Re: [R-pkg-devel] CRAN's mysterious behavior building OS/X binaries for OpenMx

On 25 September 2018 at 09:16, Joshua N Pritikin wrote: | We finally figured out why our binaries were failing to build on OS/X, | after more than a year of misery. | | We use C++ exceptions and try/catch blocks like this, | | try { | // stuff here |

Re: [R-pkg-devel] SystemRequirements: Berkeley DB STL

On 23 October 2018 at 14:02, Toby Hocking wrote: | I would like to put the https://github.com/tdhock/PeakSegDisk package on | CRAN. This package needs Berkeley DB C++ Standard Template Library. What do | I need to do to get this package (with compiled mac/windows binaries) on | CRAN? | | This C+

Re: [R-pkg-devel] Version number in check_results

On 8 November 2018 at 07:21, Lisec, Jan wrote: | [short version] | Is the depicted 'Version' in the CRAN package check results page referring to the version of the uploaded package? | | [long version] | Due to changes in a suggested package I had to update my own and fail to get it pass the CR

Re: [R-pkg-devel] FOSS license and restricted use by further dependence

Javier, On 22 November 2018 at 09:49, Javier García-Pintado wrote: | * checking CRAN incoming feasibility ... NOTE | Maintainer: ‘Javier Garcia-Pintado ’ | | New submission | | Possibly mis-spelled words in DESCRIPTION: | Kalman (11:49) Just _either_ use apostrophes around it: ie wite 'Kalm

Re: [R-pkg-devel] Suggested package relies on recent R

On 8 December 2018 at 14:41, David Hugh-Jones wrote: | Thanks guys. If CRAN already sets FORCE_SUGGESTS = false, then I think I | don't have a problem. I think you still do as long as you ignore Duncan's advice. It's not "just" about skirting CRAN tests and rules, it is about doing packaging ri

Re: [R-pkg-devel] UBSAN Problems with Memory Sanitizer

On 2 January 2019 at 16:17, Maximilian Leodolter wrote: | I just wanted to upload a new version of my package (IncDTW) but got the | message that my old version causes the following error, even though it | works perfectly fine. | | The error message says: | | runtime error: member call on addre

[R-pkg-devel] About a need for hooks from R CMD ... commands, and a question

For a few years now I had mused about how nice it would be to have other scripts triggered like `cleanup`. For Rcpp, it would be nice to run compileAttributes(). For roxygen2, it would be nice to run roxygenize() (especially if that continued to work the way it did, but I digress). That was mos

Re: [R-pkg-devel] About a need for hooks from R CMD ... commands, and a question

On 4 January 2019 at 19:24, Iñaki Ucar wrote: | On Fri, 4 Jan 2019 at 16:43, Dirk Eddelbuettel wrote: | > | > | > For a few years now I had mused about how nice it would be to have other | > scripts triggered like `cleanup`. For Rcpp, it would be nice to run | > compileAt

Re: [R-pkg-devel] About a need for hooks from R CMD ... commands, and a question

Iñaki, Duncan, Fabulous -- that is just the type of 'hack' I was hoping for in the short term. Longer term, it would indeed be nice to do something about this and create something better. I had looked once or twice at packages utils and tools but didn't quite find the right spot to connect it

Re: [R-pkg-devel] About a need for hooks from R CMD ... commands, and a question

On 4 January 2019 at 19:37, Martin Morgan wrote: | Add a tag to the DESCRIPTION file or configure.ac-like indicating the git (presumably) revision, perhaps like https://stackoverflow.com/a/11535358/547331 ? I need the path. I need to find the particular build / checkout of headers and libaries

Re: [R-pkg-devel] About a need for hooks from R CMD ... commands, and a question

On 5 January 2019 at 00:00, Iñaki Ucar wrote: | On Fri, 4 Jan 2019 at 20:10, Iñaki Ucar wrote: | > | > I see. Then I suggest the following hack (not tested). If the package | > has a vignette, put there a hidden chunk that generates a file with | > info about the branch and the path. This file w

Re: [R-pkg-devel] About a need for hooks from R CMD ... commands, and a question

Hi Duncan and Iñaki, On 4 January 2019 at 14:13, Duncan Murdoch wrote: | If you want a total hack, the help system can run R code during a build, | e.g. \Sexpr[stage=build]{paste("Built at", Sys.time())}. Certainly it | could embed some information in a help page; perhaps it could do more. |

