Re: [R-pkg-devel] Package submission failed with two warnings
On Fri, 15 May 2020 at 10:34, FARSHAD TABASINEJAD wrote: > > Dear R-package-devel experts, > > This is the first time I’m writing to this platform about a package I > recently submitted to CRAN (my first package). > While the package is already available on CRAN, I still must fix a few > warnings and one error as reported on the CRAN package check results page: > https://cran.r-project.org/web/checks/check_results_Rpvt.html > > I recently resubmitted a modified version of the package to CRAN, however, it > didn’t pass the automatic incoming checks. > > Windows: > https://win-builder.r-project.org/incoming_pretest/Rpvt_0.1.0_20200512_051950/Windows/00check.log > Status: 1 WARNING > > Debian: > https://win-builder.r-project.org/incoming_pretest/Rpvt_0.1.0_20200512_051950/Debian/00check.log > Status: 2 WARNINGs > > > 1) The first warning that appears on both Windows and Debian results is > “Insufficient package version (submitted: 0.1.0, existing: 0.1.0)”. > > Since the package is conditionally available on CRAN, do I need to modify the > package version to 0.1.1 to get rid of this warning? > Is there any way to fix this problem with the current version of the > package(0.1.0)? >From https://cran.r-project.org/web/packages/policies.html: "Updates to previously-published packages must have an increased version. Increasing the version number at each submission reduces confusion so is preferred even when a previous submission was not accepted." > > 2) The second problem appears on the Debian test results: > > * checking re-building of vignette outputs ... [8s/8s] WARNING > > Error(s) in re-building vignettes: > ... > --- re-building ‘Rpvt.Rmd’ using rmarkdown > > pandoc-citeproc: Error in $: Incompatible API versions: encoded with > [1,20] but attempted to decode with [1,17,5,4]. > > CallStack (from HasCallStack): > error, called at ./Text/Pandoc/JSON.hs:111:48 in pandoc-types-1.17.5.4 > 5tHZ3B61A58JaKOMxwGQR4:Text.Pandoc.JSON > > Error running filter /usr/bin/pandoc-citeproc: > > Filter returned error status 1 > Error: processing vignette 'Rpvt.Rmd' failed with diagnostics: > pandoc document conversion failed with error 83 --- > failed re-building ‘Rpvt.Rmd’ > > SUMMARY: processing the following file failed: > ‘Rpvt.Rmd’ > > Error: Vignette re-building failed. > Execution halted > > I’ve created this package on a Windows operating system with no problem in > creating the ‘Rpvt.Rmd’ file as is the case with the CRAN tests on > x86_64-w64-mingw32 (64-bit). > Why does it fail to create the “Rpvt.Rmd” file on x86_64-pc-linux-gnu > (Debian)? Is this something related to the citation style of the library.bib > file that I’ve used in my vignettes folder? It is the “apa-6th-edition.csl” > file downloaded from > https://raw.githubusercontent.com/citation-style-language/styles/master/apa-6th-edition.csl > >From https://cran.r-project.org/submit.html "Package authors should make all reasonable efforts to provide cross-platform portable code. Packages will not normally be accepted that do not run on at least two of the major R platforms. Cases for Windows-only packages will be considered, but CRAN may not be the most appropriate place to host them."" You might want to use win-builder (https://win-builder.r-project.org/) to test your package on other platforms. All the best, Mauricio = Department of Civil Engineering Faculty of Engineering and Sciences Universidad de La Frontera, Temuco, Chile http://hzambran.github.io/ = mailto : mauricio.zambr...@ufrontera.cl work-phone : +56 45 259 2812 = "Life goes by so fast, that if you don't stop and look around, you might miss it" (from the film Ferris Bueller's Day Off) = Linux user #454569 -- Linux Mint user -- La información contenida en este correo electrónico y cualquier anexo o respuesta relacionada, puede contener datos e información confidencial y no puede ser usada o difundida por personas distintas a su(s) destinatario(s). Si usted no es el destinatario de esta comunicación, le informamos que cualquier divulgación, distribución o copia de esta información constituye un delito conforme a la ley chilena. Si lo ha recibido por error, por favor borre el mensaje y todos sus anexos y notifique al remitente. __ 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
