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 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] 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 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] 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] 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] 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] 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

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

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 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

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

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 19:24, 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

[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] 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

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] 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] 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] 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] 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] RcppEigen and -Wno-ignored-attributes flag

On 10 September 2018 at 16:27, Τόλης Χαλκής wrote: | Dear all, | | I am developing a R package using RcppEigen on Ubuntu 18.04. Since update | 0.3.3.4.0 I get hundreds of warnings but if I add PKG_CXXFLAGS = | -Wno-ignored-attributes in Makevars the warnings disappear and the compile | time red

Re: [R-pkg-devel] Package Etiquette

Hi Joseph, On 8 September 2018 at 21:11, Joseph Wood wrote: | I’m a new developer and this is my first post. I have a question regarding | package development with regards to duplication of functionality. I read | the posting guide (https://www.r-project.org/posting-guide.html) and didn’t | see

Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

On 7 September 2018 at 13:08, Gábor Csárdi wrote: | On Fri, Sep 7, 2018 at 12:29 PM Dirk Eddelbuettel wrote: | > | > | > On 7 September 2018 at 09:27, Gábor Csárdi wrote: | > | When are users running tests for packages at all? The tests are by default | > | no even installed w

Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

On 7 September 2018 at 10:38, Hadley Wickham wrote: | On Fri, Sep 7, 2018 at 9:13 AM Iñaki Ucar wrote: | > El vie., 7 sept. 2018 a las 16:03, Ralf Stubner | > () escribió: | > > On 07.09.2018 15:52, Iñaki Ucar wrote: | > > Tests in 'inst/test' got deprecated later on: | > > | > > https://github

Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

On 7 September 2018 at 13:08, Gábor Csárdi wrote: | On Fri, Sep 7, 2018 at 12:29 PM Dirk Eddelbuettel wrote: | > | > | > On 7 September 2018 at 09:27, Gábor Csárdi wrote: | > | When are users running tests for packages at all? The tests are by default | > | no even installed w

Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

On 7 September 2018 at 09:27, Gábor Csárdi wrote: | When are users running tests for packages at all? The tests are by default | no even installed with the package. The only time I usually do this is when Which some people consider to be the wrong decision by testthat. Base R has a set of funct

Re: [R-pkg-devel] How do I prevent macOS from attempting to build my package?

On 4 September 2018 at 17:07, Uwe Ligges wrote: | Disclaimer for this field in general (as others are listening, too): we | should always try not to use it alt all and produce cross platform code. It would be nice if the CRAN system was more open so that contributed builds could be used. With m

[R-pkg-devel] How do I prevent macOS from attempting to build my package?

Package status reports come in three different severities: NOTE, WARNING, and ERROR. Motivated by Brodie's nice (dependency-free) accessor function for per-maintainer status [1], I have looked into reducing the number of ERRORs. I hit a road block. Several of my packages depend on external libr

Re: [R-pkg-devel] Changing License

On 30 August 2018 at 08:34, Charles Determan wrote: | It has come to my attention that some of the code I am distributing in one | of my packages was previously licensed under the MIT license. I have | previously released my package under the GPL-3 license. Would it be more | appropriate for me

Re: [R-pkg-devel] CRAN note: src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS

On 20 August 2018 at 22:14, Georgi Boshnakov wrote: | Hi, | | Recently the results page of my package on CRAN at | https://cran.r-project.org/web/checks/check_results_sarima.html, | started to show the NOTE below for some systems. | I am using Rcpp/RcppArmadillo without any manual interventions

Re: [R-pkg-devel] Can Submission Failure

On 7 August 2018 at 16:27, Ossenbruggen, Paul wrote: | I am new to CRAN submissions and need assistance. | | I received this set of error messages previously. I removed all these hidden files before resubmitting my package. They are back. | Question #1 How do I prevent this this? 1. (Optional)

Re: [R-pkg-devel] Correct way to set title for vignette?

