[R-pkg-devel] Building my R package: issue when importing two functions with the same name
I am building a R package, and I am facing an issue caused (as far as I understand) by the fact that some functions out of my package rely on two fuctions having the same name and coming from 2 different packages: pROC::roc spatstat::roc When checking the package via devtools::check(), I get the following warning: Warning: replacing previous import ‘spatstat::roc’ by ‘pROC::roc’ when loading ‘GmAMisc’ Note that both packages are listed among the Imports in my package's DESCRIPTION file, and that (within my functions) I have actually used spatstat::roc and pROC::roc where needed. I have done some web-search but I could not locate any workaround that actually fixes my issue. Do you have any suggestion on the matter? ** Dr Gianmarco Alberti (PhD) (currently) Research Support Officer II Department of Classics and Archaeology Faculty of Arts University of Malta (starting from 3rd September 2018) Lecturer in Spatial Forensics Department of Criminology Faculty for Social Wellbeing University of Malta https://www.researchgate.net/profile/Gianmarco_Alberti4 http://cainarchaeology.weebly.com/ ** [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Building my R package: issue when importing two functions with the same name
@Duncan: Extremely interesting...thanks. Gm ** Dr Gianmarco Alberti (PhD) (currently) Research Support Officer II Department of Classics and Archaeology Faculty of Arts University of Malta (starting from 3rd September 2018) Lecturer in Spatial Forensics Department of Criminology Faculty for Social Wellbeing University of Malta https://www.researchgate.net/profile/Gianmarco_Alberti4 http://cainarchaeology.weebly.com/ ** Il 7 ago 2018, 13:11 +0200, Duncan Murdoch , ha scritto: > On 05/08/2018 4:21 PM, Gianmarco Alberti wrote: > > I am building a R package, and I am facing an issue caused (as far as I > > understand) by the fact that some functions out of my package rely on two > > fuctions having the same name and coming from 2 different packages: > > > > pROC::roc > > spatstat::roc > > > > As Iñaki pointed out, the main issue is that you should be using Import > rather than Depends. But I didn't see mentioned the fact that the > NAMESPACE file can rename a function when you import it, e.g. > > importFrom(pROC, pROCroc = roc) > importFrom(spatstat, spatstatroc = roc) > > Now in your own functions you can use pROCroc() or spatstatroc() and > they won't conflict. > > (I was going to point you to the documentation for this, but I am not > sure it is properly documented anywhere.) > > Duncan Murdoch > > > When checking the package via devtools::check(), I get the following > > warning: > > > > Warning: replacing previous import ‘spatstat::roc’ by ‘pROC::roc’ when > > loading ‘GmAMisc’ > > > > Note that both packages are listed among the Imports in my package's > > DESCRIPTION file, and that (within my functions) I have actually used > > spatstat::roc and pROC::roc where needed. > > > > I have done some web-search but I could not locate any workaround that > > actually fixes my issue. > > > > Do you have any suggestion on the matter? > > > > ** > > Dr Gianmarco Alberti (PhD) > > (currently) > > Research Support Officer II > > Department of Classics and Archaeology > > Faculty of Arts > > University of Malta > > > > (starting from 3rd September 2018) > > Lecturer in Spatial Forensics > > Department of Criminology > > Faculty for Social Wellbeing > > University of Malta > > https://www.researchgate.net/profile/Gianmarco_Alberti4 > > http://cainarchaeology.weebly.com/ > > ** > > > > > > [[alternative HTML version deleted]] > > > > __ > > R-package-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > > __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Building my R package: issue when importing two functions with the same name
Thanks indeed for the clarification. I eventually managed to solve the issue. By the way, I have moved of the packages my package relies on to the Imports section. I have checked my package and it returned no error nor note nor warning. I have submitted it to CRAN. Thanks for your prompt feedback. Best Gm A ** Dr Gianmarco Alberti (PhD) (currently) Research Support Officer II Department of Classics and Archaeology Faculty of Arts University of Malta (starting from 3rd September 2018) Lecturer in Spatial Forensics Department of Criminology Faculty for Social Wellbeing University of Malta https://www.researchgate.net/profile/Gianmarco_Alberti4 http://cainarchaeology.weebly.com/ ** Il 7 ago 2018, 11:14 +0200, Uwe Ligges , ha scritto: > ... and even if you are importing from several packages, you should > import selective via importFrom directoves. > > If you need two functions with identical names, import at most one of > them and rather use pkg::foo syntax to access them. > > Best, > Uwe Ligges > > > > > > On 07.08.2018 10:14, Iñaki Úcar wrote: > > El mar., 7 ago. 2018 a las 9:32, Gianmarco Alberti > > () escribió: > > > > > > I am building a R package, and I am facing an issue caused (as far as I > > > understand) by the fact that some functions out of my package rely on two > > > fuctions having the same name and coming from 2 different packages: > > > > > > pROC::roc > > > spatstat::roc > > > > > > When checking the package via devtools::check(), I get the following > > > warning: > > > > > > Warning: replacing previous import ‘spatstat::roc’ by ‘pROC::roc’ when > > > loading ‘GmAMisc’ > > > > > > Note that both packages are listed among the Imports in my package's > > > DESCRIPTION file, and that (within my functions) I have actually used > > > spatstat::roc and pROC::roc where needed. > > > > I see: > > > > Depends: R (>= 3.4.0), ggplot2, ggrepel, rgdal, rgeos, raster, sp, > > spatstat, maptools, spatialEco, dismo, pROC, kimisc, corrplot, > > InPosition, lsr, gridExtra, caTools, plyr, classInt, coin, DescTools, > > rWind, shape, rworldmap, cluster, RcmdrMisc, gdistance, Hmisc > > > > In general, it is not a good idea to depend on so many packages, > > because what "Depends" do is to load and attach packages. Among other > > issues, there is one that you are already experimenting: "roc" is > > exported both by "spatstat" and "pROC", so one masks the other. > > > > The solution is to list them under "Imports" instead of "Depends". In > > fact, my advice is to put as many packages as possible under > > "Imports". Keep in "Depends" only those you would load and attach > > anyway when working with your package, because you need all the > > functions along with the ones your package exports. For the rest of > > them, just use them as package::function to avoid this kind of > > problem, and reexport functions selectively if needed. > > > > Iñaki > > > > PS: I'm taking a look at other packages and I see that you always use > > "Depends" and never "Imports". My general advice is against this > > practice. Moreover, from the "Writing R Extensions" manual: > > > > "Field ‘Depends’ should nowadays be used rarely, only for packages > > which are intended to be put on the search path to make their > > facilities available to the end user (and not to the package itself): > > for example it makes sense that a user of package 'latticeExtra' would > > want the functions of package 'lattice' made available." > > > > > > > > I have done some web-search but I could not locate any workaround that > > > actually fixes my issue. > > > > > > Do you have any suggestion on the matter? > > > > > > ** > > > Dr Gianmarco Alberti (PhD) > > > (currently) > > > Research Support Officer II > > > Department of Classics and Archaeology > > > Faculty of Arts > > > University of Malta > > > > > > (starting from 3rd September 2018) > > > Lecturer in Spatial Forensics > > > Department of Criminology > > > Faculty for Social Wellbeing > > > University of Malta > > > https://www.researchgate.net/profile/Gianmarco_Alberti4 > > > http://cainarchaeology.weebly.com/ > > > ** > > > > > > > > > [[alternative HTML version deleted]] > > > > > > __ > > > R-package-devel@r-project.org mailing list > > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > > > __ > > R-package-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-package-devel > > __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Error in curl: Failed FTP upload: 550
Hello,
Thanks for your reply.