Re: [R-pkg-devel] About a need for hooks from R CMD ... commands, and a question

On 9 January 2019 at 17:57, Iñaki Ucar wrote: | Did you check Sys.getenv("OLDPWD")? I checked with a knitr vignette | and the correct path was there. Code: [...] <>= prettyVersion <- packageVersion("someNameHere") prettyDate <- format(Sys.Date(), "%B %e, %Y") user <- Sys.getenv("USER")

Re: [R-pkg-devel] About a need for hooks from R CMD ... commands, and a question

On 10 January 2019 at 22:33, Iñaki Ucar wrote: | On Thu, 10 Jan 2019 at 21:55, Dirk Eddelbuettel wrote: | > Comes up with an empty / unset olddir when I do | > | > R CMD build someNameHere; R CMD INSTALL someNameHere_1.2.3.tar.gz | | This is quite interesting. Because if you run |

Re: [R-pkg-devel] About a need for hooks from R CMD ... commands, and a question

We have a winner! (By bending the rules.) On 10 January 2019 at 16:44, Kyle Baron wrote: | Will this work for you? | | I had to stash the working directory (when R CMD build is run) in an | environment variable via ~/.R/build.Renviron` | | $ cat ~/.R/build.Renviron | OLDWD=${PWD} That is les

Re: [R-pkg-devel] using @inheritParams in documenting data

Hi Troels, Always good to see someone work on packaging with so much energy. On 12 January 2019 at 08:46, Troels Ring wrote: | BUT where and how to put the @inheritParams CMB I cannot find documented. | Otherwise it seems to run OK I fear you are getting confused between 'roxygen2' and base R.

Re: [R-pkg-devel] check works in ubuntu linux, but get debian-CRAN C++ error

Hi Rob, On 12 January 2019 at 15:40, Robert McCulloch wrote: | checking whether the C++ compiler works... no That line is weird. It is difficult to debug from afar, and I bemoan that Kurt's system has no equivalent Docker container (or alike) to make it more reproducible. But _something_ is u

Re: [R-pkg-devel] R CMD check --as-cran problem

On 11 January 2019 at 22:51, Wang, Zhu wrote: | ** testing if installed package can be loaded | Error: package or namespace load failed for 'bujar' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): | there is no package called 'Matrix' | Error: loading failed | Execution hal

Re: [R-pkg-devel] Getting started with memory debugging

On 14 January 2019 at 09:48, Michael Chirico wrote: | Hello all, | | I'm getting started doing some debugging of memory errors and got stuck | trying to reproduce the errors found during my CRAN submission process: | | https://cran.r-project.org/web/checks/check_results_geohashTools.html | | S

Re: [R-pkg-devel] R CMD check --as-cran problem

On 14 January 2019 at 16:52, Wang, Zhu wrote: | Thanks Dirk and Klaus. The package Matrix is not used directly but it is used by package survival, which was called in Suggests. So I am not sure what is the problem. But why CRAN has no such error https://cran.r-project.org/web/checks/check_res

Re: [R-pkg-devel] R CMD check --as-cran problem

On 14 January 2019 at 13:19, Duncan Murdoch wrote: | On 14/01/2019 12:37 p.m., Dirk Eddelbuettel wrote: | > | > On 14 January 2019 at 16:52, Wang, Zhu wrote: | > | Thanks Dirk and Klaus. The package Matrix is not used directly but it is used by package survival, which was called in

Re: [R-pkg-devel] R CMD check --as-cran problem

On 14 January 2019 at 21:05, Wang, Zhu wrote: | Apologize for multiple emails but my another email with source version of the package was hold waiting for moderator approval. I now formally rejected the post. Why? There is a reason there is a size limit there. You were not asked to send your

Re: [R-pkg-devel] Imported function cannot be found.

On 18 January 2019 at 11:59, Rolf Turner wrote: | | I am build a package in which there is a function which calls upon the | function brm() from the brms package. | | In my DESCRIPTION file I have the line | | > Imports: lme4, brms, glmmTMB, MASS, lattice, Rcpp, rmutil | | In my NAMESPACE fi

Re: [R-pkg-devel] Imported function cannot be found. (Solved.)

