[R-pkg-devel] Package fails on Debian
Hi all, I am trying to get my R package to pass CRAN checks for Debian. According to ``rhub::check_on_debian()`` my error is: ``outlierComponentFactory.h:37:15: error: ‘unique_ptr’ in namespace ‘std’ does not name a template type``. I have included ``CXX_STD = CXX17`` in my Makevars file and my package passes checks for Ubuntu and Windows. I do not know how to progress and any advice is appreciated. Package: https://github.com/stcolema/MDIr Full check report: https://builder.r-hub.io/status/MDIr_0.7.0.tar.gz-1374f5af71fb4a1f903feb928f5c41f3 Thank you, Stephen [[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 fails on Debian
On Fri, 9 Dec 2022 17:29:21 + Stephen Coleman wrote: > ``outlierComponentFactory.h:37:15: error: ‘unique_ptr’ in namespace > ‘std’ does not name a template type``. Does it help to explicitly #include in outlierComponentFactory.h in order to provide the definition of the template class unique_ptr? -- Best regards, Ivan __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Do you run R on Fedora or Debian?
CRAN has sent me a notice about the following: https://www.stats.ox.ac.uk/pub/bdr/donttest/rerddapXtracto.out I can not reproduce it. I test on my Mac, the cache space is properly handled (by a package outside mine). Same with Debian on r-hub. I installed Fedora on a virtual machine, no problem (it is assigned a space in /tmp). I would really appreciate it if someone who runs Debian or Fedora could test the following: install.packages("rerddap", dependencies = TRUE) library(rerddap) cache_setup(temp_dir = TRUE) The last line should print where the cache is setup. That is called at the start of all of my functions that do downloads. If you could run that and send me the result I would appreciate it (snd privately no need to spam the list with that). I am at a loss as to how to respond to CRAN because I can't reproduce that error on anything I can test. The cacheing is actually done by the package 'crul'. Thanks, -Roy ** "The contents of this message do not reflect any position of the U.S. Government or NOAA." ** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center ***Note new street address*** 110 McAllister Way Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/ "Old age and treachery will overcome youth and skill." "From those who have been given much, much will be expected" "the arc of the moral universe is long, but it bends toward justice" -MLK Jr. __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Do you run R on Fedora or Debian?
On 10 December 2022 at 14:00, Roy Mendelssohn - NOAA Federal via R-package-devel wrote: | CRAN has sent me a notice about the following: | | https://www.stats.ox.ac.uk/pub/bdr/donttest/rerddapXtracto.out | | I can not reproduce it. I test on my Mac, the cache space is properly handled (by a package outside mine). Same with Debian on r-hub. I installed Fedora on a virtual machine, no problem (it is assigned a space in /tmp). I would really appreciate it if someone who runs Debian or Fedora could test the following: | | install.packages("rerddap", dependencies = TRUE) | library(rerddap) | cache_setup(temp_dir = TRUE) | | The last line should print where the cache is setup. That is called at the start of all of my functions that do downloads. If you could run that and send me the result I would appreciate it (snd privately no need to spam the list with that). I am at a loss as to how to respond to CRAN because I can't reproduce that error on anything I can test. The cacheing is actually done by the package 'crul'. I used r2u [1] here to install the thirty-six (!!) required dependencies in a five or so seconds [2], for convenience in Docker with the Ubuntu 22.04 image. So from docker run --rm -ti eddelbuettel/r2u:jammy bash to apt update -qq install.r rerddap and then as you requested > library(rerddap) > cache_setup(temp_dir = TRUE) [1] "/tmp/Rtmp3sVsk1/R/rerddap" > which seems correct: within the per-R-session temp directory. Hth, Dirk [1] See https://eddelbuettel.github.io/r2u/ [2] That's the point of r2u. See [1]. -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Do you run R on Fedora or Debian?