On 24 July 2018 at 16:46, Martin Møller Skarbiniks Pedersen wrote: | Hi, | | Some vignettes on Cran has the title: "Title of your vignette" | Eg. https://cran.r-project.org/package=ggpval | | The source for the vignette at | "https://raw.githubusercontent.com/s6juncheng/ggpval/master/vign

[R-pkg-devel] C++11 and deprecated warnings "noise" for auto_ptr

As some of you may have noticed, or may have been told as well in kind "fix this or else ..." email, 'R CMD check' now also marks g++-7 / g++-8 warnings of 'deprecated declarations'. This can of course be addressed in the code itself, or suppressed with the '-Wno-deprecated-declarations' flag in

Re: [R-pkg-devel] Reverse dependencies - again

On 11 July 2018 at 10:00, J C Nash wrote: | 2) Is it time to consider an effort to provide online revdep checking | that would avoid pressure on CRAN team directly and would provide | clearer indicators of the issues raised by a particular package? That is very close to my R Foundation Summit ta

Re: [R-pkg-devel] compilation flags WARNING

On 5 July 2018 at 22:19, Göran Broström wrote: | Thanks Heather and Iñaki: I understand. | | I have an old Makevars file in the src directory of the package. I | guess I can set the flags there? No, because those get scanned by R CMD check and friends. For the one you do not want, Heather's

Re: [R-pkg-devel] Questions about making a database package (Rpolyhedra)

On 29 June 2018 at 09:15, Mark van der Loo wrote: | Hi Alejandro, | | Brooke Anderson gave a nice talk at useR!2017 addressing this exact issue. | See | https://schd.ws/hosted_files/user2017/19/anderson-eddelbuettel-use_r_talk.pdf | for | the slides. The basic idea is to use an external CRAN-lik

Re: [R-pkg-devel] RcppArmadillo-based package works in every tested OS except Debian

Hi Julia, On 28 May 2018 at 16:33, Julia A. Pilowsky wrote: | I am the maintainer of the colorednoise package, which employs RcppArmadillo. The package passes all checks on my local OS X install, on win_builder, and on Travis CI's Ubuntu distribution

Re: [R-pkg-devel] Compiled code checks raise a WARNING in Fedora 28

On 23 May 2018 at 18:09, Iñaki Úcar wrote: | 2018-05-23 17:40 GMT+02:00 Dirk Eddelbuettel : | > | > On 23 May 2018 at 17:22, Iñaki Úcar wrote: | > | Hi, | > | | > | For other Fedora users that may be struggling with this too... | > | | > | Fedora 28 introduced new hardeni

Re: [R-pkg-devel] Compiled code checks raise a WARNING in Fedora 28

On 23 May 2018 at 17:22, Iñaki Úcar wrote: | Hi, | | For other Fedora users that may be struggling with this too... | | Fedora 28 introduced new hardening flags for compiled code (see [1]). | Particularly, -D_GLIBCXX_ASSERTIONS is added to the default CXXFLAGS | (verify the output of 'R CMD conf

Re: [R-pkg-devel] CRAN pretest: Overall checktime 14 min > 10 min

On 21 May 2018 at 17:46, Uwe Ligges wrote: | In addition to what Dirk said, I just added this experimental test for | CRAN incoming checks few days ago and it should not reject but lead to | manual inspection, this will be fixed on CRAN side shortly. | | Nevertheless: The idea is that we have t

Re: [R-pkg-devel] CRAN pretest: Overall checktime 14 min > 10 min

I can't speak to the recent increase on Windows. It may be load; it may be related to R 3.5.0 --- but I'd even whittle things down from 5+ minutes. At one point in the past we were told to aim for 1 minute, give or take. So e.g. Rcpp has been using a scheme for _many_ years where I take a cue fr

Re: [R-pkg-devel] questions about promptPackage(); -package.Rd; help(package="")

Ben, Been meaning to write a short blog post about it as it also affects two (old) packages of mine. My favourite is to just rely on the Rd macros to the fullest, and I generally just hand-edit it -- no promptPackage() use. See eg this side-by-side diff of the first of the two I need to update;