On 18 January 2019 at 15:13, Rolf Turner wrote: | | Thanks Dirk. Your suggestion worked perfectly. (See inline below.) Glad to hear. | On 1/18/19 2:50 PM, Dirk Eddelbuettel wrote: | > | > On 18 January 2019 at 11:59, Rolf Turner wrote: [...] | > Which of these packages uses Rcp

Re: [R-pkg-devel] LaTeX warnings on debian builds only

On 18 January 2019 at 10:42, Adam Price wrote: | Windows and OS X builds work fine, but I don't have access to a debian | machine that I can reproduce this on. I currently cannot reproduce this You do -- RHub, ie https://builder.r-hub.io.. It's so worth it. Please explore it. As a community w

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

On 6 February 2019 at 15:26, Ivan Krylov wrote: | The version of R I'm currently using is 3.3.3 (2017-03-06) from Debian | stable, which might explain the differences in utils:::format.person. In case you were unaware you _can_ get current R versions, now R 3.5.2, for Debian stable thanks to the

Re: [R-pkg-devel] Possible Rtools path problem

The R-on-Windows FAQ has recommends to NOT install in a path with spaces. The R Installer on Windows defaults to a path with spaces. I cannot reconcile it either. Such is life, sometimes. But when I had to work on that platform in the past I put my open source stuff into c:/opt/ -- so maybe tr

Re: [R-pkg-devel] List of reverse dependencies, including archived packages

On 26 February 2019 at 20:38, Uwe Ligges wrote: | | | On 26.02.2019 18:59, Iñaki Ucar wrote: | > On Tue, 26 Feb 2019 at 18:38, Oliver Dechant wrote: | >> | >> Somewhat relatedly is there a way to monitor when a package has new | >> reverse depends or imports added? | > | > I don't know of any

Re: [R-pkg-devel] Debian check string include

On 27 February 2019 at 14:17, Horia Yeb wrote: | rcpp_throwchart.cpp:6:10: fatal error: String.h: No such file or directory Did you mean the standard C header string.h? Or did you mean Rcpp's own Rcpp/String.h ? It is included for you by Rcpp.h. | Also would it be possible to submit a Windows

Re: [R-pkg-devel] What to do when a dependency falls off CRAN

Neal, "It's complicated". To a first appromimation, a dependency is a risk. As an illustration, I taught CRANberries a few years in its run to also consider disappearing packages. Right now, it knows about 3685 packages which are (or were at some point) "archived". This is an imprecise count

Re: [R-pkg-devel] package cartograflow_0.0.0.9000.tar.gz

On 25 March 2019 at 22:12, cartograf...@gmail.com wrote: | Hello, | I've submitted my package cartograflow and I received an email from your teeam that it does not pass the incoming checks automatically.Debian:

[R-pkg-devel] R 3.6.0, rpath and StagedInstall

I have one (or two) packages that use an external library. So we use -rpath to tell the dynamic linker about it. But R 3.6.0 dislikes this and howls about an absolute path ending in error. So we use StagedInstall: No. Which gets a NOTE. Which is still not ideal and I would like to avoid it, bu

Re: [R-pkg-devel] What version does "CRAN check list" refer to ?

On 5 April 2019 at 11:29, Jose V. Die wrote: | I am working on my first package and I released a new version (1.0.11). The CRAN checks link shows the last updated for today although the check details section refers to version 1.0.1. | | So, I’m confused about it. Are those check results from

Re: [R-pkg-devel] attempt to re-insert old removed package

On 5 April 2019 at 13:30, peter dalgaard wrote: | For most packages[*], I assume that you can just take on the role as maintainer, bump the version number and resubmit. If you don't actually maintain it, then of course it might fall of CRAN again after a while. | | -pd | | [*] Actually, I exp

Re: [R-pkg-devel] set PKG_CONFIG_PATH before installing a package

On 8 April 2019 at 10:59, Travers Ching wrote: | I think the correct way to do it is through the configure script. See | for example the Cairo package that uses pkg-config. Configure scripts | are slightly hard to work through in my experience, but are worth it | if you need customization of t

Re: [R-pkg-devel] SHLIB_OPENMP_*FLAGS in Makefiles

On 15 April 2019 at 11:21, Jarrett Phillips wrote: | In checking my R package via devtools::check and devtools::check_built, I | received the following NOTE which I am unsure how to fix. My package | contains compiled code (via Rcpp). Within my .cpp file I have the following | line: | | #define

Re: [R-pkg-devel] Submitting a package whose unit tests sometimes fail because of server connections

On 16 April 2019 at 11:40, Will wrote: | Some things I have considered include: | |1. Skipping all unit tests on CRAN (using something like |*testtht::skip_on_cran*). This would immediately fix the problem, and as |a mitigating factor we report automated test result and coverage on t