I had a similar problem and today it was solved. What I did was first, solve any possible dependency issue of the archived package, check your package against r-devel, using --as-cran, and then write to CRAN saying that your package is currently archived because of ., but you are submitting a new version that corrects all the problems. IHTH. Kind regards Mauricio Mauricio Zambrano-Bigiarini, PhD = Department of Civil Engineering Faculty of Engineering and Sciences Universidad de La Frontera, Temuco, Chile http://hzambran.github.io/ = mailto : mauricio.zambr...@ufrontera.cl work-phone : +56 45 259 2812 = "A people that values its privileges above its principles soon loses both". (Dwight D. Eisenhower) = Linux user #454569 -- Linux Mint user On Tue, 17 Mar 2020 at 17:27, Gianmarco Alberti wrote: > > 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 -- La información contenida en este correo electrónico y cualquier anexo o respuesta relacionada, puede contener datos e información confidencial y no puede ser usada o difundida por personas distintas a su(s) destinatario(s). Si usted no es el destinatario de esta comunicación, le informamos que cualquier divulgación, distribución o copia de esta información constituye un delito conforme a la ley chilena. Si lo ha recibido por error, por favor borre el mensaje y todos sus anexos y notifique al remitente. __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Manual inspection of a new CRAN submission
Thank you very much Duncan for the information. BTW, it is incredible to me how the quality control of packages submitted to CRAN has improved in the last decade. Now the automatic procedures are able to identify even "little" things (e.g., broken links, misspelled words, size of vignettes, etc). Thank you very much for all the effort and dedication of the CRAN Repository Maintainers. Kind regards, Mauricio = "Success is not final, failure is not fatal. It is the courage to continue that counts. (Winston Churchill) = Linux user #454569 -- Linux Mint user On Wed, 18 Dec 2019 at 19:50, Duncan Murdoch wrote: > > On 18/12/2019 5:01 p.m., Mauricio Zambrano-Bigiarini wrote: > > Dear List, > > > > Today I submitted a package to CRAN, and after correcting some NOTEs, > > I got the following automatic message: > > > > "package mypackage_0.1-2.tar.gz has been auto-processed and is pending > > a manual inspection of this new CRAN submission. A CRAN team member > > will typically respond to you within the next 10 working days. For > > technical reasons you may receive a second copy of this message when a > > team member triggers a new check." > > > > > > Could somebody give a short explanation about what type of checkings > > are made in this "manual inspection" ? > > > > Basically they're checking whether you are following the guidelines at > https://cran.r-project.org/web/packages/policies.html. Not all of those > things can be checked automatically, and many people claim to be > following them when they actually are not. > > Duncan Murdoch -- La información contenida en este correo electrónico y cualquier anexo o respuesta relacionada, puede contener datos e información confidencial y no puede ser usada o difundida por personas distintas a su(s) destinatario(s). Si usted no es el destinatario de esta comunicación, le informamos que cualquier divulgación, distribución o copia de esta información constituye un delito conforme a la ley chilena. Si lo ha recibido por error, por favor borre el mensaje y todos sus anexos y notifique al remitente. __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Manual inspection of a new CRAN submission
Dear List, Today I submitted a package to CRAN, and after correcting some NOTEs, I got the following automatic message: "package mypackage_0.1-2.tar.gz has been auto-processed and is pending a manual inspection of this new CRAN submission. A CRAN team member will typically respond to you within the next 10 working days. For technical reasons you may receive a second copy of this message when a team member triggers a new check." Could somebody give a short explanation about what type of checkings are made in this "manual inspection" ? Thak in advance for your help, Mauricio Mauricio Zambrano-Bigiarini, PhD = Department of Civil Engineering Faculty of Engineering and Sciences Universidad de La Frontera, Temuco, Chile http://hzambran.github.io/ = mailto : mauricio.zambr...@ufrontera.cl work-phone : +56 45 259 2812 = "Success is not final, failure is not fatal. It is the courage to continue that counts. (Winston Churchill) = Linux user #454569 -- Linux Mint user -- La información contenida en este correo electrónico y cualquier anexo o respuesta relacionada, puede contener datos e información confidencial y no puede ser usada o difundida por personas distintas a su(s) destinatario(s). Si usted no es el destinatario de esta comunicación, le informamos que cualquier divulgación, distribución o copia de esta información constituye un delito conforme a la ley chilena. Si lo ha recibido por error, por favor borre el mensaje y todos sus anexos y notifique al remitente. __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Appropriate place to post about CRAN check environments etc.