Re: [R-pkg-devel] Explicitly Calling a Method of a specific Class in a Function

On 6 May 2018 at 11:42, Dr. rer. nat. Michael Thrun wrote: | Dear Developers, | I have currently one note in one of my packages I am unable to solve at my own: | “ | checking dependencies in R code ... NOTE | Unexported object imported by a ':::' call: ‘sp:::plot.SpatialPolygons’ | See the note

Re: [R-pkg-devel] CRAN pretest archived because of 2 NOTEs

On 18 April 2018 at 11:36, Gertjan van den Burg wrote: | While waiting to get this message posted to the list, I've solved the | problem by copying the stdlib rand() and srand() functions into my | package under a different name. This makes the check pass and ensures my | RNG does not interfere

Re: [R-pkg-devel] registering native routines

On 10 April 2018 at 23:30, Rampal Etienne wrote: | Yes, I followed all those suggestions but it did not fix the x64 notes. | Indeed I am using Windows. I am going to try this on a Linux system. You could consider the R Hub service at https://builder.r-hub.io/ and/or via the CRAN package rh

Re: [R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission Boom 0.8

On 4 April 2018 at 14:15, Steven Scott wrote: | These appear to be caused by an ill formed std::set or std::function in the | STL implementation of the host machine. If I'm reading that wrong someone | please let me know. AFAICT it needs C++11 explicitly set which that machine (with a new clang-

Re: [R-pkg-devel] Using shared libraries

On 28 March 2018 at 19:47, Ogan Mancarci wrote: | I have been looking for ways to use shared libraries in packages in CRAN | and be able to write tests for them. Well the basic problem here is that shared libraries are in fact provided by the _operating system_ and hence you just introduced an OS

Re: [R-pkg-devel] Avoid reprocessing Rmd vignette

On 18 March 2018 at 21:57, Tim Keitt wrote: | That's a great idea, however my problem is with building a vignette, not | running tests, unless they are linked in some way I'm not understanding. Similar idea applies: condition, just as Inaki and Thierry suggested. An example for a conditional vig

Re: [R-pkg-devel] Avoid reprocessing Rmd vignette

Tim, On 18 March 2018 at 18:58, Tim Keitt wrote: | I have an Rmd vignette that runs some benchmarks. It takes long enough (20+ | minutes) that eg TravisCI will choke. I've not tried submitting to CRAN. | What is the best practice for handling this situation? Do I generate | HTML/PDF output locall

Re: [R-pkg-devel] [FORGED] Re: How to (conditionally) use an archived package (without Suggests)?

On 25 February 2018 at 16:45, Hugh Parsonage wrote: | Not to mention a drat repository you can just fork with a single click! Yes, very easy -- but marginally expensive as you get the content (ie drat code history) mirrored. If you're at ease with git you can do it all by hand too. We still use

Re: [R-pkg-devel] [FORGED] Re: How to (conditionally) use an archived package (without Suggests)?

On 25 February 2018 at 15:00, Marius Hofert wrote: | okay, so (afaik) this is just a github repos which contains an exact | copy of the github version of the problematic package (here: loon). I Be very careful with terminology here: -- "github repo" is to most people a source code repo -- drat

Re: [R-pkg-devel] How to (conditionally) use an archived package (without Suggests)?

On 25 February 2018 at 14:20, meik michalke wrote: | Am Sonntag, 25. Februar 2018, 06:35:52 CET schrieb Dirk Eddelbuettel: | > On 25 February 2018 at 11:51, meik michalke wrote: | > | 'Additional_repositories' is meant for R package repositories, it won't | > | work wi

Re: [R-pkg-devel] How to (conditionally) use an archived package (without Suggests)?

On 25 February 2018 at 11:51, meik michalke wrote: | 'Additional_repositories' is meant for R package repositories, it won't work | with source code git repos. if a package is in 'Suggests' and can't be found You missed the part where we create packages ("R CMD build") out of source repos, and

Re: [R-pkg-devel] [FORGED] Re: How to (conditionally) use an archived package (without Suggests)?