I build the package manually, and then uploaded it here:
https://win-builder.r-project.org/upload.aspx
I got the following:
Access to the path 'C:\Inetpub\ftproot\R-release\GmAMisc_1.1.0.tar.gz' is
denied.
in both cases: R-devel and R-release.
I don’t have any clue….
Best regards
Dr Gianmarco Alberti (PhD Udine)
Lecturer in Spatial Forensics
Coordinator of the BA course in Criminology
Department of Criminology
Faculty for Social Wellbeing
Room 332, Humanities B (FEMA)
University of Malta, Msida, Malta (Europe) - MSD 2080
tel +356 2340 3718
Academic profiles
https://www.researchgate.net/profile/Gianmarco_Alberti4
https://malta.academia.edu/GianmarcoAlberti
Google Scholar profile
https://scholar.google.com/citations?user=tFrJKQ0J=en
Correspondence Analysis website
http://cainarchaeology.weebly.com/
R packages on CRAN:
CAinterprTools
https://cran.r-project.org/web/packages/CAinterprTools/index.html
GmAMisc
https://cran.r-project.org/package=GmAMisc
movecost
https://cran.r-project.org/web/packages/movecost/index.html
On 21 Feb 2020, 14:30 +0100, Ivan Krylov , wrote:
> 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 package manually (i.e. issue the command
> R CMD build . in package directory), then upload the resulting file
> using cURL or any other FTP client?
>
> curl -T yourfile.tar.gz ftp://win-builder.r-project.org/R-devel/
>
> You can also try the alternative upload page at
> https://win-builder.r-project.org/upload.aspx
>
> If manual FTP uploading works while devtools::check_win_devel()
> doesn't, some debugging may be required. For example, try
>
> trace(devtools:::upload_ftp, quote({str(file); str(url)}))
>
> before running check_win_devel() or check_win_release() to see which
> arguments does devtools:::check_win call upload_ftp with.
>
> --
> Best regards,
> Ivan
[[alternative HTML version deleted]]
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] note about mispelled words
Hello, I am checking a package of mine, and I got only 1 note regarding possibly misspelled words in the DESCRIPTION. The issue I am facing is that those 6 words are not actually misspelled, being either first or last names of individuals (actually, statistician; e.g., Kruskall, Brainerd). Shall I have to do something (removing those; which does not make sense), or upon submitting my new version of the package there is a way to make clear that that note can be ignored? By the way, those names were already there in earlier versions of the package and no note cropped out in those occasions. Thank you Best GmA Dr Gianmarco Alberti (PhD Udine) Lecturer in Spatial Forensics Coordinator of the BA course in Criminology Department of Criminology Faculty for Social Wellbeing Room 332, Humanities B (FEMA) University of Malta, Msida, Malta (Europe) - MSD 2080 tel +356 2340 3718 Academic profiles https://www.researchgate.net/profile/Gianmarco_Alberti4 https://malta.academia.edu/GianmarcoAlberti Google Scholar profile https://scholar.google.com/citations?user=tFrJKQ0J=en Correspondence Analysis website http://cainarchaeology.weebly.com/ R packages on CRAN: CAinterprTools https://cran.r-project.org/web/packages/CAinterprTools/index.html GmAMisc https://cran.r-project.org/package=GmAMisc movecost https://cran.r-project.org/web/packages/movecost/index.html [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] note about dependency on archived package
Further to my earlier email, I understand that my package has been archived since my last version on CRAN (1.1.0) had among its dependencies a package that has been archived. Now my question: How can I bring my package (actually the new version 1.1.1 that I’m trying to check) back to life (i.e., CRAN) again? Best Gm Dr Gianmarco Alberti (PhD Udine) Lecturer in Spatial Forensics Coordinator of the BA course in Criminology Department of Criminology Faculty for Social Wellbeing Room 332, Humanities B (FEMA) University of Malta, Msida, Malta (Europe) - MSD 2080 tel +356 2340 3718 Academic profiles https://www.researchgate.net/profile/Gianmarco_Alberti4 https://malta.academia.edu/GianmarcoAlberti Google Scholar profile https://scholar.google.com/citations?user=tFrJKQ0J=en Correspondence Analysis website http://cainarchaeology.weebly.com/ R packages on CRAN: CAinterprTools https://cran.r-project.org/web/packages/CAinterprTools/index.html GmAMisc https://cran.r-project.org/package=GmAMisc movecost https://cran.r-project.org/web/packages/movecost/index.html On 17 Mar 2020, 21:22 +0100, Gianmarco Alberti , wrote: > Hello, > > After checking my package with win builder, I got 1 note that I seem to not > fully understand: > > CRAN repository db overrides: > X-CRAN-Comment: Archived on 2020-03-17 as depends on archived package >'spatialEco'. > > Do you have any suggestion? > There is not reference to that package in my NAMESPACE, nor it is listed > among the dependencies. > > Full log here: > https://win-builder.r-project.org/98x9zsbaHsp1/00check.log > > Best > Gm > > ******** > Dr Gianmarco Alberti (PhD Udine) > Lecturer in Spatial Forensics > Coordinator of the BA course in Criminology > Department of Criminology > Faculty for Social Wellbeing > Room 332, Humanities B (FEMA) > University of Malta, Msida, Malta (Europe) - MSD 2080 > tel +356 2340 3718 > > Academic profiles > https://www.researchgate.net/profile/Gianmarco_Alberti4 > https://malta.academia.edu/GianmarcoAlberti > > Google Scholar profile > https://scholar.google.com/citations?user=tFrJKQ0J=en > > Correspondence Analysis website > http://cainarchaeology.weebly.com/ > > R packages on CRAN: > CAinterprTools > https://cran.r-project.org/web/packages/CAinterprTools/index.html > > GmAMisc > https://cran.r-project.org/package=GmAMisc > > movecost > https://cran.r-project.org/web/packages/movecost/index.html > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] note about dependency on archived package
Hello, After checking my package with win builder, I got 1 note that I seem to not fully understand: CRAN repository db overrides: X-CRAN-Comment: Archived on 2020-03-17 as depends on archived package 'spatialEco'. Do you have any suggestion? There is not reference to that package in my NAMESPACE, nor it is listed among the dependencies. Full log here: https://win-builder.r-project.org/98x9zsbaHsp1/00check.log Best Gm Dr Gianmarco Alberti (PhD Udine) Lecturer in Spatial Forensics Coordinator of the BA course in Criminology Department of Criminology Faculty for Social Wellbeing Room 332, Humanities B (FEMA) University of Malta, Msida, Malta (Europe) - MSD 2080 tel +356 2340 3718 Academic profiles https://www.researchgate.net/profile/Gianmarco_Alberti4 https://malta.academia.edu/GianmarcoAlberti Google Scholar profile https://scholar.google.com/citations?user=tFrJKQ0J=en Correspondence Analysis website http://cainarchaeology.weebly.com/ R packages on CRAN: CAinterprTools https://cran.r-project.org/web/packages/CAinterprTools/index.html GmAMisc https://cran.r-project.org/package=GmAMisc movecost https://cran.r-project.org/web/packages/movecost/index.html [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] package test returns error when R version 4.1.0
