 Thread Tomas Kalibera
On 3/5/20 9:45 AM, Rolf Turner wrote: On 5/03/20 9:04 pm, Tomas Kalibera wrote: On 3/5/20 4:26 AM, John Lawson wrote: I see this error on the CRAN Check report Fatal error: the condition has length > 1 The problem is that the condition t1 == "I" & t2 == "

Re: [R-pkg-devel] Errors in make check in Windows 10 with OpenBLAS

2020-03-19 Thread Tomas Kalibera
Hi Erin, this comes from examples in ?str. Could you please try to find a minimal example to reproduce on your system based on that? I would look for "line needs" in ?str and experiment with reducing the example there while still getting the error. Once it is minimal, could you please try

Re: [R-pkg-devel] Strange leftovers after check by CRAN

2020-03-20 Thread Tomas Kalibera
On 3/19/20 6:03 PM, Max Turgeon wrote: > Is there perhaps a typo in the environment variable name? This line suggests > there should be an underscore at the beginning too: > > https://github.com/wch/r-source/blob/trunk/src/library/tools/R/check.R#L6028 Also the correct name is in R Internals,

Re: [R-pkg-devel] Errors in make check in Windows 10 with OpenBLAS

2020-03-20 Thread Tomas Kalibera
glish_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252" > > enc2native("\uff21") > [1] "A" > > enc2native("\u4e2d") > [1] "" > > Sys.setlocale("LC_CTYPE", "English_United States.28605

Re: [R-pkg-devel] Errors in make check in Windows 10 with OpenBLAS

2020-03-20 Thread Tomas Kalibera
     > c.ch <http://c.ch> w.ch <http://w.ch> c.fw w.fw >      > 64   64   32   64 >     >> stopifnot(unname(ncc) == c(64,64, 32, 64)) >     >> ## nchar.max: 1st line needs an increase of  2 in order to > see  1  (in >      > UTF-$ >

Re: [R-pkg-devel] Errors in make check in Windows 10 with OpenBLAS

2020-03-21 Thread Tomas Kalibera
onv.def win_iconv.o > > Just the  -march=native -pipe > > Erin Hodgess, PhD > mailto: erinm.hodg...@gmail.com <mailto:erinm.hodg...@gmail.com> > > > On Fri, Mar 20, 2020 at 9:01 AM Tomas Kalibera > mailto:tomas.kalib...@gmail.com>> wrote: > > Th

Re: [R-pkg-devel] Problem with Check --as-cran

2020-03-23 Thread Tomas Kalibera
The problem is with if (class(data) != "matrix") stop("The data field should be an array or a data frame") Please use inherits() instead of checking class(), see this for more details https://developer.r-project.org/Blog/public/2019/11/09/when-you-think-class.-think-again Best Tomas On

Re: [R-pkg-devel] use of getNativeSymbolInfo

2020-03-24 Thread Tomas Kalibera
On 2/9/20 5:14 PM, Benjamin Tyner wrote: Hello, Using package nlme as an example, where there is a registered routine fit_gnls: > library(nlme) > getDLLRegisteredRoutines("nlme")$.C$fit_gnls $name [1] "fit_gnls" $address attr(,"class") [1] "RegisteredNativeSymbol" $dll DLL name: nlme

Re: [R-pkg-devel] data and load version 3

2020-06-30 Thread Tomas Kalibera
On 6/30/20 11:48 AM, Göran Broström wrote: On 2020-06-30 01:07, Jeff Newmiller wrote: Your choice. Do you want to support people using older versions of R, or not? Is that all? No point at all with version 3 in packages? Why was it introduced? I have seen an argument for version 2: "...

Re: [R-pkg-devel] warning: type of ‘zhpevx_’ does not match original declaration [-Wlto-type-mismatch]

2020-07-06 Thread Tomas Kalibera
My recommendation would be to try to minimize the example (package) as much as possible so that it still has the problem, and then try to investigate why exactly/where is the type mismatch. This is what helped me debug similar issues - sometimes it was hard to tell from the Fortran warnings

Re: [R-pkg-devel] how to prevent a small package from yielding a large installed size?

2020-06-15 Thread Tomas Kalibera
On 6/15/20 6:52 PM, Duncan Murdoch wrote: On 15/06/2020 12:30 p.m., Daniel Kelley wrote: Duncan, thanks very much for that very helpful hint.  I got as follows.   My guess is that the first column in rdx$variables is an address offset, and so it seems that the lion's share of the storage is

Re: [R-pkg-devel] Anyone Know How To Setup Wine for Windows Testing?

2020-09-09 Thread Tomas Kalibera
On 7/16/20 7:57 PM, Steve Bronder wrote: On Wed, Jul 15, 2020 at 2:22 PM Neal Fultz wrote: If you don't mind multi-gig docker containers, this can be helpful: https://github.com/scottyhardy/docker-wine It doesn't work with 64 bit versions of R as far as I could tell, but 32 bit did install

Re: [R-pkg-devel] Compiling 32-bit on Windows using 64-bit gcc and -m32

2020-09-09 Thread Tomas Kalibera
On 9/7/20 7:07 PM, b...@denney.ws wrote: Hello, My question is: Can I use the 64-bit gcc to build a 32-bit package with the -m32 command line option with Rtools? And, can that work for CRAN? Or more generally, is there a work-around for needing lots of RAM during compilation with the