Perfect. Thanks. That is what I am seeing and that is what is expected. I have even gotten into a debugger, and looked at to where the file was downloaded, right after the download, and it is in a proper temporary space. Dirk if you really want to be a glutton for punishment, could you try this: install.packages("rerddapXtracto", dependencies = TRUE) library(rerddapXtracto) xcoord <- mbnms$Longitude ycoord <- mbnms$Latitude dataInfo <- rerddap::info('etopo180') parameter = 'altitude' xName <- 'longitude' yName <- 'latitude' bathy <- rxtractogon (dataInfo, parameter = parameter, xcoord = xcoord, ycoord = ycoord) What you would be looking for is any sign that this has left a file in cache in the user's space. I don't find any in my virtual machine Assuming that pans out, now my question is how to respond to CRAN. I can give you one guess who from CRAN sent me the notice, As I said, I don't know how to fix something when everything I am have available to behaves properly. Thanks, -Roy > On Dec 10, 2022, at 2:16 PM, Dirk Eddelbuettel wrote: > > > On 10 December 2022 at 14:00, Roy Mendelssohn - NOAA Federal via > R-package-devel wrote: > | CRAN has sent me a notice about the following: > | > | https://www.stats.ox.ac.uk/pub/bdr/donttest/rerddapXtracto.out > | > | I can not reproduce it. I test on my Mac, the cache space is properly > handled (by a package outside mine). Same with Debian on r-hub. I > installed Fedora on a virtual machine, no problem (it is assigned a space in > /tmp). I would really appreciate it if someone who runs Debian or Fedora > could test the following: > | > | install.packages("rerddap", dependencies = TRUE) > | library(rerddap) > | cache_setup(temp_dir = TRUE) > | > | The last line should print where the cache is setup. That is called at the > start of all of my functions that do downloads. If you could run that and > send me the result I would appreciate it (snd privately no need to spam the > list with that). I am at a loss as to how to respond to CRAN because I can't > reproduce that error on anything I can test. The cacheing is actually done > by the package 'crul'. > > I used r2u [1] here to install the thirty-six (!!) required dependencies in a > five or so seconds [2], for convenience in Docker with the Ubuntu 22.04 > image. So from > > docker run --rm -ti eddelbuettel/r2u:jammy bash > > to > > apt update -qq > install.r rerddap > > and then as you requested > >> library(rerddap) >> cache_setup(temp_dir = TRUE) > [1] "/tmp/Rtmp3sVsk1/R/rerddap" >> > > which seems correct: within the per-R-session temp directory. > > Hth, Dirk > > [1] See https://eddelbuettel.github.io/r2u/ > [2] That's the point of r2u. See [1]. > > -- > dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ** "The contents of this message do not reflect any position of the U.S. Government or NOAA." ** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center ***Note new street address*** 110 McAllister Way Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: roy.mendelss...@noaa.gov www: https://www.pfeg.noaa.gov/ "Old age and treachery will overcome youth and skill." "From those who have been given much, much will be expected" "the arc of the moral universe is long, but it bends toward justice" -MLK Jr. __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Do you run R on Fedora or Debian?
On Sat, 10 Dec 2022 14:00:22 -0800 Roy Mendelssohn - NOAA Federal via R-package-devel wrote: > cache_setup(temp_dir = TRUE) Unfortunately, it prints a path under tempdir() for me on my Debian oldstable machine. I see that the error came from the "donttest" check from an extra test that's not on by default with --as-cran. Unfortunately, not even running _R_CHECK_DONTTEST_EXAMPLES_=true \ _R_CHECK_THINGS_IN_OTHER_DIRS_=TRUE R CMD check --as-cran \ --run-donttest rerddapXtracto_1.1.3.tar.gz reproduces the issue for me. As a measure of last resort, could it help to manually go over rerddapXtracto examples and see if any are wrapped in \donttest{} and may be missing a cache setting? -- Best regards, Ivan __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Do you run R on Fedora or Debian?