Re: [R-pkg-devel] dtrti2 error on CRAN checks

On 17 April 2019 at 11:06, Benjamin Christoffersen wrote: | Since the start of April, I have gotten some errors on the Debian | machines on the check on CRAN for my package dynamichazard. The places | where I get the errors seems to come down to LAPACK's dtrtri routine. | I have tried to reproduc

Re: [R-pkg-devel] long file names in tar

On 18 April 2019 at 10:37, Steven Scott wrote: | My Boom package makes a C++ library available to package authors (mainly | me). The wrapped library is used outside of R and must comply with | external style rules such as UseLongDescriptiveNames, and files must be | named for the class they cont

[R-pkg-devel] CRAN macOS build failure

A (somewhat resource-heavy) package of mine (RQuantLib) now fails to build on macOS: clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/Rcpp/include" -I/usr/local/include -Wal

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

On 10 May 2019 at 16:49, Iñaki Ucar wrote: | On Fri, 10 May 2019 at 15:42, Wang, Zhu wrote: | > | > 00install.out | > | > ** testing if installed package can be loaded from temporary location | > ** checking absolute paths in shared objects and dynamic libraries | > mv: cannot move '/media/sf

Re: [R-pkg-devel] Compilation used the "non-portable flag"

On 10 May 2019 at 20:32, Goldfeld, Keith wrote: | Good afternoon – | | I am submitting an update to my package ‘simstudy’, and the ran the rhub checks. I received a note from one of the four platforms (the other three passed). The Ubuntu Linux 16.04 objected to the compilation flags: | | * ch

Re: [R-pkg-devel] Compilation used the "non-portable flag"

On 15 May 2019 at 11:49, Gábor Csárdi wrote: | Thinking about this a bit more, I think this might be a bug in R CMD | check, actually. | | I understand that these flags are not portable, and yes, they should | be reported if they are specified in the packages's Makevars* files. | But in this cas

Re: [R-pkg-devel] R CMD check works but with devtools::check() examples fail

Barbara, On 15 May 2019 at 17:09, Barbara Lerner wrote: | I have just upgraded to R 3.6.0 and when building and checking my | package, R CMD check passes all the checks, including running the | examples, but devtools::check reports a failure when running the | examples.  I have also run the e

Re: [R-pkg-devel] R CMD check works but with devtools::check() examples fail

Hi Barbara, On 16 May 2019 at 16:48, Barbara Lerner wrote: | This is very helpful, thank you!  The R Internals document gave me the | clues that I need. Great! | I am pretty certain that more things are being checked than before as | problems are being reported with code that has not change

Re: [R-pkg-devel] R CMD check works but with devtools::check() examples fail

On 17 May 2019 at 08:33, Rainer Krug wrote: | Interesting discussion - because I had similar issues. | | @Dirk: You are developing packages fir ages - do you probably have a template make file you could share (as I assume, you use make) which is doing all these checks? Nothing special -- just

Re: [R-pkg-devel] Non-portable flags.

on.site: Set variable _R_CHECK_COMPILATION_FLAGS_KNOWN_ to white-list compiler flags pulled in Debian's gcc configuration * configure{,.ac}: Applied two upstream patches from this week to accommodate gfortran 8 changes related to C to Fortran calls -- Dirk Eddelbuettel Sat, 11 May 2019 13:58:42 -

Re: [R-pkg-devel] Non-portable flags.

On 4 June 2019 at 17:35, Rolf Turner wrote: | Thanks Dirk. I did an upgrade and the NOTE went away, so I guess that | all is well. Yes. | I'm never sure about upgrading with "sudo apt whatever", so I was a bit | apprehensive. For the record I did: | | sudo apt update | sudo apt u

Re: [R-pkg-devel] Travis/appveyor with CXX14/17

On 7 June 2019 at 10:13, Tim Keitt wrote: | I bumped a package to CXX14/17 and it failed on Travis/Appveyor while | checking fine locally. I assume I need to request different compilers or Correct. Working with a seriously outdated base layer of Ubuntu is a key bug^Hfeature of Travis. Maddenin

Re: [R-pkg-devel] R CMD build: "Error in if (any(update))"

On 10 June 2019 at 13:21, Rob Foxall wrote: | I've got an R package that I periodically create in what I assume is | an old-fashioned way: | | Within R: use "package.skeleton" | Outside of R: update e.g. .rd files as appropriate | Command window: run the following commands | R CMD build packageN