Hello, Thanks for your reply. I got mixed results using: devtools::check_win_oldrelease() - STATUS OK (R version 4.0.5) - https://win-builder.r-project.org/7qy6PL8C7ye7 devtools::check_win_release() - 1 ERROR (R version 4.1.0) - https://win-builder.r-project.org/hlA15dFq5BdR devtools::check_win_devel() - 1 ERROR (R Under development (unstable) - https://win-builder.r-project.org/uQ0LGZ7v0E5h The reported error is to be: ERROR: lazy loading failed for package ‘movecost’ Since I couldn’t understand the actual underlying issue, I ran devtools::check_rhub() (as described in my earlier email) which brought to the fore the Bioconductor issue. I have tested the package on Win (R version 4.1) and everything was fine. I hope I have addressed your question. Please let me know if you need any other relevant info from my end. Best Gm Dr Gianmarco Alberti (PhD Udine) Lecturer in Spatial Forensics Coordinator of the BA dissertations Department of Criminology Faculty for Social Wellbeing Room 332, Humanities B (FEMA) University of Malta, Msida, Malta (Europe) - MSD 2080 tel +356 2340 3718 Academic profiles https://www.researchgate.net/profile/Gianmarco_Alberti4 https://malta.academia.edu/GianmarcoAlberti Google Scholar profile https://scholar.google.com/citations?user=tFrJKQ0J=en Correspondence Analysis website http://cainarchaeology.weebly.com/ R packages on CRAN: CAinterprTools https://cran.r-project.org/web/packages/CAinterprTools/index.html GmAMisc https://cran.r-project.org/package=GmAMisc movecost https://cran.r-project.org/web/packages/movecost/index.html On 5 Jul 2021, 11:20 +0200, Uwe Ligges , wrote: > What happens when you test it on winbuilder? > It is configured like the CRAN incoming checks and there should be all > relevant packages available. > > Best, > Uwe Ligges > > > On 05.07.2021 11:16, Gianmarco Alberti wrote: > > Hello, > > Further to my earlier email, I think I have located a likely issue, and I > > would appreciate feedback. > > > > I ran devtools::check_rhub(), and somewhere in the flood of the output I > > got there is the following message: > > > > Bioconductor does not yet build and check packages for R version 4.2 > > > > The complete report that I got from devtools::check_rhub() is here: > > https://builder.r-hub.io/status/movecost_1.2.tar.gz-cbda0dbe4d7a414498921e9ab2a54aaf > > > > > > Any idea about how to proceed in order for me to get my package on CRAN? > > I am noticing that I am not the only one experiencing that isse > > (https://github.com/r-hub/rhub/issues/471). > > > > Best > > GmA > > > > > > Dr Gianmarco Alberti (PhD Udine) > > Lecturer in Spatial Forensics > > Coordinator of the BA dissertations > > Department of Criminology > > Faculty for Social Wellbeing > > Room 332, Humanities B (FEMA) > > University of Malta, Msida, Malta (Europe) - MSD 2080 > > tel +356 2340 3718 > > > > Academic profiles > > https://www.researchgate.net/profile/Gianmarco_Alberti4 > > https://malta.academia.edu/GianmarcoAlberti > > > > Google Scholar profile > > https://scholar.google.com/citations?user=tFrJKQ0J=en > > > > Correspondence Analysis website > > http://cainarchaeology.weebly.com/ > > > > R packages on CRAN: > > CAinterprTools > > https://cran.r-project.org/web/packages/CAinterprTools/index.html > > > > GmAMisc > > https://cran.r-project.org/package=GmAMisc > > > > movecost > > https://cran.r-project.org/web/packages/movecost/index.html > > > > On 5 Jul 2021, 09:49 +0200, Gianmarco Alberti , > > wrote: > > > Good morning, > > > > > > I got stuck on what follows. > > > I have tested a new version of my package locally (on a MAC), and > > > everything is fine. > > > > > > I got mixed results using: > > > devtools::check_win_oldrelease() - STATUS OK (R version 4.0.5) - > > > https://win-builder.r-project.org/7qy6PL8C7ye7 > > > > > > devtools::check_win_release() - 1 ERROR (R version 4.1.0) - > > > https://win-builder.r-project.org/hlA15dFq5BdR > > > > > > devtools::check_win_devel() - 1 ERROR (R Under development (unstable) - > > > https://win-builder.r-project.org/uQ0LGZ7v0E5h > > > > > > The reported error seems to be: > > > ERROR: lazy loading failed for package ‘movecost' > > > > > > > > > I have asked a friend to run devtools::check() on his
[R-pkg-devel] package test returns error when R version 4.1.0
Good morning, I got stuck on what follows. I have tested a new version of my package locally (on a MAC), and everything is fine. I got mixed results using: devtools::check_win_oldrelease() - STATUS OK (R version 4.0.5) - https://win-builder.r-project.org/7qy6PL8C7ye7 devtools::check_win_release() - 1 ERROR (R version 4.1.0) - https://win-builder.r-project.org/hlA15dFq5BdR devtools::check_win_devel() - 1 ERROR (R Under development (unstable) - https://win-builder.r-project.org/uQ0LGZ7v0E5h The reported error seems to be: ERROR: lazy loading failed for package ‘movecost' I have asked a friend to run devtools::check() on his Win-based machine (running R version 4.1.0), and the test returned no problems (0 error, 0 warning, 0 notes). Since I cannot reproduce the error neither on my computer nor on a win-based machine, I am at loss of understanding where the issue actually lies. I would really appreciate any help and/or suggestion. Best Gianmarco Dr Gianmarco Alberti (PhD Udine) Lecturer in Spatial Forensics Coordinator of the BA dissertations Department of Criminology Faculty for Social Wellbeing Room 332, Humanities B (FEMA) University of Malta, Msida, Malta (Europe) - MSD 2080 tel +356 2340 3718 Academic profiles https://www.researchgate.net/profile/Gianmarco_Alberti4 https://malta.academia.edu/GianmarcoAlberti Google Scholar profile https://scholar.google.com/citations?user=tFrJKQ0J=en Correspondence Analysis website http://cainarchaeology.weebly.com/ R packages on CRAN: CAinterprTools https://cran.r-project.org/web/packages/CAinterprTools/index.html GmAMisc https://cran.r-project.org/package=GmAMisc movecost https://cran.r-project.org/web/packages/movecost/index.html [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] package test returns error when R version 4.1.0