On 25 February 2018 at 11:50, Marius Hofert wrote: | perfectly works (even if you don't have loon) *except* for the check | (--as-cran) to give me the warning: | * checking dependencies in R code ... WARNING | '::' or ':::' import not declared from: ‘loon’ | 'loadNamespace' or 'requireNamespace' c

Re: [R-pkg-devel] How to (conditionally) use an archived package (without Suggests)?

On 24 February 2018 at 19:41, Duncan Murdoch wrote: | Don't throw an error, work around it. If you have no alternative code, | then don't test the "bar" code unless "bar" is installed. | | The basic idea is that your package should pass tests without errors | even if "bar" is not available. 1

Re: [R-pkg-devel] How to (conditionally) use an archived package (without Suggests)?

On 25 February 2018 at 00:45, Marius Hofert wrote: | A package 'foo' uses a package 'bar' (in Imports). 'bar' has been | archived and the maintainer of 'foo' was asked to fix the dependency | on 'bar' according to WRE 1.1.3.1. | | Working with 'bar::' everywhere (and requireNamespace("bar", quiet

Re: [R-pkg-devel] header file for "flockfile" function under windows

On 20 February 2018 at 20:56, Carmen M. Livi wrote: | I am using file-locking functions in C that can be found in the | in Unix | | extern void flockfile (FILE *__stream) __THROW; | extern int ftrylockfile (FILE *__stream) __THROW __wur; | extern void funlockfile (FILE *__stream) __THROW; | |

Re: [R-pkg-devel] MAX_ARGS limitation in foreign function calls

On 20 February 2018 at 09:33, Udaya B. Kogalur wrote: | We are hitting the MAX_ARGS ceiling in our R-C function calls in the | development of randomForestSRC. This limits to number of arguments to | 65 using .Call(). Is there a work around for this dilemma? Thank | you. The easiest is to avoid

Re: [R-pkg-devel] R package CRAN check error

On 16 February 2018 at 20:46, Georgi Boshnakov wrote: | You get a source package suitable for submission by running `R CMD check namepackage' or the equivalent devtools::build() Close: "R CMD build namepackage" creates the tar.gz file. And "R CMD check --as-cran namepackage_*.tar.gz" checks it

Re: [R-pkg-devel] R package CRAN check error

Ilaria, On 16 February 2018 at 12:34, Ilaria Amerise wrote: | on submitting a new version of a package I got a rejection because of | the following Error in the CRAN-check. | | Any help would be highly appreciated. | | * using R version 3.4.3 (2017-11-30) | * using platform: x86_64-apple-darwin

Re: [R-pkg-devel] CRAN submission: Packages accepted if they run on two major R platforms

Carmen, On 16 February 2018 at 17:59, Carmen M. Livi wrote: | I am new here and have a question regarding package submissions: | | "CRAN Repository Policy" states that "packages will not be accepted that | do not run on at least two major R platforms". | | My package runs on MAC and Linux. So

Re: [R-pkg-devel] configuration failed on win-builder

Hi Carmen, On 15 February 2018 at 19:45, Carmen M. Livi wrote: | when submiting my R-package to CRAN I get the following error from the | windows machine: | | * installing *source* package 'spp' ... | ./configure.win: 2: Syntax error: word unexpected (expecting ")") | ERROR: configuration faile

Re: [R-pkg-devel] Windows binaries

On 14 February 2018 at 21:14, Kapur, Kush wrote: | Dear R development team, We're only regular list members here -- just like you. | I have also submitted the Windows binaries for the ssrm.logmer package using build_win function in devtools. Not sure I follow. You generally upload a _source_ t

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

On 14 February 2018 at 17:12, Baptiste Auguie wrote: | Thanks Ralf, now it makes more sense to me. I had misunderstood the | situation on CRAN and r-hub and thought they used an external Lapack on | linux. This has been unchanged over the many years that you had these battles: - on Windows it is