On 10 December 2022 at 14:27, Roy Mendelssohn - NOAA Federal wrote: | Perfect. Thanks. That is what I am seeing and that is what is expected. I have even gotten into a debugger, and looked at to where the file was downloaded, right after the download, and it is in a proper temporary space. | | Dirk if you really want to be a glutton for punishment, could you try this: | | install.packages("rerddapXtracto", dependencies = TRUE) | library(rerddapXtracto) | xcoord <- mbnms$Longitude | ycoord <- mbnms$Latitude | dataInfo <- rerddap::info('etopo180') | parameter = 'altitude' | xName <- 'longitude' | yName <- 'latitude' | bathy <- rxtractogon (dataInfo, parameter = parameter, xcoord = xcoord, | ycoord = ycoord) | | What you would be looking for is any sign that this has left a file in cache in the user's space. I don't find any in my virtual machine As luck would have it [1] I still had that container session open in a tab from byobu [2] so continuing (and another 102 (!!!) packages as binaries installed in three or four seconds, gotta bless #r2u) > install.packages("rerddapXtracto", dependencies = TRUE) # argument is > > redundant, btw Install system packages as root... Reading package lists... Done Building dependency tree... Done Reading state information... Done Ign https://r2u.stat.illinois.edu/ubuntu jammy InRelease Hit https://r2u.stat.illinois.edu/ubuntu jammy Release [ ... many lines from r2u & bspm processing omitted ... ] Setting up r-cran-plotdap (1.0.0-1.ca2204.1) ... Setting up r-cran-rerddapxtracto (1.1.3-1.ca2204.1) ... Processing triggers for libc-bin (2.35-0ubuntu3.1) ... > library(rerddapXtracto) > xcoord <- mbnms$Longitude > ycoord <- mbnms$Latitude > dataInfo <- rerddap::info('etopo180') > parameter = 'altitude' > xName <- 'longitude' > yName <- 'latitude' > bathy <- rxtractogon (dataInfo, parameter = parameter, xcoord = xcoord, > ycoord = ycoord) > > getwd() [1] "/" > Nothing spewn to stdout. Jumping into the same Docker session via the much-underappreciated backdoor trick: edd@rob:~/git/digest(master)$ docker ps CONTAINER ID IMAGECOMMAND CREATED STATUS PORTS NAMES 18f6bf0e3bb1 eddelbuettel/r2u:jammy "bash"39 minutes ago Up 39 minutes nervous_black edd@rob:~/git/digest(master)$ docker exec -ti nervous_black bash root@18f6bf0e3bb1:/# ls bin boot dev etc home lib lib32 lib64 libx32 media mnt opt proc root run sbin srv sys tmp usr var root@18f6bf0e3bb1:/# cd ~ root@18f6bf0e3bb1:~# ls root@18f6bf0e3bb1:~# we see no files in / (where we started) or $HOME. | Assuming that pans out, now my question is how to respond to CRAN. I can give you one guess who from CRAN sent me the notice, As I said, I don't know how to fix something when everything I am have available to behaves properly. I have no idea. But I would trust Ivan's advice as he is essentially always spot on and minimize / control interaction. If CRAN reports this to you, they see it. You should have access to `tempdir()` and friends to make things per-session, or else you need to ask the user (once) and then store in user-supplied location. I think that was discussed here recently. Good luck, Dirk [1] Also commonly called 'attention deficit disorder' [2] A more user-friendly variant of tmux | Thanks, | | -Roy | | > On Dec 10, 2022, at 2:16 PM, Dirk Eddelbuettel wrote: | > | > | > On 10 December 2022 at 14:00, Roy Mendelssohn - NOAA Federal via R-package-devel wrote: | > | CRAN has sent me a notice about the following: | > | | > | https://www.stats.ox.ac.uk/pub/bdr/donttest/rerddapXtracto.out | > | | > | I can not reproduce it. I test on my Mac, the cache space is properly handled (by a package outside mine). Same with Debian on r-hub. I installed Fedora on a virtual machine, no problem (it is assigned a space in /tmp). I would really appreciate it if someone who runs Debian or Fedora could test the following: | > | | > | install.packages("rerddap", dependencies = TRUE) | > | library(rerddap) | > | cache_setup(temp_dir = TRUE) | > | | > | The last line should print where the cache is setup. That is called at the start of all of my functions that do downloads. If you could run that and send me the result I would appreciate it (snd privately no need to spam the list with that). I am at a loss as to how to respond to CRAN because I can't reproduce that error on anything I can test. The cacheing is actually done by the package 'crul'. | > | > I used r2u [1] here to install the thirty-six (!!) required dependencies in a | > five or so seconds [2], for convenience in Docker with the Ubuntu 22.04 | > image. So from | > | > docker run --rm -ti eddelbuettel/r2u:jammy bash | > | > to | > | > apt update -qq | > install.r rerddap | > | > and then as you requested | > | >> library(rerd
Re: [R-pkg-devel] Do you run R on Fedora or Debian?