Re: [R-pkg-devel] Another CRAN-only bug

On 12 June 2019 at 21:57, David Hugh-Jones wrote: | Not for the first time, my package has a bug that isn't found on rhub, | travis, appveyor, or my local machine, but is found on CRAN. This time it's | Windows-only, so I can't even download a Docker image and investigate that | way. Two options

Re: [R-pkg-devel] R CMD check Rcpp_1.0.1.tar.gz error

Howdy, There is a dedicated list for Rcpp we recommend users use... On 17 June 2019 at 20:56, Wang, Zhu wrote: | installing *source* package 'Rcpp' ... | ** package 'Rcpp' successfully unpacked and MD5 sums checked | ** using non-staged installation | ** libs | g++ -std=gnu++11 -I"/usr/shar

Re: [R-pkg-devel] CRAN NOTE: SHLIB_OPENMP_*FLAGS in Makefiles

Hi Charith, On 19 June 2019 at 16:41, Charith Karunarathna wrote: | I got the following NOTES after submitting my R package to CRAN for the first time. | " | Flavor: r-devel-windows-ix86+x86_64 | Check: use of SHLIB_OPENMP_*FLAGS in Makefiles, Result: NOTE | src/Makevars.win: SHLIB_OPENMP_C

Re: [R-pkg-devel] VignetteBuilder field

On 3 July 2019 at 19:43, Michael Gruenstaeudl wrote: | Assume an R package `myPackage` that contains the folder `vignettes`, in | which the TEX-file `PACViR_Vignette.tex` and two image files | (`image1.pdf` and `image2.pdf`) are located. The TEX-file compiles | nicely without the need to use S

Re: [R-pkg-devel] Writing a data package with large files

index.html and I include the main gist / abstract: Hosting Data Packages via drat: A Case Study with Hurricane Exposure Data G. Brooke Anderson and Dirk Eddelbuettel The R Journal (2017) 9:1, pages 486-497. Abstract Data-only packages offer a way to provide extended functionality for oth

Re: [R-pkg-devel] Difficulty installing my package from drat repository

On 10 July 2019 at 05:53, Alex Hallam wrote: | I am working on a data package. Due to the size of the package I opted | to store the package as a drat repo. | | I am able to install my package locally, but I can't seem to install the | package | from the drat repo. The error I get is: | | ``` |

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

On 14 July 2019 at 17:06, Travers Ching wrote: | For maximum compatibility in a package, personally I would use version 2. Why are you against the futures and all the new shiny things? ;-) Duncan put it well in his follow-up message. We might as well use this as a nudge towards upgrading to cu

Re: [R-pkg-devel] help troubleshooting travis-ci issues?

On 5 August 2019 at 00:13, Iñaki Ucar wrote: | On Mon, 5 Aug 2019 at 00:08, Ben Bolker wrote: | > | > | > Yeah, I might try that, or I might try installing the downstream | > packages that are causing problems from Rutter's repo. | | AFAICT from the build log, the packages that are causing pr

Re: [R-pkg-devel] Error ... could not find function ...

On 14 August 2019 at 17:44, Rolf Turner wrote: | > Error in cpp_object_initializer(.self, .refClassDef, ...) : | > could not find function "cpp_object_initializer" This can happen when a package using Rcpp Modules is not fully loaded. While I am not familiar with eiher package here, try `impo

Re: [R-pkg-devel] Linking with software dependencies

On 24 August 2019 at 18:16, Sameh M. Abdulah wrote: | (1) My package requires a pre-installation of Intel MKL. Is there any way to include the MKL installation with the package. This (or a related) question was discussed here (or on a related list ?) very recently. The recommendation, that I co

Re: [R-pkg-devel] Last released version FAIL

Hi Christiane, On 26 August 2019 at 09:32, Cristiane Hayumi Taniguti wrote: | My name is Cristiane, I am mantainer of onemap package. The current version | of the package in CRAN is having problems passing to cran check | . I | alr

Re: [R-pkg-devel] third part software dependency

On 30 August 2019 at 11:10, Serguei Sokol wrote: | I am preparing a new package r2sundials for submission to cran. It | depends on third part software | (https://computing.llnl.gov/projects/sundials). This will be my first | submission of the kind so I am wondering how it is supposed to be tes

Re: [R-pkg-devel] third part software dependency

On 30 August 2019 at 07:24, Dirk Eddelbuettel wrote: | | On 30 August 2019 at 11:10, Serguei Sokol wrote: | | I am preparing a new package r2sundials for submission to cran. It | | depends on third part software | | (https://computing.llnl.gov/projects/sundials). This will be my first

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

On 3 September 2019 at 15:37, Tomas Kalibera wrote: | Yes, that seems to be an upstream problem. Maybe checking with the documentation for Armadillo documentation at http://arma.sourceforge.net/docs.html (large page, see about the various #define in config.hpp near the bottom) could be of help.