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

On 12 February 2018 at 22:16, Baptiste Auguie wrote: | As far as I can tell Armadillo added specialised methods for banded | matrices; the routines used to solve non-banded matrices probably haven't | changed. | | Coming back to the error itself, what puzzles me is that it seems to be | precisely

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

hich builds on my local mac but fails the online r-hub build | (interestingly, on a linux machine, which also puzzled me about cda's logs) | | https://builder.r-hub.io/status/isolve_1.0.tar.gz-757573eaf5b0cb30d8154d7b8f7e2bc7 | | Thanks for any advice, | | baptiste | | | | | | |

Re: [R-pkg-devel] R-devel warning: You used a knitr feature that depends on the digest package.

On 7 February 2018 at 15:03, luke-tier...@uiowa.edu wrote: | The problem is that this is an indirect dependency with knitr needing | digest and codetools to implement a feature (cacheing) that is being | asked for. And there is no obvious way (to me at least) of finding out | that these are needed

Re: [R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission huxtable 2.0.2

On 7 February 2018 at 11:53, David Hugh-Jones wrote: | Hi guys, | | I've been having some problems with updating my 'huxtable' package on CRAN. | The latest issue is that I run a test which renders a rmarkdown document to | PDF, using rmarkdown::render. This passes R CMD check fine on my machine,

Re: [R-pkg-devel] New CRAN package assistance

On 7 February 2018 at 21:54, Huw Campbell wrote: | I have just submitted a package for CRAN which works on my Mac and linux | boxes, but there are notes for Windows and my license file. There is little | indication as to what the actual problems are. | | The library is a simple binding for the sn

Re: [R-pkg-devel] fftw linking

On 4 February 2018 at 15:38, Denis Rastegaev wrote: | I try to upload my package on CRAN but the package | does not pass the incoming checks. How to link external | compiler with fftw? CRAN is a treasure trove with over 12k packages. Learn to search it. For example, package fftwtools has this li

Re: [R-pkg-devel] Working with R-devel

On 24 January 2018 at 07:55, William Dunlap wrote: | On Linux you can trace all the getenv calls with ltrace. It only | works on ELF files, not sh scripts: | | % R CMD ltrace -e getenv `R RHOME`/bin/*/R | libR.so->getenv("R_HOME") |= "/home/R/R-3.4.3/lib64/R" | libR.so->getenv("R

Re: [R-pkg-devel] Working with R-devel

On 24 January 2018 at 07:03, luke-tier...@uiowa.edu wrote: | If you are picking up an R 3.4.x that is trying to load a package | built by R-devel you should also see a warning that the package was | built under R version 3.5.0 Yes, I am of course very aware of the issue. But we had to separate o

Re: [R-pkg-devel] FIXED -- Working with R-devel

Thanks to Martin, my 'RD' script now points to ~/.R/check.Renviron-Rdevel in which I also set (or re-set) R_LIBS="/usr/local/lib/R-devel/site-library/" after having added this (for good measure) to my 'RD' script: unset R_PROFILE R_RENVIRON R_LIBS export R_CHECK_ENVIRON=~/.R/check.Ren

Re: [R-pkg-devel] Working with R-devel

On 24 January 2018 at 12:00, Martin Maechler wrote: | > Uwe Ligges | > I guess you actually pick up anotehr version of R. | > Carefully check what is on your PATH and perhaps some Renviron files | > that may be around? I did, a million times, hence the frustration. | Yes exact

[R-pkg-devel] Working with R-devel

I am going in circles here and have lost my way. I used to have means to build R-devel (still do) and use it for local testing (no longer do). - Fresh build of R-devel - One entry in .libPaths() - I can install Rcpp, it ends up in that .libPaths() - I can load - With the _exact same settings

Re: [R-pkg-devel] Licensing of an R package

On 19 January 2018 at 10:00, Dirk Eddelbuettel wrote: | Also look eg at our Rblpapi package. The Bloomberg API is not open source, | but they allow distribution of the (pre-built) library and headers. Our | package, building on top, is GPL-2+. No issues. (This example is extra fun Correction