Thanks for the effort. Yep that is what I see when I run in my virtual machine. I will play with it some more, and hopefully someone from CRAN will see this and chime in. I am more than willing to try to fix this, I just can not reproduce the error. -Roy > On Dec 10, 2022, at 2:53 PM, Dirk Eddelbuettel wrote: > > > On 10 December 2022 at 14:27, Roy Mendelssohn - NOAA Federal wrote: > | Perfect. Thanks. That is what I am seeing and that is what is expected. > I have even gotten into a debugger, and looked at to where the file was > downloaded, right after the download, and it is in a proper temporary space. > | > | Dirk if you really want to be a glutton for punishment, could you try this: > | > | install.packages("rerddapXtracto", dependencies = TRUE) > | library(rerddapXtracto) > | xcoord <- mbnms$Longitude > | ycoord <- mbnms$Latitude > | dataInfo <- rerddap::info('etopo180') > | parameter = 'altitude' > | xName <- 'longitude' > | yName <- 'latitude' > | bathy <- rxtractogon (dataInfo, parameter = parameter, xcoord = xcoord, > | ycoord = ycoord) > | > | What you would be looking for is any sign that this has left a file in > cache in the user's space. I don't find any in my virtual machine > > As luck would have it [1] I still had that container session open in a tab > from byobu [2] so continuing (and another 102 (!!!) packages as binaries > installed in three or four seconds, gotta bless #r2u) > >> install.packages("rerddapXtracto", dependencies = TRUE) # argument is > >> redundant, btw > Install system packages as root... > Reading package lists... Done > Building dependency tree... Done > Reading state information... Done > Ign https://r2u.stat.illinois.edu/ubuntu jammy InRelease > Hit https://r2u.stat.illinois.edu/ubuntu jammy Release > [ ... many lines from r2u & bspm processing omitted ... ] > Setting up r-cran-plotdap (1.0.0-1.ca2204.1) ... > Setting up r-cran-rerddapxtracto (1.1.3-1.ca2204.1) ... > Processing triggers for libc-bin (2.35-0ubuntu3.1) ... >> library(rerddapXtracto) >> xcoord <- mbnms$Longitude >> ycoord <- mbnms$Latitude >> dataInfo <- rerddap::info('etopo180') >> parameter = 'altitude' >> xName <- 'longitude' >> yName <- 'latitude' >> bathy <- rxtractogon (dataInfo, parameter = parameter, xcoord = xcoord, >> ycoord = ycoord) >> >> getwd() > [1] "/" >> > > Nothing spewn to stdout. Jumping into the same Docker session via the > much-underappreciated backdoor trick: > > edd@rob:~/git/digest(master)$ docker ps > CONTAINER ID IMAGECOMMAND CREATED STATUS > PORTS NAMES > 18f6bf0e3bb1 eddelbuettel/r2u:jammy "bash"39 minutes ago Up 39 > minutes nervous_black > edd@rob:~/git/digest(master)$ docker exec -ti nervous_black bash > root@18f6bf0e3bb1:/# ls > bin boot dev etc home lib lib32 lib64 libx32 media mnt opt proc > root run sbin srv sys tmp usr var > root@18f6bf0e3bb1:/# cd ~ > root@18f6bf0e3bb1:~# ls > root@18f6bf0e3bb1:~# > > we see no files in / (where we started) or $HOME. > > | Assuming that pans out, now my question is how to respond to CRAN. I can > give you one guess who from CRAN sent me the notice, As I said, I don't > know how to fix something when everything I am have available to behaves > properly. > > I have no idea. But I would trust Ivan's advice as he is essentially always > spot on and minimize / control interaction. If CRAN reports this to you, > they see it. You should have access to `tempdir()` and friends to make things > per-session, or else you need to ask the user (once) and then store in > user-supplied location. I think that was discussed here recently. > > Good luck, Dirk > > [1] Also commonly called 'attention deficit disorder' > [2] A more user-friendly variant of tmux > > > | Thanks, > | > | -Roy > | > | > On Dec 10, 2022, at 2:16 PM, Dirk Eddelbuettel wrote: > | > > | > > | > On 10 December 2022 at 14:00, Roy Mendelssohn - NOAA Federal via > R-package-devel wrote: > | > | CRAN has sent me a notice about the following: > | > | > | > | https://www.stats.ox.ac.uk/pub/bdr/donttest/rerddapXtracto.out > | > | > | > | I can not reproduce it. I test on my Mac, the cache space is properly > handled (by a package outside mine). Same with Debian on r-hub. I > installed Fedora on a virtual machine, no problem (it is assigned a space in > /tmp). I would really appreciate it if someone who runs Debian or Fedora > could test the following: > | > | > | > | install.packages("rerddap", dependencies = TRUE) > | > | library(rerddap) > | > | cache_setup(temp_dir = TRUE) > | > | > | > | The last line should print where the cache is setup. That is called at > the start of all of my functions that do downloads. If you could run that > and send me the result I would appreciate it (snd privately no need to spam > the lis
