[R-pkg-devel] Win-builder: Author field differs from that derived from Authors@R

2019-02-06 Thread Ivan Krylov
asilief [aut, cph], Alex Kargovsky [aut, cph], Knut Franke >> [cph], Alexander Semke [cph], Tilman Benkert [cph], Kasper Peeters >> [cph], Russell Standish [cph], Ivan Krylov [cre, cph]' >> Authors@R: 'Miquel Garriga [aut, cph], Stefan Gerlach [aut, cph], >> Ion Vasilief

[R-pkg-devel] Robj: reading proprietary format - first time packaging

2019-01-29 Thread Ivan Krylov
Hi! Not being able to find an R package that would let me import an Origin(R)[0] OPJ file, I found liborigin[1] and used Rcpp (thanks, Dirk Eddelbuettel!) to create the package which I titled Ropj[2]. Right now it only understands the absolute minimum of what I needed to import, but I intend to

Re: [R-pkg-devel] How to obtain intercept of intercept-only glm in Fortran?

2019-05-11 Thread Ivan Krylov
On Fri, 10 May 2019 16:17:42 + "Wang, Zhu" wrote: > Are there any examples or links for me to follow through more closely? Calling R functions from C++ is described at and elsewhere in Rcpp documentation. An example follows:

Re: [R-pkg-devel] R CMD check ERROR (strange to me)

2019-05-10 Thread Ivan Krylov
On Thu, 9 May 2019 23:19:46 + "Wang, Zhu" wrote: > I have encountered some strange error (see 00install.out). It seems to have been stripped by the attachment filter, and there are no compilation errors on my system. Can you include the relevant lines from 00install.out inline? -- Best

Re: [R-pkg-devel] Need help for Debian check error

2019-04-30 Thread Ivan Krylov
On Tue, 30 Apr 2019 19:53:49 + "Zhang, Lixiang" wrote: > I don't know why is that happening and how should I fix it. Thanks a > lot for your help. The e-mail from CRAN also said, >> More details are given in the directory: followed by a link scrambled by your e-mail software. When you

Re: [R-pkg-devel] parallel computing slower than sequential computing

2019-04-30 Thread Ivan Krylov
On Mon, 29 Apr 2019 23:44:42 + "Wang, Zhu" wrote: > sessionInfo() > R version 3.5.2 (2018-12-20) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 18.04.2 LTS Which BLAS implementation do you use? One popular implementation, OpenBLAS, spawns multiple threads to do some

Re: [R-pkg-devel] How to obtain intercept of intercept-only glm in Fortran?

2019-05-06 Thread Ivan Krylov
On Sat, 4 May 2019 22:41:16 + "Wang, Zhu" wrote: > In an R package I would like to compute intercept for an > intercept-only GLM in a Fortran subroutine. If all else fails, you could use R API [*] to call coef(glm.fit(...)), though it might require writing a C or C++ wrapper to avoid

Re: [R-pkg-devel] "Progress reports" for examples in packages.

2019-07-02 Thread Ivan Krylov
Could R CMD check be using valgrind to run the examples? Valgrind has to interpret CPU instructions manually to be able to warn about results of code execution depending on memory values it considers undefined, so it is much slower than execution on a real CPU. One way to verify that on a

Re: [R-pkg-devel] No protocol specified

2019-08-25 Thread Ivan Krylov
On Fri, 23 Aug 2019 09:18:07 +0200 "Dr. rer. nat. Michael Thrun" wrote: >> No protocol specified > > Can anyone translate this note to me in a way that I know what the > issue is? I might be mistaken, but "No protocol specified" is an error frequently returned by an X server [*] when a

Re: [R-pkg-devel] please help understand an error in openMP statements

2019-09-13 Thread Ivan Krylov
On Thu, 12 Sep 2019 16:12:17 -0500 Marcin Jurek wrote: > U_NZentries.cpp:258:19: error: ‘covparms’ not specified in enclosing > ‘parallel’ > 258 | covmat= MaternFun(dist,covparms) + diagmat(nug) ; // summation from > arma > | ~^~~ This might be a compiler

Re: [R-pkg-devel] "Additional issues" show WRITE outside an array

2019-07-26 Thread Ivan Krylov
On Fri, 26 Jul 2019 01:50:36 -0500 Jiahuan ye wrote: > I am very confused what causes the ERROR. Your code on line 197 of src/min_wgss.cpp causes memory access outside the block that had been allocated for the best_change_point vector. I have not read the code in depth, but it looks like the