Re: [R-pkg-devel] Licensing of an R package

Chris, I am with Duncan here. You can license _your_ package any way you want and prefer. I like GPL. You seem to imply that the GPL license prohibits linking against commercial code. If that were the case we'd never have R, Emacs, gcc/g++, ... on Windows or macOS or any of the now-essentially

Re: [R-pkg-devel] Imports: vs Suggests:

Hugh, You may be looking at this from the wrong angle. "Imports" is really an updated variant of "Depends". Both of them declaure _unconditional_ use of another package. (How they are used is the fine distinction between loading and attaching which we'll skip here). The key point is that a pack

Re: [R-pkg-devel] Portable method of stripping debug symbols

On 4 January 2018 at 00:27, Thibault Vatter wrote: | We faced a problem when we tried Dirk's solution for our package | rvinecopulib: there is a strip binary on OS X but it doesn't work as the | linux one. | | As such, to avoid calling OS X's strip which doesn't work, we use: | | strippedLib: $(

Re: [R-pkg-devel] Portable method of stripping debug symbols

Christopher, On 3 January 2018 at 21:59, Christopher Lalansingh wrote: | I'm running into troubles with the total size of my package and I've found that when using Rcpp, one can reduce the size of shared objects by stripping out debug symbols by including `-Wl,-S' in PKG_LIBS. Unfortunately thi

Re: [R-pkg-devel] File name error

Cristine, On 21 December 2017 at 08:21, Blume Christine wrote: | I also had troubles with debian (Fedora only gave warnings) May I ask you to be a little more careful in your attribution? Yes, it is too that the instance labeleb 'r-devel-debian' gave you an error. But that was not because of

Re: [R-pkg-devel] Debian: example file is no longer read correctly

On 20 December 2017 at 15:32, Göran Broström wrote: | > Or can someone tell me how to install the package using R devel on Linux? | | Good question (which I missed). I do it like this: | | (i) Download and unpack the tarball R-devel in ~/src/ | (ii) ./configure and make | (iii) Start R-devel

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

On 19 December 2017 at 13:41, Ralf Stubner wrote: | On 19.12.2017 09:38, Baptiste Auguie wrote: | > Thanks for the pointer to `arma::solve_opts::no_band`, it sounds like a | > good solution (assuming the compiler will then skip all the parts | > related to banded inversion routines). I've been una

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

On 18 December 2017 at 13:12, Ralf Stubner wrote: | On 18.12.2017 08:37, Baptiste Auguie wrote: | > What I don't really understand (because of the templating system etc.) is | > why this new routine in Armadillo would be needed at all, when cda does not | > solve banded linear systems. I wonder if

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

On 17 December 2017 at 17:50, Dirk Eddelbuettel wrote: | In short, but relying on (Rcpp)Armadillo, you are submit to it changing its That should have read: "... by relying on (Rcpp)Armadillo, you are subject to ..." My bad. | solver and it seems to have done so recently. A

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

On 17 December 2017 at 17:21, Dirk Eddelbuettel wrote: | | ** testing if installed package can be loaded | | Error: package or namespace load failed for ‘cda’ in dyn.load(file, DLLpath | | = DLLpath, ...): | | unable to load shared object ‘/home/hornik/tmp/R.check/r- | | release-gcc/Work/build

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

On 17 December 2017 at 19:15, Baptiste Auguie wrote: | Hi, | | The CRAN maintainers recently informed me that my cda package now fails on | CRAN. The root cause seems to be this error: | | ** testing if installed package can be loaded | Error: package or namespace load failed for ‘cda’ in dyn.lo

Re: [R-pkg-devel] CRAN check FAIL due to pragmas in headers and code

On 14 December 2017 at 03:04, brodie gaslam via R-package-devel wrote: | This leads me to think that it is (maybe) possible that this is an issue with the latest version of the check tool? Which is what I tried to explain to Inaki when he first filed on as an Rcpp issue ticket: Sometimes you nee