Hello, Further to my earlier email, I think I have located a likely issue, and I would appreciate feedback. I ran devtools::check_rhub(), and somewhere in the flood of the output I got there is the following message: Bioconductor does not yet build and check packages for R version 4.2 The complete report that I got from devtools::check_rhub() is here: https://builder.r-hub.io/status/movecost_1.2.tar.gz-cbda0dbe4d7a414498921e9ab2a54aaf Any idea about how to proceed in order for me to get my package on CRAN? I am noticing that I am not the only one experiencing that isse (https://github.com/r-hub/rhub/issues/471). Best GmA Dr Gianmarco Alberti (PhD Udine) Lecturer in Spatial Forensics Coordinator of the BA dissertations Department of Criminology Faculty for Social Wellbeing Room 332, Humanities B (FEMA) University of Malta, Msida, Malta (Europe) - MSD 2080 tel +356 2340 3718 Academic profiles https://www.researchgate.net/profile/Gianmarco_Alberti4 https://malta.academia.edu/GianmarcoAlberti Google Scholar profile https://scholar.google.com/citations?user=tFrJKQ0J=en Correspondence Analysis website http://cainarchaeology.weebly.com/ R packages on CRAN: CAinterprTools https://cran.r-project.org/web/packages/CAinterprTools/index.html GmAMisc https://cran.r-project.org/package=GmAMisc movecost https://cran.r-project.org/web/packages/movecost/index.html On 5 Jul 2021, 09:49 +0200, Gianmarco Alberti , wrote: > Good morning, > > I got stuck on what follows. > I have tested a new version of my package locally (on a MAC), and everything > is fine. > > I got mixed results using: > devtools::check_win_oldrelease() - STATUS OK (R version 4.0.5) - > https://win-builder.r-project.org/7qy6PL8C7ye7 > > devtools::check_win_release() - 1 ERROR (R version 4.1.0) - > https://win-builder.r-project.org/hlA15dFq5BdR > > devtools::check_win_devel() - 1 ERROR (R Under development (unstable) - > https://win-builder.r-project.org/uQ0LGZ7v0E5h > > The reported error seems to be: > ERROR: lazy loading failed for package ‘movecost' > > > I have asked a friend to run devtools::check() on his Win-based machine > (running R version 4.1.0), and the test returned no problems (0 error, 0 > warning, 0 notes). > > Since I cannot reproduce the error neither on my computer nor on a win-based > machine, I am at loss of understanding where the issue actually lies. > > I would really appreciate any help and/or suggestion. > > Best > Gianmarco > > > > > > Dr Gianmarco Alberti (PhD Udine) > Lecturer in Spatial Forensics > Coordinator of the BA dissertations > Department of Criminology > Faculty for Social Wellbeing > Room 332, Humanities B (FEMA) > University of Malta, Msida, Malta (Europe) - MSD 2080 > tel +356 2340 3718 > > Academic profiles > https://www.researchgate.net/profile/Gianmarco_Alberti4 > https://malta.academia.edu/GianmarcoAlberti > > Google Scholar profile > https://scholar.google.com/citations?user=tFrJKQ0J=en > > Correspondence Analysis website > http://cainarchaeology.weebly.com/ > > R packages on CRAN: > CAinterprTools > https://cran.r-project.org/web/packages/CAinterprTools/index.html > > GmAMisc > https://cran.r-project.org/package=GmAMisc > > movecost > https://cran.r-project.org/web/packages/movecost/index.html > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] package test returns error when R version 4.1.0
Dear All, Thanks for the useful discussion. After Uwe’s prompt, I have tested the package again, and everything is fine now. Was it a CRAN issue? Whatever the issue was, I am glad my new version is bound to be on CRAN soon (I have just submitted it). Best Gianmarco Dr Gianmarco Alberti (PhD Udine) Lecturer in Spatial Forensics Coordinator of the BA dissertations Department of Criminology Faculty for Social Wellbeing Room 332, Humanities B (FEMA) University of Malta, Msida, Malta (Europe) - MSD 2080 tel +356 2340 3718 Academic profiles https://www.researchgate.net/profile/Gianmarco_Alberti4 https://malta.academia.edu/GianmarcoAlberti Google Scholar profile https://scholar.google.com/citations?user=tFrJKQ0J=en Correspondence Analysis website http://cainarchaeology.weebly.com/ R packages on CRAN: CAinterprTools https://cran.r-project.org/web/packages/CAinterprTools/index.html GmAMisc https://cran.r-project.org/package=GmAMisc movecost https://cran.r-project.org/web/packages/movecost/index.html On 7 Jul 2021, 16:47 +0200, Uwe Ligges , wrote: > Can you pls try again now. > > Best, > Uwe Ligges > > On 06.07.2021 23:18, Murray Efford wrote: > > I also get from Winbuilder: > > > > ** byte-compile and prepare package for lazy loading > > ERROR: lazy loading failed for package 'secr' > > > > even for the tar.gz of the version secr 4.4.4 that currently passes all > > checks on CRAN. Perhaps it is significant that secr also imports from > > raster that had a new version on CRAN 18th June. > > > > Murray Efford > > > > > > From: R-package-devel on behalf of > > Duncan Murdoch > > Sent: 07 July 2021 08:28 > > To: Alex Chubaty > > Cc: r-package-devel@r-project.org > > Subject: Re: [R-pkg-devel] package test returns error when R version 4.1.0 > > > > On 06/07/2021 4:15 p.m., Alex Chubaty wrote: > > > Thanks for the suggestion Duncan. > > > > > > The same code version ran on winbuilder last week, but it's broken this > > > week. > > > > If that happened with a released version of R, then it could be that > > some new package version is causing the problem, or it could be a > > transient problem on Winbuilder. > > > > Devel versions of R change every day, so there are more possibilities > > for origins of the problem there. > > > > Duncan Murdoch > > > > > > > > I'll compare the dependencies between the two packages and focus on > > > those used by both for now, to see if it's caused by a broken dependency. > > > > > > Alex > > > > > > > > > On Tue, Jul 6, 2021 at 2:08 PM Duncan Murdoch > > <mailto:murdoch.dun...@gmail.com>> wrote: > > > > > > Both NegLogoR and movecost have a lot of hard dependencies -- so many > > > that I'm unwilling to install them with the limited bandwidth that I > > > have right now. I suspect that's related to the problem: some > > > dependency install is failing, and that causes something else to fail, > > > and that leads to the not-very-informative failure messages. > > > > > > This kind of problem is quite a lot of work to debug. If I were going > > > to attempt to do it, I would go for a bisection strategy: > > > > > > - Do you have any old revision which succeeds? If so, use bisection > > > on the revisions until you find the change which first triggers the > > > error. > > > > > > - Perhaps no versions succeed, because something external to your > > > package has triggered the error. In this case, bisection would work on > > > the dependencies: cut out half of the dependencies and all the code > > > that depends on those. Have you fixed the error? If so, add back half > > > of the dependencies, otherwise cut out half of the remaining ones. > > > > > > - If you're still getting the errors after cutting out all of the > > > dependencies, then start cutting out code and data. Etc. > > > > > > In any case, try to find a version of the package that doesn't trigger > > > the error, and a minimal change to it that does. Then perhaps you'll > > > understand the root cause of the error. > > > > > > Duncan Murdoch > > > > > > On 06/07/2021 3:11 p.m., Alex Chubaty wrote: > > > > FWIW I'm having the same issue with package NetLogoR ( > > > > https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fg