Re: [R-pkg-devel] debugging memory errors

2019-11-06 Thread Ivan Krylov
On Wed, 6 Nov 2019 08:43:50 -0600 Marcin Jurek wrote: > I have very little clue what to do, above all because I don't know > how to reproduce the error. Using AddressSanitizer to find memory errors in R packages requires the R installation to be built with AddressSanitizer, too. I found it

Re: [R-pkg-devel] potential memory leak using openMP

2019-11-15 Thread Ivan Krylov
On Fri, 15 Nov 2019 10:49:25 -0600 Marcin Jurek wrote: > 1) what should I do to reproduce the error? The following is a quick, unchecked suggestion, but: `R CMD check --use-valgrind` just adds `-d valgrind` to the command line, while the report you are seeing can only be obtained with

Re: [R-pkg-devel] Fix non-ASCII characters in R packages

2019-12-02 Thread Ivan Krylov
On Mon, 2 Dec 2019 10:57:51 -0300 Rafael Pereira wrote: > checking data for non-ASCII characters ... NOTE Note: found 58 marked > Latin-1 strings > > I have used to code below to identify my scripts that have strings > using non-ASCII characters. I don't think it's about non-ASCII in source

Re: [R-pkg-devel] checking CRAN incoming feasibility NOTE

2019-10-06 Thread Ivan Krylov
On Sat, 5 Oct 2019 16:52:16 -0500 "R. Mark Sharp" wrote: > MIT + file LICENSE > File 'LICENSE': > Copyright 2017-2019 R. Mark Sharp > > Permission is hereby granted, <...> Note that for packages licensed under MIT license, the LICENSE file should only contain the lines: >> YEAR:

Re: [R-pkg-devel] Adding .exes to R package?

2020-01-23 Thread Ivan Krylov
On Wed, 22 Jan 2020 20:54:40 + Jonathan Greenberg wrote: > Are there reasonable tutorials on how to do this? If you absolutely have to do this, take a look at the tinytex package. It is basically an installer for a preselected set of packages from TeX Live inside a platform-specific

Re: [R-pkg-devel] finding "logo.jpg" [was: "try" malfunctions on Ubuntu Linux 16.04 LTS, R-release, GCC]

2020-02-03 Thread Ivan Krylov
On Mon, 3 Feb 2020 13:30:11 -0600 Spencer Graves wrote: > logo.jpg <- paste(R.home(), "doc", "html", "logo.jpg", sep > = .Platform$file.sep) I wonder whether file.path(R.home('doc'), 'html', 'logo.jpg') would be more portable. Are there R installations built without the HTML docs? -- Best

Re: [R-pkg-devel] Catching console messages from libGL

2020-02-17 Thread Ivan Krylov
On Mon, 17 Feb 2020 14:56:31 -0500 Duncan Murdoch wrote: > So how do I capture stderr (or, off topic here, how do I get libGL to > be quiet)? libGL seems to only offer bad news in this regard: it writes directly to stderr [1] and does not seem to offer a way to silence the _LOADER_FATAL

Re: [R-pkg-devel] CRAN Package Check Results - No protocol specified (OS X only)

2020-02-18 Thread Ivan Krylov
On Mon, 17 Feb 2020 19:28:43 -0500 Dominic Comtois wrote: > a bunch of warnings with "No protocol specified" messages "No protocol specified" is printed by the X11 client library when it fails to connect to the X server. I think that these indicate a problem with setup of the macOS testing

Re: [R-pkg-devel] Error in curl: Failed FTP upload: 550

2020-02-21 Thread Ivan Krylov
On Fri, 21 Feb 2020 14:04:24 +0100 Gianmarco Alberti wrote: > I have also used: > check_win_devel() and check_win_release() out of devtools, but I keep > getting the following message: > Error in curl::curl_fetch_memory(url, handle = h) : > Failed FTP upload: 550 Does it work if you build the

Re: [R-pkg-devel] Need help to resolve NOTEs in auto check

2020-01-22 Thread Ivan Krylov
Hello Ian, On Wed, 22 Jan 2020 10:29:51 + Ian Walker wrote: > * checking CRAN incoming feasibility ... NOTE > Maintainer: ‘Ian Walker < > i.wal...@bath.ac.uk > >’ This NOTE is there for CRAN staff to have another look at the Maintainer: field in case this is someone's first submission or