Re: [R-pkg-devel] set pkg_config for 3rd party software

On 5 September 2019 at 16:53, Ralf Stubner wrote: | I don't know what is best, but here are three alternatives: | | * Use PKG_CHECK_MODULES which sets up default variables with _CFLAGS | and _LIBS suffix after searching for a library with pkg-config, c.f. | https://autotools.io/pkgconfig/pkg_che

Re: [R-pkg-devel] set pkg_config for 3rd party software

Martin, And not to beat a dead horse, but isn't the root cause the outdated rpm? So can't you replace / update that package? That's what I do over in the .deb world, and for Ubuntu it is particularly easy with PPAs. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ___

Re: [R-pkg-devel] set pkg_config for 3rd party software

Martin, On 6 September 2019 at 07:19, Dirk Eddelbuettel wrote: | So can't you replace / update that package? That's what I do over in the | .deb world, and for Ubuntu it is particularly easy with PPAs. And then there is of course this too: edd@rob:~$ pkg-config --modversion nlo

Re: [R-pkg-devel] Require -package.Rd?

Wolfgang, Joris, This may not necessarily work -- see "Goodhart's Law" [1] Once you impose something like this, (some) will skirt it with just the minimum requirement of an (essentially) empty file. An existing set of examples is provided by the vignettes of (at least) one developer which each

Re: [R-pkg-devel] Resubmitting after a few days

On 24 September 2019 at 11:43, Roy Mendelssohn - NOAA Federal via R-package-devel wrote: | A few days ago I had to resubmit because an external URL I was using in my vignette changed and the nightly builds were issuing warnings. This morning a user reported a bug. I have the fix and a new v

Re: [R-pkg-devel] Appropriate usage of 'Suggests' -- package installed conditional on other software not found

Charles, On 3 October 2019 at 10:10, Driver, Charles wrote: | I have a function that outputs / compiles some latex. To do this I use Sys.which('pdflatex') and if nothing is found, prompt the user whether to install tinytex package. So, normally I understand the use of 'Suggests' in the packag

Re: [R-pkg-devel] Appropriate usage of 'Suggests' -- package installed conditional on other software not found

Hi John, On 3 October 2019 at 13:56, Fox, John wrote: | > On Oct 3, 2019, at 9:11 AM, Dirk Eddelbuettel wrote: | > On 3 October 2019 at 10:10, Driver, Charles wrote: | > | I have a function that outputs / compiles some latex. To do this I use Sys.which('pdflatex') and

Re: [R-pkg-devel] Appropriate usage of 'Suggests' -- package installed conditional on other software not found

John, On 3 October 2019 at 15:26, Fox, John wrote: | In the original context of this thread, a simple error message indicating that LaTeX is absent probably would suffice. Yes, I agree. Hence this earlier comment of mine you choose not to reply to: | > Anyway, this is going off-topic. It mig

Re: [R-pkg-devel] Appropriate usage of 'Suggests' -- package installed conditional on other software not found

On 3 October 2019 at 21:38, Driver, Charles wrote: | Since texi2dvi does more advanced checking than my simple Sys.which('pdflatex') , it sounds like I should rely on an error from that as cause for the message / prompt. Right. The corrolary is that if texi2dvi fails, simply installing tinyte

Re: [R-pkg-devel] missing wget, cmake, pkg-config,..etc

On 7 October 2019 at 11:42, Sameh M. Abdulah wrote: | I am using some tools through my package installation such as wget, cmake, pkg-config. The users complain that the installation failed because of missing such tools on their system. They need to install them separately before installation

Re: [R-pkg-devel] Please help

Bahadir, On 16 October 2019 at 19:12, Max Turgeon wrote: | It may help to look at what other packages linking to RcppArmadillo have done and try to reproduce it/adapt it to your setting. Packages using the package generator RcppArmadillo.package.skeleton() get these two templates via the skele