[R-pkg-devel] no visible binding for global variable ‘degree_C’ - CRAN check note
In my iemisc package, I am using the units package. This is an example of how I am using the set_units function: T <- 20 set_units(T, degree_C) Upon checking iemisc with devtools for CRAN submission, I receive the following note under "checking R code for possible problems": no visible binding for global variable ‘degree_C’ Please tell me how to avoid that note in my R packages. Thank you. Irucka -- -- No fear, Only Love! / ¡No temas, solamente amor! -Irucka Ajani Embry, 15 March 2020 Family Partners: http://www.sustainlex.org/ https://www.schoolingsolutions.com/ --- The business collaboration between EConsulting (tm) [https://www.econsultingllc.org/] and EcoC^2S, is Getting Back to Nature. Getting Back to Nature LocalHarvest -- https://www.localharvest.org/getting-back-to-nature-M73453 Getting Back to Nature -- https://www.gettingback2nature.farm/ -- Irucka and his twin brother, Obiora, are featured in the Middle Tennessee Local Table Magazine Annual issue. The article discusses their family farm history and the current work that they are doing under Getting Back to Nature. The full magazine can be found here [the article begins on page 18 of the PDF document]: https://media.gettingback2nature.farm/pdf/LocalTable_ANNUAL_2020_lo_res.pdf -- Obiora and Irucka were interviewed separately in early 2020 for the Natural Resources Defense Council's (NRDC) "Regenerative Agriculture: Farm Policy for the 21st Century: Policy Recommendations to Advance Regenerative Agriculture" report written By Arohi Sharma, Lara Bryant, and Ellen Lee. The PDF report is available below: https://www.nrdc.org/sites/default/files/regenerative-agriculture-farm-policy-21st-century-report.pdf EcoC2S -- https://www.ecoccs.com/ Principal, Irucka Embry, EIT Services: Growing Food Healthy Living Mentor Data Analysis with R R Training Chemistry and Mathematics Tutoring Free/Libre and Open Source Software (FLOSS) Consultation __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] no visible binding for global variable ‘degree_C’ - CRAN check note
You can declare degree_C as a variable before using set_units(): degree_C <- NULL set_units(T, degree_C) you could use globalVariables() somewhere at the top-level in your package: utils::globalVariables("degree_C") or you could supply degree_C as a literal character string: set_units(T, "degree_C") On Sat, Dec 10, 2022 at 11:13 PM EcoC2S - Irucka Embry wrote: > > In my iemisc package, I am using the units package. > > This is an example of how I am using the set_units function: > > T <- 20 > > set_units(T, degree_C) > > Upon checking iemisc with devtools for CRAN submission, I receive the > following note under "checking R code for possible problems": > > no visible binding for global variable ‘degree_C’ > > Please tell me how to avoid that note in my R packages. > > Thank you. > > Irucka > > -- > -- > No fear, Only Love! / ¡No temas, solamente amor! > -Irucka Ajani Embry, 15 March 2020 > > Family Partners: > http://www.sustainlex.org/ > https://www.schoolingsolutions.com/ > > --- > > The business collaboration between EConsulting (tm) > [https://www.econsultingllc.org/] and EcoC^2S, is Getting Back to > Nature. > > Getting Back to Nature LocalHarvest -- > https://www.localharvest.org/getting-back-to-nature-M73453 > Getting Back to Nature -- https://www.gettingback2nature.farm/ > > -- Irucka and his twin brother, Obiora, are featured in the Middle > Tennessee Local Table Magazine Annual issue. The article discusses their > family farm history and the current work that they are doing under > Getting > Back to Nature. The full magazine can be found here [the article begins > on > page 18 of the PDF document]: > > https://media.gettingback2nature.farm/pdf/LocalTable_ANNUAL_2020_lo_res.pdf > > -- Obiora and Irucka were interviewed separately in early 2020 for the > Natural Resources Defense Council's (NRDC) "Regenerative Agriculture: > Farm > Policy for the 21st Century: Policy Recommendations to Advance > Regenerative > Agriculture" report written By Arohi Sharma, Lara Bryant, and Ellen Lee. > The PDF report is available below: > > https://www.nrdc.org/sites/default/files/regenerative-agriculture-farm-policy-21st-century-report.pdf > > EcoC2S -- https://www.ecoccs.com/ > Principal, Irucka Embry, EIT > > Services: > Growing Food > Healthy Living Mentor > Data Analysis with R > R Training > Chemistry and Mathematics Tutoring > Free/Libre and Open Source Software (FLOSS) Consultation > > __ > 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