Re: [R-pkg-devel] package test returns error when R version 4.1.0
Thank you all. I appreciate your help and discussion so far. To complicate the matter further, I have done an experiment. I have tried to test a new version which is 99.9% identical to the last official one on CRAN because I wanted to understand if the issue was with some new code added to the version I have been testing in the last couple of days. The new version 1.2 (virtually identical to the 1.1 on CRAN) did not pass the tests as per my earlier description. Same errors. The only Ok is on my computer and with devtools’ winoldrealeases() I really don’t know that to do next. Best Gm Dr Gianmarco Alberti (PhD Udine) Lecturer in Spatial Forensics Coordinator of the BA dissertations Department of Criminology Faculty for Social Wellbeing Room 332, Humanities B (FEMA) University of Malta, Msida, Malta (Europe) - MSD 2080 tel +356 2340 3718 Academic profiles https://www.researchgate.net/profile/Gianmarco_Alberti4 https://malta.academia.edu/GianmarcoAlberti Google Scholar profile https://scholar.google.com/citations?user=tFrJKQ0J=en Correspondence Analysis website http://cainarchaeology.weebly.com/ R packages on CRAN: CAinterprTools https://cran.r-project.org/web/packages/CAinterprTools/index.html GmAMisc https://cran.r-project.org/package=GmAMisc movecost https://cran.r-project.org/web/packages/movecost/index.html Il 6 lug 2021, 14:53 +0200, brodie gaslam via R-package-devel , ha scritto: > > > On Tuesday, July 6, 2021, 8:09:18 AM EDT, dbosa...@gmail.com > > wrote: > > > > Martin: > > > > What I suggested was he remove the LazyData entry from the description file > > if he was NOT lazy loading data. If someone is lazy loading data, then that > > is a different situation, and they obviously need to set the entry. > > > > But clearly Gm has a different problem. He has now tried "LazyData: true", > > "LazyData: false", and removing the LazyData entry entirely. And he is > > still getting this error: > > > > * installing *source* package 'movecost' ... > > ** using staged installation > > ** R > > ** data > > ** byte-compile and prepare package for lazy loading > > ERROR: lazy loading failed for package 'movecost' > > * removing 'd:/RCompile/CRANguest/R-release/lib/movecost' > > FWIW I think this is lazy loading of the code, which I think is > different to what LazyData controls. This is described in > R-Internals: > > https://cran.r-project.org/doc/manuals/R-ints.html#Lazy-loading > > I know nothing about it so I will not comment further. > > Best, > > B. > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] package test returns error when R version 4.1.0
Hello, Thank you all for the suggestions. I am starting being a bit worried because I seem not being able to fix the issue. I have never experienced issues with this package (movecost); the last new version I have released to CRAN was released a couple of weeks ago with no issue whatsoever. The new version I am trying to get on CRAN has just one difference: the ‘chorn’ package has been added to the dependencies. Now, I have tried to drop that new dependency, and I have run the tests. Same result. The test using devtools::check_win_release() and devtools::check_win_devel() both return 1 error (lazy loading failed for package ‘movecost’) The test using devtools::check_win_oldrelease() is OK. I also tried to keep the new dependency and to drop the lazy download instead (in DESCRIPTION I have put LazyData: false). I got the same results as above. The package checks perfectly on my MAC, and checked perfectly when I asked a Win users to test the package on his PC (with the latest version of R). I am really scratching my head. Best Gm Dr Gianmarco Alberti (PhD Udine) Lecturer in Spatial Forensics Coordinator of the BA dissertations Department of Criminology Faculty for Social Wellbeing Room 332, Humanities B (FEMA) University of Malta, Msida, Malta (Europe) - MSD 2080 tel +356 2340 3718 Academic profiles https://www.researchgate.net/profile/Gianmarco_Alberti4 https://malta.academia.edu/GianmarcoAlberti Google Scholar profile https://scholar.google.com/citations?user=tFrJKQ0J=en Correspondence Analysis website http://cainarchaeology.weebly.com/ R packages on CRAN: CAinterprTools https://cran.r-project.org/web/packages/CAinterprTools/index.html GmAMisc https://cran.r-project.org/package=GmAMisc movecost https://cran.r-project.org/web/packages/movecost/index.html On 5 Jul 2021, 13:25 +0200, dbosa...@gmail.com, wrote: > For the lazy loading error, if you are not intentionally lazy loading data, > you should remove the lazy loading entry from the description file. > Previously this was not causing any problems with the CRAN checks, but now it > is. > > -Original Message- > From: R-package-devel On Behalf Of > Gianmarco Alberti > Sent: Monday, July 5, 2021 5:27 AM > To: r-package-devel@r-project.org; Uwe Ligges > > Subject: Re: [R-pkg-devel] package test returns error when R version 4.1.0 > > Hello, > Thanks for your reply. > > I got mixed results using: > devtools::check_win_oldrelease() - STATUS OK (R version 4.0.5) - > https://win-builder.r-project.org/7qy6PL8C7ye7 > > devtools::check_win_release() - 1 ERROR (R version 4.1.0) - > https://win-builder.r-project.org/hlA15dFq5BdR > > devtools::check_win_devel() - 1 ERROR (R Under development (unstable) - > https://win-builder.r-project.org/uQ0LGZ7v0E5h > > The reported error is to be: > ERROR: lazy loading failed for package ‘movecost’ > > Since I couldn’t understand the actual underlying issue, I ran > devtools::check_rhub() (as described in my earlier email) which brought to > the fore the Bioconductor issue. > > I have tested the package on Win (R version 4.1) and everything was fine. > > I hope I have addressed your question. > Please let me know if you need any other relevant info from my end. > > Best > Gm > > > Dr Gianmarco Alberti (PhD Udine) > Lecturer in Spatial Forensics > Coordinator of the BA dissertations > Department of Criminology > Faculty for Social Wellbeing > Room 332, Humanities B (FEMA) > University of Malta, Msida, Malta (Europe) - MSD 2080 tel +356 2340 3718 > > Academic profiles > https://www.researchgate.net/profile/Gianmarco_Alberti4 > https://malta.academia.edu/GianmarcoAlberti > > Google Scholar profile > https://scholar.google.com/citations?user=tFrJKQ0J=en > > Correspondence Analysis website > http://cainarchaeology.weebly.com/ > > R packages on CRAN: > CAinterprTools > https://cran.r-project.org/web/packages/CAinterprTools/index.html > > GmAMisc > https://cran.r-project.org/package=GmAMisc > > movecost > https://cran.r-project.org/web/packages/movecost/index.html > > On 5 Jul 2021, 11:20 +0200, Uwe Ligges , > wrote: > > What happens when you test it on winbuilder? > > It is configured like the CRAN incoming checks and there should be all > > relevant packages available. > > > > Best, > > Uwe Ligges > > > > > > On 05.07.2021 11:16, Gianmarco Alberti wrote: > > > Hello, > > > Further to my earlier email, I think I have located a likely issue, and I > > > would appreciate feedback. > > > > &g