Re: [R-pkg-devel] R package which creates a directory in the user home dir

Sigbert, One approach you could consider is to _package_ the data in a (standard R) package upon which you can have a Suggests: relationship using a Additional_repositories: entry in DESCRIPTION. That is fully compliant and compatible with the CRAN Policy, and has been done before -- in fact th

Re: [R-pkg-devel] Advice about non-replicable error in CRAN R CMD check

David, On 21 October 2019 at 11:30, Dueber, David wrote: | When I submitted my package (BifactorIndicesCalculator: https://github.com/ddueber/BifactorIndicesCalculator) to CRAN, the automated checks returned an error for the development release of R in Windows. The log file is (https://win-b

Re: [R-pkg-devel] cargo not installed on Windows auto-check server

Hi Antoine, On 22 October 2019 at 16:40, Pelletier Antoine wrote: | I am triying to upload to CRAN a package which relies on a Rust library. | Rust compiler rustc and Rust package manager cargo are system requirements | to the package. Source code of the package is available at | https://gitlab.

Re: [R-pkg-devel] License of pre-built vignettes

On 25 October 2019 at 22:45, Mark van der Loo wrote: | Adding a static PDF vignette is very easy. I have written about it here: | http://www.markvanderloo.eu/yaRb/2019/01/11/add-a-static-pdf-vignette-to-an-r-package/ And I am doing just that for more and more packages of mine. It is "wrong" in

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

Hi Viktor, On 2 November 2019 at 13:09, Viktor Gal wrote: | I’m developing an ML library that has R bindings… when installing the library with R CMD INSTALL the R process is running out of memory (50G+ ram) when doing: | ** byte-compile and prepare package for lazy loading | | any ideas how i

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

Hi Victor, On 2 November 2019 at 13:58, Viktor Gal wrote: | so the project is open source, you can reproduce the error yourself (but note it’ll take a long time to actually compile it). steps for reproducing: | git clone https://github.com/shogun-toolbox/shogun.git | cd shogun | git checkout fe

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

On 6 November 2019 at 08:43, Marcin Jurek wrote: | Hello, I'm trying to submit my package to CRAN and received the following | error message: | | Error(s) in re-building vignettes: | --- re-building ‘GPvecchia_vignette.Rmd’ using rmarkdown | .../RcppArmadillo/include/armadillo_bits/subview_meat.

Re: [R-pkg-devel] R-hub PREPERROR on Ubuntu Linux 16.04 LTS, R-release, GCC not on other platforms

On 8 November 2019 at 10:14, R. Mark Sharp wrote: | Should I ignore this problem with regard to going forward with a submission to CRAN? | | It looks like some CRAN packages that I am dependent on are not available on the Ubuntu Linux 16.04 LTS platform. | | #> Failed with error: ‘there is no

Re: [R-pkg-devel] Install Package from GitHub in Vignette

On 11 November 2019 at 12:44, Daniel Sjoberg wrote: | Thank you Ben. That is a great suggestion. While searching for | instructions on using pre-compiled vignettes, I came across a few posts | recommending the dependency package be stored in a drat repository on | GitHub and using the DESCRIPTIO

Re: [R-pkg-devel] Install Package from GitHub in Vignette

by with Sweave only, hence not depending on anything that could change or break. For html, there is also a solution by Henrik involving his R.rsp package. See eg https://stackoverflow.com/a/2491/143305 Dirk | On Mon, Nov 11, 2019 at 1:23 PM Dirk Eddelbuettel wrote: | | > | > On 11 Nove

Re: [R-pkg-devel] Using FORTRAN libraries and compiler options

On 14 November 2019 at 16:42, Rampal S. Etienne wrote: | I couldn't find a call to dgemm in the mvtnorm package. Do you have | other suggestions for packages that may be calling this? The mirror of CRAN at GitHub allows convenient search. Looking for 'user:cran dgemm' give 620+ code hits; the pa

Re: [R-pkg-devel] compression of vignettes

On 21 November 2019 at 16:43, Joris Meys wrote: | The workflow as described in the manual : | https://cran.r-project.org/doc/manuals/R-exts.html#Checking-and-building-packages | | is as follows : | | R CMD build pkg --compact-vignettes | R CMD check pkg_x.y.z.tar.gz --as-cran | | In a basic T

Re: [R-pkg-devel] how to change from -fsanitize=undefined to -fsanitize=address

Youyi, It looks like you are trying to debug a _current_ SAN / ASAN / UBSAN error against your package by leaning on documentation I wrote five years ago specifically for another package (called "sanitizers") used to validate the initial Docker container builds I made (and to ensure the error th