Re: [R-pkg-devel] For reproducibility issue

2020-01-17 Thread Ivan Krylov
On Fri, 17 Jan 2020 13:55:39 + وليد خلف معوض المطيرى wrote: > So, does anyone have an idea of how to solve this issue. "Writing R Extensions", 1.6. Writing portable packages: >> Compiled code should not call the system random number generators >> such as rand, drand48 and random, but

Re: [R-pkg-devel] Checkpoint package failing CRAN checks

2020-01-10 Thread Ivan Krylov
I wonder why does vignettes/checkpoint.Rmd run the following: > example_project <- tempdir() Now example_project contains the path of per-session temporary directory... > dir.create(example_project, recursive = TRUE, showWarnings = FALSE) ...so there should be no need to create it... >

Re: [R-pkg-devel] rhub, docker and Bioconductor

2020-01-07 Thread Ivan Krylov
On Tue, 7 Jan 2020 13:54:38 + Christian Martin Hennig wrote: > Are there any other options apart from rhub/docker to get wiser about > my errors and issues (error on debian-clang in a routine that shows > nothing suspicious on my machine I cannot answer your original questions, but I can

Re: [R-pkg-devel] suggestion: conda for third-party software

2020-01-07 Thread Ivan Krylov
On Tue, 7 Jan 2020 15:49:45 +0100 Serguei Sokol wrote: > Currently, many R packages include TPS as part of them thus bloating > their sizes and often duplicating files on a given system.  And even > when TPS is not included in an R package but is just installed on a > system, it is not so

Re: [R-pkg-devel] Installed package size

2020-03-12 Thread Ivan Krylov
On Thu, 12 Mar 2020 15:16:13 + Carsten Croonenbroeck wrote: > I would like to know what's the maximum size and if there's a way > around that limit. Here's what CRAN policy [*] says about that: >> As a general rule, neither data nor documentation should exceed 5MB >> (which covers several

Re: [R-pkg-devel] An invalid URLs

2020-03-13 Thread Ivan Krylov
On Fri, 13 Mar 2020 09:49:03 +0800 (GMT+08:00) jared_wood wrote: > Status: 403 > > Message: Forbidden > > > > I don’t know why. The URL was picked up in the article of this > database and I can open it. To be fair, my requests to this service are also blocked unless I use Tor

Re: [R-pkg-devel] More GitHub problems

2020-04-21 Thread Ivan Krylov
On Mon, 20 Apr 2020 23:44:43 -0500 Spencer Graves wrote: > Is there a way to restore the functionality of a local clone of a > GitHub repository after the SSH key it used was replaced? Does `git remote -v` in the repo directory show https://github.com/... or g...@github.com:... or ssh://...

Re: [R-pkg-devel] An invalid URLs

2020-03-13 Thread Ivan Krylov
On Fri, 13 Mar 2020 11:02:06 +0300 Ivan Krylov wrote: > the remote server could deny requests from such automated user > agents, only allowing clients that look like browsers Here is what I have been able to observe: If wait for some time, then try to access http://www.malacards.org/

Re: [R-pkg-devel] /usr/bin/ld: cannot find -ludev

2020-04-26 Thread Ivan Krylov
On Sun, 26 Apr 2020 15:39:50 + "Sameh M. Abdulah" wrote: > Yes, I think I will need it Could you tell us why your package needs it? Perhaps there is a way to make it an optional dependency. > since I know that this is an OS libs It is true that libudev is required for successful bootup of

Re: [R-pkg-devel] Help Debugging Debian Error

2020-05-15 Thread Ivan Krylov
On Fri, 15 May 2020 03:50:12 -0400 Paul Hibbing wrote: > Complete output: > > library(testthat) > > library(PAutilities) > > > > test_check("PAutilities") It seems to me that the R process crashes while running your tests, but since testthat::test_check captures everything to

Re: [R-pkg-devel] OpenMP variable not specified in enclosing 'parallel'

2020-03-23 Thread Ivan Krylov
On Mon, 23 Mar 2020 15:29:20 +0100 Emil Sjørup wrote: > const int iMaxLag = 20; > error: ‘iMaxLag’ not specified in enclosing ‘parallel’ > error: ‘iMaxLag’ is predetermined ‘shared’ for ‘shared’ This looks like a compiler bug to me. g++ seems to forget the rule that "const" variables are

[R-pkg-devel] Guidelines on use of snow-style clusters in R packages?