Re: [R-pkg-devel] CRAN check FAIL due to pragmas in headers and code

On 14 December 2017 at 00:58, Iñaki Úcar wrote: | Hi all, | | Three days ago, Patrick Perry posted the following on R-devel: | | 2017-12-11 16:32 GMT+01:00 Patrick Perry : | > A recent change to r-devel causes an R CMD check warning when a C file | > includes a "#pragma GCC diagnostic ignored" p

Re: [R-pkg-devel] Rcpp Copyright Query

ht holders relating to the Rcpp package: | - Copyright (C) 2010 - 2012 Dirk Eddelbuettel and Romain Francois "Missing"? Sorry, but who is missing what? Presumably you are not _including_ Rcpp in your package and as such you are not _(re-)distributing_ the sources over which other people have a

Re: [R-pkg-devel] Error in re-building vignettes (SOLVED)

On 6 December 2017 at 11:40, Göran Broström wrote: | Hi again, | | today I INSTALLED R-devel (2017-12-05 r73849) and updated all packages | | > update.packages(checkBuilt = TRUE) | | and rebuilt eha_2.5.1 and now all checks passed! Maybe the update of | packages was necessary. Very much so,

Re: [R-pkg-devel] Testing for a Specific R Error

On 2 December 2017 at 08:38, Bill Denney wrote: | Hi, | | I got a message last night that some of the tests in the PKNCA package do not follow best practices. ("Do not test the exact format of R messages (from R itself or from other packages): They change, and they can be translated.") Speci

Re: [R-pkg-devel] Errors in the pre-test after submitting the R package

Hi Senren, On 30 November 2017 at 16:49, Tan, Senren wrote: | Thank you very much for your reply. My pleasure. You did well here. | I have been trying to look at the R package fftw developed by Olaf and Uwe over the last few days. And I have tried to make use of the configure.ac. file in the

Re: [R-pkg-devel] Errors in the pre-test after submitting the R package

On 28 November 2017 at 11:01, Ege Rubak wrote: | The obvious place to look for pointers of how to detect and link | correctly to fftw would be in the current CRAN package `fftwtools` that | does it without any Rcpp: | https://github.com/krahim/fftwtools And there is also fftw by Olaf and Uwe (!

Re: [R-pkg-devel] Errors in the pre-test after submitting the R package

On 27 November 2017 at 21:24, Tan, Senren wrote: | I have been developing an R package using Rcpp to call C++ functions that use the C subroutine library 'fftw3' that implements fast Fourier transform algorithm. Since I have the C library 'fftw3' installed on my laptop (running MacOS), when I c

Re: [R-pkg-devel] Installing Tests with R Build

On 23 November 2017 at 08:07, Joshua Ulrich wrote: | On Wed, Nov 22, 2017 at 4:21 PM, Bill Denney wrote: | > I have a package that I'm trying to make a validation vignette for. The validation vignette is intended to assist users with documentation that the tests work. | > | > When running R BU

Re: [R-pkg-devel] dependencies

On 21 November 2017 at 19:20, Cathy Lee Gierke wrote: | Thanks Bryan. All of my imports are in the namespace. Can you tell me why | this one should be in the description file? Because you need an entry in the DESCRIPTION file _and_ an entry in NAMESPACE. Dirk -- http://dirk.eddelbuettel.com

Re: [R-pkg-devel] Why would src/Makevars be ignored?

On 21 November 2017 at 16:51, Duncan Murdoch wrote: | According to section 1.2.1 "Using Makevars" in Writing R Extensions, | R_HOME/etcR_ARCH/Makeconf is included after Makevars, so what you're | seeing is by design. I believe this is so that packages are built with | tools compatible with tho

[R-pkg-devel] Why would src/Makevars be ignored?

Having a bit of a puzzle with a package at work (which I can't share). In src/Makevars I override CC, CXX, CXX11, CXX14 to point to a specific (version) of g++ on my system, say g++-x.y. I also set CXX_STD=CXX14 Only it doesn't work. I need an extra dot.RMakevars and an invocation via R_MAKE

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