Re: [R-pkg-devel] package test returns error when R version 4.1.0
Hello, Thank you. Yes I just tried that option, but I still get the same error: https://win-builder.r-project.org/2OF2vD11Uxe3 Gm Dr Gianmarco Alberti (PhD Udine) Lecturer in Spatial Forensics Coordinator of the BA dissertations Department of Criminology Faculty for Social Wellbeing Room 332, Humanities B (FEMA) University of Malta, Msida, Malta (Europe) - MSD 2080 tel +356 2340 3718 Academic profiles https://www.researchgate.net/profile/Gianmarco_Alberti4 https://malta.academia.edu/GianmarcoAlberti Google Scholar profile https://scholar.google.com/citations?user=tFrJKQ0J=en Correspondence Analysis website http://cainarchaeology.weebly.com/ R packages on CRAN: CAinterprTools https://cran.r-project.org/web/packages/CAinterprTools/index.html GmAMisc https://cran.r-project.org/package=GmAMisc movecost https://cran.r-project.org/web/packages/movecost/index.html On 5 Jul 2021, 23:46 +0200, dbosa...@gmail.com, wrote: > Gm: > > Did you try completely removing the LazyData line from the description file? > > David > > From: Gianmarco Alberti > Sent: Monday, July 5, 2021 5:13 PM > To: r-package-devel@r-project.org; Uwe Ligges > ; dbosa...@gmail.com > Subject: RE: [R-pkg-devel] package test returns error when R version 4.1.0 > > Hello, > Thank you all for the suggestions. > > I am starting being a bit worried because I seem not being able to fix the > issue. > > I have never experienced issues with this package (movecost); > the last new version I have released to CRAN was released a couple of weeks > ago with no issue whatsoever. > > The new version I am trying to get on CRAN has just one difference: the > ‘chorn’ package has been added to the dependencies. > Now, I have tried to drop that new dependency, and I have run the tests. Same > result. > The test using devtools::check_win_release() and devtools::check_win_devel() > both return 1 error (lazy loading failed for package ‘movecost’) > > The test using devtools::check_win_oldrelease() is OK. > > > I also tried to keep the new dependency and to drop the lazy download instead > (in DESCRIPTION I have put LazyData: false). I got the same results as above. > > The package checks perfectly on my MAC, and checked perfectly when I asked a > Win users to test the package on his PC (with the latest version of R). > > > I am really scratching my head. > > Best > Gm > > > Dr Gianmarco Alberti (PhD Udine) > Lecturer in Spatial Forensics > Coordinator of the BA dissertations > Department of Criminology > Faculty for Social Wellbeing > Room 332, Humanities B (FEMA) > University of Malta, Msida, Malta (Europe) - MSD 2080 > tel +356 2340 3718 > > Academic profiles > https://www.researchgate.net/profile/Gianmarco_Alberti4 > https://malta.academia.edu/GianmarcoAlberti > > Google Scholar profile > https://scholar.google.com/citations?user=tFrJKQ0J=en > > Correspondence Analysis website > http://cainarchaeology.weebly.com/ > > R packages on CRAN: > CAinterprTools > https://cran.r-project.org/web/packages/CAinterprTools/index.html > > GmAMisc > https://cran.r-project.org/package=GmAMisc > > movecost > https://cran.r-project.org/web/packages/movecost/index.html > > On 5 Jul 2021, 13:25 +0200, dbosa...@gmail.com, wrote: > > > For the lazy loading error, if you are not intentionally lazy loading data, > > you should remove the lazy loading entry from the description file. > > Previously this was not causing any problems with the CRAN checks, but now > > it is. > > > > -Original Message- > > From: R-package-devel On Behalf Of > > Gianmarco Alberti > > Sent: Monday, July 5, 2021 5:27 AM > > To: r-package-devel@r-project.org; Uwe Ligges > > > > Subject: Re: [R-pkg-devel] package test returns error when R version 4.1.0 > > > > Hello, > > Thanks for your reply. > > > > I got mixed results using: > > devtools::check_win_oldrelease() - STATUS OK (R version 4.0.5) - > > https://win-builder.r-project.org/7qy6PL8C7ye7 > > > > devtools::check_win_release() - 1 ERROR (R version 4.1.0) - > > https://win-builder.r-project.org/hlA15dFq5BdR > > > > devtools::check_win_devel() - 1 ERROR (R Under development (unstable) - > > https://win-builder.r-project.org/uQ0LGZ7v0E5h > > > > The reported error is to be: > > ERROR: lazy loading failed for package ‘movecost’ > > > > Since I couldn’t understand the actual underlying issue, I ran > > devtools::ch
[R-pkg-devel] ERROR: lazy loading failed for package 'movecost'
Hello, I am in the process of checking my ‘movecost’ package before submitting to CRAN. As usual, I have tested my package locally (on my MAC) using devtools::check() and everything is fine, getting 0 error, 0 warnings and 0 notes. Also, as I routinely do, I used (A) devtools::check_win_devel(); in the returned email, the status was OK (https://win-builder.r-project.org/lWar6m662wl3). BUT, I got 1 error from both: (B) devtools::check_win_release() (https://win-builder.r-project.org/6ZzaipUr9rPF) (C) devtools::check_win_oldrelease() (https://win-builder.r-project.org/yXHZoOCov7xH) I cannot really figure out what is actually causing the error (Im not a specialist in programming and the like): ERROR: lazy loading failed for package ‘movecost' Any hint/elucidation on the matter, so that I can spot what is causing the error, would be appreciated. Thank you for your time and consideration. Best Gianmarco Dr Gianmarco Alberti (PhD Udine) Lecturer in Spatial Forensics Coordinator of the BA dissertations Department of Criminology Faculty for Social Wellbeing Room 332, Humanities B (FEMA) University of Malta, Msida, Malta (Europe) - MSD 2080 tel +356 2340 3718 Academic profiles https://www.researchgate.net/profile/Gianmarco_Alberti4 https://malta.academia.edu/GianmarcoAlberti Google Scholar profile https://scholar.google.com/citations?user=tFrJKQ0J=en Correspondence Analysis website http://cainarchaeology.weebly.com/ R packages on CRAN: CAinterprTools https://cran.r-project.org/web/packages/CAinterprTools/index.html GmAMisc https://cran.r-project.org/package=GmAMisc movecost https://cran.r-project.org/web/packages/movecost/index.html [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] ‘Package required and available but unsuitable version’ and notes about examples execution time