2020-05-24 Thread Ivan Krylov
Some of the packages I use make it possible to run some of the computations in parallel. For example, sNPLS::cv_snpls calls makeCluster() itself, makes sure that the package is loaded by workers, exports the necessary variables and stops the cluster after it is finished. On the other hand,

Re: [R-pkg-devel] "non-ASCII input" and "--data-compress" ignored

2020-07-17 Thread Ivan Krylov
On Fri, 17 Jul 2020 02:02:36 -0500 Spencer Graves wrote: > If I copy this URL into a browser and back out again, I get > the following: > > > https://www.americansecurityproject.org/ASP%20Reports/Ref%200072%20-%20North%20Korea%E2%80%99s%20Nuclear%20Program%20.pdf > > >   However, if I

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

2020-06-30 Thread Ivan Krylov
On Mon, 29 Jun 2020 22:55:02 +0200 Göran Broström wrote: > After googling for a while (found nothing relevant in 'WRE'), I > understand that I have two options: (i) Change 'Depends' in > DESCRIPTION as suggested, and (ii) using save with 'version = 2' for > the new files. One of the steps

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

2020-06-30 Thread Ivan Krylov
On Tue, 30 Jun 2020 11:48:29 +0200 Göran Broström wrote: > No point at all with version 3 in packages? Format version 3 [1] introduces support for ALTREP objects [2]. Examples of where ALTREP might be useful include really long integer vectors, like 1:1e10. -- Best regards, Ivan [1]

Re: [R-pkg-devel] package installation and linking with JAGS

2020-07-08 Thread Ivan Krylov
On Wed, 8 Jul 2020 11:06:31 +0200 Frantisek Bartos wrote: >Check: for GNU extensions in Makefiles, Result: WARNING This warning is easy to deal with: >JAGS_ROOT ?= c:/progra~1/JAGS/JAGS-4.3.0 Use plain "=" macro definitions, since others aren't considered portable enough. >SOURCES=

Re: [R-pkg-devel] Valgrind warning on saveRDS, about object in external pointer

2020-07-08 Thread Ivan Krylov
On Wed, 08 Jul 2020 19:23:41 +0300 David Cortes wrote: >- The warning is about an un-initialized value allocated in a call to >C++ std::vector::reserve, which is called on a C++ vector member of the >struct in the external pointer. I'm ready to admit that I didn't read the code well enough, but

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

2020-07-07 Thread Ivan Krylov
On Tue, 7 Jul 2020 03:00:23 + Pierre Lafaye de Micheaux wrote: >Should I just write something like (adding the middle instruction >below to my existing code above)?: > >#ifdef FC_LEN_T >typedef long long int FC_LEN_T; No, I don't think that would help. What _might_ help is adapting the

Re: [R-pkg-devel] Valgrind warning on saveRDS, about object in external pointer

2020-07-15 Thread Ivan Krylov
On Wed, 08 Jul 2020 22:43:13 +0300 David Cortes wrote: > About the source code: it actually complains about line > fit_model.cpp:751 : > hplane_root->reserve(exp_nodes); My fault. I was reading the GitHub source code instead of CRAN package source code. > I’m not able to reproduce the warning

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

2020-07-06 Thread Ivan Krylov
On Fri, 3 Jul 2020 00:15:27 + Pierre Lafaye de Micheaux wrote: >Found the following significant warnings: >myzhpevx.cpp:13:23: warning: type of _zhpevx__ does not match > original declaration [-Wlto-type-mismatch] I managed to reproduce the warning on R-devel r78607 built with

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

2020-06-15 Thread Ivan Krylov
On Mon, 15 Jun 2020 12:52:20 -0400 Duncan Murdoch wrote: > maybe someone else can suggest how to read an object from > the .rdb file using R code. Internally R uses C code for this. This function seems to work for me: # filename: the .rdb file # offset, size: the pair of values from the .rdx

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

2020-06-15 Thread Ivan Krylov
On Mon, 15 Jun 2020 11:13:21 + Daniel Kelley wrote: > A possible clue is that I get a large-file note on macOS, but not > when I use rhub for test linux builds, or winbuilder for a windows > build. I do not have ready access to either linux or windows > machines, to examine those builds in