Re: [R-pkg-devel] bioRxiv Preprint as Vignette

On 30 November 2019 at 19:55, Charith Karunarathna wrote: | I am just wondering about how I can include a bioRxiv preprint as the vignette of my R package. It's a pdf file already in bioRxiv. Could you please let me know how I can include that file as vignette? Sure. "Just do it" -- in the sen

Re: [R-pkg-devel] casen 0.1: strange pre-test results

On 30 November 2019 at 18:29, Mauricio Vargas wrote: | This is the 1st time that the pre-checks shows strange errors for me. The | results are here | https://win-builder.r-project.org/incoming_pretest/casen_0.1.0.9000_20191130_185019/ Following that URL to https://win-builder.r-project.org/

Re: [R-pkg-devel] how to change from -fsanitize=undefined to -fsanitize=address

On 30 November 2019 at 23:24, Youyi Fong wrote: | Here is a solution worked out by the wonderful staff from our scientific | computing support team at the Fred Hutchinson Cancer Research Center. I | really don't know how Dan did it, but the way he explained to me was that | he came across this gi

Re: [R-pkg-devel] Including in my vignette a figure drawn outside R

On 3 December 2019 at 15:36, Michael Dewey wrote: | I am planning to include a flow-chart in the vignette of one of my | packages (metap). I am planning to draw it using dot from Graphviz. I | know that there is Rgraphviz which would do the whole thing in R but I | do this sort of thing rarely

Re: [R-pkg-devel] How to account for optional packages not necessarily on CRAN

roject.org/archive/2017/RJ-2017-026/index.html Hosting Data Packages via drat: A Case Study with Hurricane Exposure Data G. Brooke Anderson and Dirk Eddelbuettel , The R Journal (2017) 9:1, pages 486-497. Abstract Data-only packages offer a way to provide extended functionality for ot

Re: [R-pkg-devel] reduce size of shared objects

On 11 December 2019 at 14:07, Guido Kraemer wrote: | I am building an R package (https://github.com/gdkrmr/zarr-R) that wraps | a couple of C++ headers and the resulting shared object is huge (>20Mb, | see https://travis-ci.org/gdkrmr/zarr-R). I have tried to set the | following in `./src/Make

Re: [R-pkg-devel] Proper way to ask a user to set permanent variables?

Jonathan, In all but one (maybe two?) of my packages I found relying on options() sufficient. I usually follow the somewhat-common pattern of creating a package-local environment in R/init.R or R/zzz.R. I then fill it with values reflecting options() (often under a tag starting with the package

Re: [R-pkg-devel] Alternatives to R-devel on a Mac for package checking?

Jonathan, Rocker should be building weekly r-devel and drd (similar, was meant to be a littler "lighter", effectively the same) images. As Merlise noticed, somehow the cronjob push to the Docker Hub build service started to fail -- this sadly happens once in a while so I manually triggered a re

Re: [R-pkg-devel] warnings by 3rd party headers

On 16 January 2020 at 17:06, Iñaki Ucar wrote: | On Thu, 16 Jan 2020 at 16:58, Guido Kraemer wrote: | > | > I need to distribute some 3rd party headers with my package. The headers | > make R CMD check produce warnings: | > | > File which contains pragma(s) suppressing important diagnostics:

Re: [R-pkg-devel] Proper way to ask a user to set permanent variables?

On 17 January 2020 at 09:49, Zhian Kamvar wrote: | Options are not persistent between sessions unless the user wants them to | be. You can have users set the options in their .Rprofile either in the | working directory of the project or their home directory. This is the Yes, precisely. | method

Re: [R-pkg-devel] How to provide a finalized PDF file in a package?

On 21 January 2020 at 17:58, Ralf Stubner wrote: | On Tue, Jan 21, 2020 at 5:50 PM Gábor Csárdi wrote: | > | > While R.rsp is a great workaround, I wish we had a better solution for | > including a static PDF file in a package, one that does not require 6 | > additional packages to leave a file

Re: [R-pkg-devel] Alternatives to R-devel on a Mac for package checking?

Just to close one loop here: On 15 January 2020 at 16:53, Dirk Eddelbuettel wrote: | Rocker should be building weekly r-devel and drd (similar, was meant to be a | littler "lighter", effectively the same) images. | | As Merlise noticed, somehow the cronjob push to the Docker Hub bui

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