Hello, I am in the process of testing a new version of my GmAMisc package before submitting it to CRAN. I have checked it using: (a) devtools::check_win_devel() https://win-builder.r-project.org/T9yi5bawc203 (b) devtools::check_win_release() https://win-builder.r-project.org/VACDopQ9QBMi (c) devtools::check_win_oldrelease() https://win-builder.r-project.org/yoIK3iE7IZqk Now, (a) returns 2 notes about functions’ examples whose execution time is larger than 10 sec This didn’t happen when testing earlier versions of the same package. I did not make any major change to those functions, excluding updating some chunks of code to adapt them to the new structure of the ‘spatstat' package. Most of my functions whose execution time is larger than 10 sec are feature Monte Carlo-based resampling; I have tried to reduce the number of randomised iterations (e.g., from 199 to 99) but no significant changes were produced when it comes to the execution time. (b) returns the same two notes as (a) (c) returns 1 error: Package required and available but unsuitable version: ‘spatstat.linnet' I am wondering: (1) are the 2 notes returned by (a) and (b) a relevant obstacle when it comes to getting my new version on CRAN? I am a little concerned because I do not know how to reduce the execution time further. (2) why the difference between (a)-(b) and (c) when it comes to the error related to spatstat.linnet? Is the error returned by (c) fatal in anticipation of submitting the package to CRAN? If it is, how can I tackle that? Thank you in advance for any help on the above issues. Best Gm Dr Gianmarco Alberti (PhD Udine) Lecturer in Spatial Forensics Coordinator of the BA dissertations Department of Criminology Faculty for Social Wellbeing Room 332, Humanities B (FEMA) University of Malta, Msida, Malta (Europe) - MSD 2080 tel +356 2340 3718 Academic profiles https://www.researchgate.net/profile/Gianmarco_Alberti4 https://malta.academia.edu/GianmarcoAlberti Google Scholar profile https://scholar.google.com/citations?user=tFrJKQ0J=en Correspondence Analysis website http://cainarchaeology.weebly.com/ R packages on CRAN: CAinterprTools https://cran.r-project.org/web/packages/CAinterprTools/index.html GmAMisc https://cran.r-project.org/package=GmAMisc movecost https://cran.r-project.org/web/packages/movecost/index.html [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] ‘Package required and available but unsuitable version’ and notes about examples execution time
Hello, Thank you very much for your prompt reply on a weekend. I am testing my examples locally, and I am noticing that they did not get slower actually. So far I have tested 3 of them and they are in the order of 3 or 4 seconds. So, shall I repeat the test later (or another day)? When it comes to your second question, in my new version’s DESCRIPTION file the following are mentioned (Imports): spatstat.geom (>= 1.65-5), spatstat.core (>= 1.65-5), spatstat.linnet (>= 2.0-0), spatstat (>= 2.0-0) Any further hint? Thank you for your time Best Gianmarco Dr Gianmarco Alberti (PhD Udine) Lecturer in Spatial Forensics Coordinator of the BA dissertations Department of Criminology Faculty for Social Wellbeing Room 332, Humanities B (FEMA) University of Malta, Msida, Malta (Europe) - MSD 2080 tel +356 2340 3718 Academic profiles https://www.researchgate.net/profile/Gianmarco_Alberti4 https://malta.academia.edu/GianmarcoAlberti Google Scholar profile https://scholar.google.com/citations?user=tFrJKQ0J=en Correspondence Analysis website http://cainarchaeology.weebly.com/ R packages on CRAN: CAinterprTools https://cran.r-project.org/web/packages/CAinterprTools/index.html GmAMisc https://cran.r-project.org/package=GmAMisc movecost https://cran.r-project.org/web/packages/movecost/index.html On 21 Mar 2021, 13:46 +0100, Duncan Murdoch , wrote: > On 21/03/2021 7:18 a.m., Gianmarco Alberti wrote: > > Hello, > > > > I am in the process of testing a new version of my GmAMisc package before > > submitting it to CRAN. > > > > I have checked it using: > > (a) devtools::check_win_devel() > > https://win-builder.r-project.org/T9yi5bawc203 > > > > (b) devtools::check_win_release() > > https://win-builder.r-project.org/VACDopQ9QBMi > > > > (c) devtools::check_win_oldrelease() > > https://win-builder.r-project.org/yoIK3iE7IZqk > > > > Now, > > (a) returns 2 notes about functions’ examples whose execution time is > > larger than 10 sec > > This didn’t happen when testing earlier versions of the same package. I did > > not make any major change to those functions, excluding updating some > > chunks of code to adapt them to the new structure of the ‘spatstat' > > package. Most of my functions whose execution time is larger than 10 sec > > are feature Monte Carlo-based resampling; I have tried to reduce the number > > of randomised iterations (e.g., from 199 to 99) but no significant changes > > were produced when it comes to the execution time. > > Did the examples actually become slower? You can time them locally: > you won't get the same timings as Win-builder, but relative timings > should be roughly proportional. > > If they did become slower, then you really should modify the examples. > This might mean using an unrealistically small number of iterations; > that's better than not running them at all, because at least it will > show users how your functions work. > > Or maybe Win-builder was under heavy load, and that's why the timings > are slower. You could take a chance and submit with a note about this. > > > > > (b) returns the same two notes as (a) > > > > (c) returns 1 error: > > Package required and available but unsuitable version: ‘spatstat.linnet' > > How are you stating your dependency on this package? Your current > version only mentions "spatstat (>= 1.56-0)". CRAN has spatstat.linnet > 2.0-0, but perhaps Win-builder hadn't updated its old release library to > that version when you ran your test. > > Duncan Murdoch > > > > > I am wondering: > > (1) are the 2 notes returned by (a) and (b) a relevant obstacle when it > > comes to getting my new version on CRAN? I am a little concerned because I > > do not know how to reduce the execution time further. > > > > (2) why the difference between (a)-(b) and (c) when it comes to the error > > related to spatstat.linnet? Is the error returned by (c) fatal in > > anticipation of submitting the package to CRAN? If it is, how can I tackle > > that? > > > > > > Thank you in advance for any help on the above issues. > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] package not passing automatic checks: no clue as to what is causing 2 notes