On 21 July 2015 at 11:46, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 21/07/2015 9:01 AM, ProfJCNash wrote: There has been some disagreement on where it is appropriate to post questions about package checking procedures, including the building of the environment e.g., R-devel under Linux Mint. In looking at https://www.r-project.org/mail.html, it seems to me that the procedures belong with r-package-devel, but there doesn't seem to be a good home for the consequent need to build R-devel to do this. Have I missed the appropriate list? It seems to me that the volume of queries of this sort, and the success of WinBuilder, suggest we could seriously use similar a Linbuilder and MacBuilder (and possibly others). There's a lot of duplicated effort being wasted on the R-devel side in particular. Is there sufficient interest to - make the effort to emulate Winbuilder for Linux and/or Mac - coordinate the volunteer effort - fund/support the necessary infrastructure (it could be worth a modest contribution to save effort)? For the record, I'm willing to participate. I've managed to set up Linux Mint VirtualBox instances that run R current and R devel for testing, though I find I must do more work than I'd like to maintain things, likely as a result of my own limited skills. That sounds like the sort of project the R Consortium would support. They are just getting started, but soon they will have a committee set up to decide on projects, and presumably soon after that will have a process in place to solicit them. Duncan Murdoch In my humble opinion, such a project could be of great utility to several people that is starting to migrate to GNU/Linux, or to people willing to test their packages with the latest development version of R but without all the knowledge to properly set up the environment on their local machines. If I can contribute to a LinBuilder (e.g., testing), I would be willing to do it. Kind regards, Mauricio Zambrano-Bigiarini, PhD = Dept. of Civil Engineering Faculty of Engineering and Sciences Universidad de La Frontera PO Box 54-D, Temuco, Chile = mailto : mauricio.zambr...@ufrontera.cl work-phone : +56 45 259 2812 http://ingenieriacivil.ufro.cl/ = When the pupil is ready, the master arrives. (Zen proverb) = Linux user #454569 -- Linux Mint user __ 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] Setting up R-devel in Linux Mint 17.1 64-bit
= When the pupil is ready, the master arrives. (Zen proverb) = Linux user #454569 -- Linux Mint user On 20 July 2015 at 18:35, Dirk Eddelbuettel e...@debian.org wrote: On 20 July 2015 at 18:05, MAURICIO ZAMBRANO BIGIARINI wrote: | Dear list, | | I'm trying to set up the development version of R (R-devel ) for | testing some packages before submitting them to CRAN. I'm using Linux | Mint 17.1 64-bit, which is an Ubuntu-based distro. | | I followed the advice of Dirk on | https://stat.ethz.ch/pipermail/r-sig-debian/2012-August/001935.html | | | Everything seems to run fine until .configure: | | R is now configured for x86_64-unknown-linux-gnu | | Source directory: . | Installation directory:/usr/local/lib/R-devel | | C compiler:ccache gcc -std=gnu99 -g -O2 | Fortran 77 compiler: gfortran -g -O2 | | C++ compiler: ccache g++ -g -O2 | C++11 compiler:ccache g++ -std=c++11 -g -O2 | Fortran 90/95 compiler:gfortran -g -O2 | Obj-C compiler: | | Interfaces supported: X11, tcltk | External libraries:readline, BLAS(generic), LAPACK(generic), curl | Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU | Options enabled: shared R library, R profiling | | Capabilities skipped: | Options not enabled: shared BLAS, memory profiling | | Recommended packages: no Looks good but ... | | | However, when running make, I got an error saying: | | /usr/bin/ld: ../appl/dchdc.o: relocation R_X86_64_32 against | `.rodata' can not be used when making a shared object; recompile with | -fPIC | | | I would highly appreciate any advice on how to solve this issue (or | what should I recompile with -fPIC and how). ... naybe your R was built without shared library support? The binaries resulting from my configuration (ie the Debian or Ubuntu packages obtained either from the distro themselves or the CRAN mirrors) have 'pic' set: edd@max:~$ grep -i pic /etc/R/Makeconf CPICFLAGS = -fpic CXXPICFLAGS = -fpic CXX1XPICFLAGS = -fpic DYLIB_LDFLAGS = -shared -fopenmp# $(CFLAGS) $(CPICFLAGS) FCPICFLAGS = -fpic FPICFLAGS = -fpic SHLIB_LDFLAGS = -shared# $(CFLAGS) $(CPICFLAGS) ## We want to ensure libR is picked up from $(R_HOME)/lib ALL_CFLAGS = $(R_XTRA_CFLAGS) $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS) ALL_CXXFLAGS = $(R_XTRA_CXXFLAGS) $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS) ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS) ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS) ALL_FFLAGS = $(R_XTRA_FFLAGS) $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS) $(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $ -o $@ $(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $ -o $@ edd@max:~$ Here /etc/R/Makefonf is just a convenient link to $(R_HOME)/etc/Makeconf. Dirk Thank you very much Dirk, but I forgot to mention that this is my very first time trying to set up R-devel. In my ~/SVN/R-devel/trunk/Makeconf file I currently don't have the first two lines you mentioned: CPICFLAGS = -fpic CXXPICFLAGS = -fpic and instead of SHLIB_LDFLAGS = -shared# $(CFLAGS) $(CPICFLAGS) I have DYLIB_LDFLAGS = -shared -fopenmp# $(DYLIBS_LTO) how can I be sure that I I enabled the shared library support ? Mauricio __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Setting up R-devel in Linux Mint 17.1 64-bit