Re: [R-pkg-devel] package CatDataAnalysis

2020-06-28 Thread Ivan Krylov
On Sun, 28 Jun 2020 11:07:46 -0500 Charles Geyer wrote: >Please note that I made Alan Agresti (with his acquiescence) the >author of the package Sorry to derail this, but is it possible for Alan Agresti to add a line to the page [*] allowing redistribution of the data, preferably under the

Re: [R-pkg-devel] R package does not find DLL routine

2020-06-28 Thread Ivan Krylov
On Sun, 28 Jun 2020 12:43:53 +0200 Lisa GM wrote: > "sum_c" not resolved from current namespace (sum) As mentioned by Dirk Eddelbuettel, this is not the way R packages are supposed to be built [*], but if you are absolutely positive you cannot build the DLL from source together with the

Re: [R-pkg-devel] [External] Guidelines on use of snow-style clusters in R packages?

2020-06-13 Thread Ivan Krylov
On Wed, 3 Jun 2020 08:54:56 -0500 (CDT) luke-tier...@uiowa.edu wrote: > If you use [a cluster] passed to you it would be best to leave > it in the state you found it at least as far as the search path and > global environment are concerned. Thanks for this advice! I guess that clusterExport() is

Re: [R-pkg-devel] [R] a question of etiquette

2020-06-03 Thread Ivan Krylov
On Tue, 2 Jun 2020 20:33:56 -0400 Avraham Adler wrote: > If there is a term which reflects that mechanism from a discipline > other than biology, please let me know. I think that "copyleft" is the term you are looking for. The Wikipedia page [*] defines it as >> the practice of offering people

Re: [R-pkg-devel] Note: information on .o files is not available / Found '_exit', possibly from '_exit' (C)

2020-07-17 Thread Ivan Krylov
On Fri, 17 Jul 2020 11:25:40 +0200 Fabio Sigrist wrote: > Found '_exit', possibly from '_exit' (C) > Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) > Found 'exit', possibly from 'exit' (C), 'stop' (Fortran) > Found 'printf', possibly from 'printf' (C) A curious

Re: [R-pkg-devel] os/x compiled w/ openmp?

2020-07-21 Thread Ivan Krylov
On Mon, 13 Jul 2020 10:14:14 -0400 Joshua N Pritikin wrote: > Is this the best place to ask? R-SIG-Mac [*] is probably a better place for this. The short answer is that OpenMP support has been dropped from the compiler supplied with macOS, but there are workarounds [**]. -- Best regards, Ivan

Re: [R-pkg-devel] "non-ASCII input" and "--data-compress" ignored

2020-07-20 Thread Ivan Krylov
On Fri, 17 Jul 2020 18:08:24 -0500 Spencer Graves wrote: >   I tried escaping "%" every time it occurred without success, > but adding "\encoding{UTF-8}" as the 4th line of > nuclearWeaponStates.Rd eliminated that problem. Glad it works for you, but you might want to check that the link

Re: [R-pkg-devel] Etiquette for package submissions that do not automatically pass checks?

2020-08-17 Thread Ivan Krylov
Dear Cesko, On Fri, 14 Aug 2020 21:08:55 +0200 Cesko Voeten wrote: > The package contains functionality to run on cluster nodes that were > set up by the user and needs to access its own internal functions > from there. Apologies for derailing the thread, but I had a similar problem a few

Re: [R-pkg-devel] Formatting .Rbuildignore

2020-08-17 Thread Ivan Krylov
On Mon, 17 Aug 2020 15:56:07 +0200 Thierry Onkelinx wrote: > Can we add blank lines in .Rbuildignore? Or lines with only comments > (line starting with #)? .Rbuildignore is not documented [1] to allow comments, but the current implementation does skip empty lines [2] since 2010 [3] (otherwise

Re: [R-pkg-devel] How to retrieve a flag set in configure.ac (filled in Makevars.in) during package installation in an R or C++ script ?

2020-08-17 Thread Ivan Krylov
On Sat, 15 Aug 2020 19:50:41 +0530 Akshit Achara wrote: > To access these files, I need to use the path of libminizinc (which > can change per installation). I want to extract this path from either > Makevars or configure to use it in my package. Just as Makevars is generated during