Dear All, I trust this email finds you doing well. I had planned to release a new version of my package, and everything was checking perfectly on my machine and using the ‘devtools’ functions check_win_oldrelease(), check_win_release(), and check_win_devel(). However, after submitting the package to CRAN, I have been notified that the package does not pass the automatic incoming checks. I had a look at the log file (https://win-builder.r-project.org/incoming_pretest/movecost_2.0_20230412_090758/Windows/00check.log) and I see two notes which I do not understand: * checking HTML version of manual ... [6s] NOTE Encountered the following conversion/validation errors: 'CreateProcess' failed to run 'd:\rtools43\x86_64-w64-mingw32.static.posix\bin\tidy.exe -language en -qe --drop-empty-elements no D:\temp\Rtmp29JsRe\file2426857b24734' 'CreateProcess' failed to run 'd:\rtools43\x86_64-w64-mingw32.static.posix\bin\tidy.exe -language en -qe --drop-empty-elements no D:\temp\Rtmp29JsRe\file2426857b24734' * checking for detritus in the temp directory ... NOTE Found the following files/directories: 'lastMiKTeXException' Do you have any suggestion as to what can possibly cause those issues, and how to fix them? Thanks -- Dr Gianmarco Alberti | Lecturer in Spatial Forensics BA, MA, PhD (Udine) - Coordinator of the BA dissertations Department of Criminology - Faculty for Social Wellbeing Room 332, Humanities B (FEMA) University of Malta Msida - MSD 2080 (Malta) +356 2340 3718 Google Scholar: https://scholar.google.com/citations?user=tFrJKQ0J=en ResearchGate: https://www.researchgate.net/profile/Gianmarco_Alberti4 Academia: https://malta.academia.edu/GianmarcoAlberti movecost: https://CRAN.R-project.org/package=movecost chisquare: https://CRAN.R-project.org/package=chisquare CAinterprTools: https://CRAN.R-project.org/package=CAinterprTools [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] package not passing automatic checks: no clue as to what is causing 2 notes
Thanks you! Kind regards Gm -- Dr Gianmarco Alberti | Lecturer in Spatial Forensics BA, MA, PhD (Udine) - Coordinator of the BA dissertations Department of Criminology - Faculty for Social Wellbeing Room 332, Humanities B (FEMA) University of Malta Msida - MSD 2080 (Malta) +356 2340 3718 Google Scholar: https://scholar.google.com/citations?user=tFrJKQ0J=en ResearchGate: https://www.researchgate.net/profile/Gianmarco_Alberti4 Academia: https://malta.academia.edu/GianmarcoAlberti movecost: https://CRAN.R-project.org/package=movecost chisquare: https://CRAN.R-project.org/package=chisquare CAinterprTools: https://CRAN.R-project.org/package=CAinterprTools On 12 Apr 2023, 11:08 +0200, Uwe Ligges , wrote: > Indeed, a hicc up of the Windows builder. > Should be resolved. > > Best, > Uwe Ligges > > > On 12.04.2023 10:48, Gianmarco Alberti wrote: > > Hello, > > Thanks for your prompt advices. > > > > I am not an expert…. > > > > I have sent an email to explain that those are likely to be issues on the > > CRAN’s end, and to inform that I would not mind to wait a while and re-do > > the entire submission procedure. > > > > Thank you again > > Gm > > > > -- > > Dr Gianmarco Alberti | Lecturer in Spatial Forensics > > BA, MA, PhD (Udine) - Coordinator of the BA dissertations > > > > Department of Criminology - Faculty for Social Wellbeing > > Room 332, Humanities B (FEMA) > > University of Malta > > Msida - MSD 2080 (Malta) > > +356 2340 3718 > > > > Google Scholar: https://scholar.google.com/citations?user=tFrJKQ0J=en > > ResearchGate: https://www.researchgate.net/profile/Gianmarco_Alberti4 > > Academia: https://malta.academia.edu/GianmarcoAlberti > > movecost: https://CRAN.R-project.org/package=movecost > > chisquare: https://CRAN.R-project.org/package=chisquare > > CAinterprTools: https://CRAN.R-project.org/package=CAinterprTools > > On 12 Apr 2023, 10:16 +0200, Ivan Krylov , wrote: > > > В Wed, 12 Apr 2023 10:05:32 +0200 > > > Gianmarco Alberti пишет: > > > > > > > 'CreateProcess' failed to run > > > > 'd:\rtools43\x86_64-w64-mingw32.static.posix\bin\tidy.exe -language > > > > en -qe --drop-empty-elements no D:\temp\Rtmp29JsRe\file2426857b24734' > > > > > > This is a (transient?) problem on the machine running the check: > > > something completely prevented HTML Tidy from running, even before the > > > process would have tried to load the required DLLs. Nothing to do with > > > your package. > > > > > > > * checking for detritus in the temp directory ... NOTE > > > > Found the following files/directories: 'lastMiKTeXException' > > > > > > I think this is a false positive too. Some other package may have > > > failed to compile its PDF documentation (at the same time?), which > > > caused MiKTeX to create this file in the temp directory. Your PDF > > > manual check resulted in an OK. > > > > > > Does the automatic e-mail include the instructions on where to reply > > > with this explanation? > > > > > > -- > > > Best regards, > > > Ivan > > > > [[alternative HTML version deleted]] > > > > __ > > R-package-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-package-devel [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] package not passing automatic checks: no clue as to what is causing 2 notes
Hello, Thanks for your prompt advices. I am not an expert…. I have sent an email to explain that those are likely to be issues on the CRAN’s end, and to inform that I would not mind to wait a while and re-do the entire submission procedure. Thank you again Gm -- Dr Gianmarco Alberti | Lecturer in Spatial Forensics BA, MA, PhD (Udine) - Coordinator of the BA dissertations Department of Criminology - Faculty for Social Wellbeing Room 332, Humanities B (FEMA) University of Malta Msida - MSD 2080 (Malta) +356 2340 3718 Google Scholar: https://scholar.google.com/citations?user=tFrJKQ0J=en ResearchGate: https://www.researchgate.net/profile/Gianmarco_Alberti4 Academia: https://malta.academia.edu/GianmarcoAlberti movecost: https://CRAN.R-project.org/package=movecost chisquare: https://CRAN.R-project.org/package=chisquare CAinterprTools: https://CRAN.R-project.org/package=CAinterprTools On 12 Apr 2023, 10:16 +0200, Ivan Krylov , wrote: > В Wed, 12 Apr 2023 10:05:32 +0200 > Gianmarco Alberti пишет: > > > 'CreateProcess' failed to run > > 'd:\rtools43\x86_64-w64-mingw32.static.posix\bin\tidy.exe -language > > en -qe --drop-empty-elements no D:\temp\Rtmp29JsRe\file2426857b24734' > > This is a (transient?) problem on the machine running the check: > something completely prevented HTML Tidy from running, even before the > process would have tried to load the required DLLs. Nothing to do with > your package. > > > * checking for detritus in the temp directory ... NOTE > > Found the following files/directories: 'lastMiKTeXException' > > I think this is a false positive too. Some other package may have > failed to compile its PDF documentation (at the same time?), which > caused MiKTeX to create this file in the temp directory. Your PDF > manual check resulted in an OK. > > Does the automatic e-mail include the instructions on where to reply > with this explanation? > > -- > Best regards, > Ivan [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