On 20 July 2015 at 20:29, peter dalgaard pda...@gmail.com wrote: Oi! Could you guys move to r-devel? This has nothing to do with _package_ development. Thanks for the advice. I was not sure about the list I should have submitted this message, but looking at http://www.r-project.org/mail.html: R-package-devel is to get help about package development in R,... If you are having problems developing a package or passing R CMD check, this is the place to ask! R-devel: This list is intended for questions and discussion about code development in R. ... The list is also for proposals of new functionality for R, and pre-testing of new versions. It is meant particularly for those who maintain an active position in the development of R. and as my original intend was to passing R CMD check--as-cran using the development version of R, I chose r-package-devel. I'll create a shorten version of this message in r-devel (not sure if this is the right way of moving a message from one mailing list to another). Mauricio -Peter D On 21 Jul 2015, at 00:49 , MAURICIO ZAMBRANO BIGIARINI mauricio.zambr...@ufrontera.cl wrote: -- Forwarded message -- From: Dirk Eddelbuettel e...@debian.org Date: 20 July 2015 at 19:21 Subject: Re: [R-pkg-devel] Setting up R-devel in Linux Mint 17.1 64-bit To: MAURICIO ZAMBRANO BIGIARINI mauricio.zambr...@ufrontera.cl Cc: Dirk Eddelbuettel e...@debian.org, r-package-devel@r-project.org On 20 July 2015 at 18:56, MAURICIO ZAMBRANO BIGIARINI wrote: | how can I be sure that I I enabled the shared library support ? edd@max:~/svn/r-devel$ ./configure --help | grep enable-R-sh --enable-R-shlibbuild the shared/dynamic library 'libR' [no] edd@max:~/svn/r-devel$ Make sure you set --enable-R-shlib. It is in the script which you linked to in your previous email. I thought I did it already when running configure: ./configure --prefix=/usr/local/lib/R-devel --enable-R-shlib --with-blas --with-lapack --with-readline --without-recommended-packages I just tried to run again your script (mentioned in my previous e-mail) from scratch and I'm still getting an error: R is now configured for x86_64-unknown-linux-gnu Source directory: . Installation directory:/usr/local/lib/R-devel C compiler:ccache gcc -ggdb -pipe -std=gnu99 -Wall -pedantic Fortran 77 compiler: ccache gfortran -g -O2 C++ compiler: ccache g++ -ggdb -pipe -Wall -pedantic C++11 compiler:ccache g++ -std=c++11 -ggdb -pipe -Wall -pedantic Fortran 90/95 compiler:ccache gfortran -g -O2 Obj-C compiler: Interfaces supported: X11, tcltk External libraries:readline, BLAS(generic), LAPACK(generic), curl Additional capabilities: PNG, JPEG, TIFF, NLS, cairo, ICU Options enabled: shared R library, R profiling Capabilities skipped: Options not enabled: shared BLAS, memory profiling Recommended packages: no make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/doc/manual' make[1]: Nothing to be done for `front-matter'. make[1]: Nothing to be done for `html-non-svn'. make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/doc/manual' SVN-REVISION is unchanged make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/m4' make[1]: Nothing to be done for `R'. make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/m4' make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/tools' make[1]: Nothing to be done for `R'. make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/tools' make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/doc' make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/doc/html' make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/doc/html' make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/doc/manual' make[2]: Nothing to be done for `R'. make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/doc/manual' make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/doc' make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/etc' make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/etc' make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/share' make[1]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/share' make[1]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src' make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/scripts' creating src/scripts/R.fe make[3]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/scripts' make[3]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/scripts' make[2]: Leaving directory `/home/hzambran/SVN/R-devel/trunk/src/scripts' make[2]: Entering directory `/home/hzambran/SVN/R-devel/trunk/src/include' config.status: creating src/include/config.h config.status: src/include/config.h is unchanged Rmath.h is unchanged make[3]: Entering
