Re: [R-pkg-devel] checking CRAN incoming feasibility
On 17 January 2024 at 09:42, Simon Urbanek wrote: | that check always hangs for me (I don't think it likes NZ ;)), so I just use | | _R_CHECK_CRAN_INCOMING_REMOTE_=0 R CMD check --as-cran ... You can also set it in Renviron files consulted just for checks: $ grep INCOMING_= ~/.R/check.Renviron* /home/edd/.R/check.Renviron:_R_CHECK_CRAN_INCOMING_=FALSE /home/edd/.R/check.Renviron-Rdevel:_R_CHECK_CRAN_INCOMING_=TRUE $ Best, Dirk | | Cheers, | Simon | | | > On Jan 16, 2024, at 6:49 PM, Rolf Turner wrote: | > | > | > On Tue, 16 Jan 2024 16:24:59 +1100 | > Hugh Parsonage wrote: | > | >>> Surely the software just has to check | >> that there is web connection to a CRAN mirror. | >> | >> Nope! The full code is in tools:::.check_package_CRAN_incoming (the | >> body of which filled up my entire console), but to name a few checks | >> it has to do: check that the name of the package is not the same as | >> any other, including archived packages (which means that it has to | >> download the package metadata), make sure the licence is ok, see if | >> the version number is ok. 10 minutes is quite a lot though. I suspect | >> the initial connection may have been faulty. | > | > Well, it may not have been 10 minutes, but it was at least 5. The | > problem is persistent/repeatable. I don't believe that there is any | > faulty connection. | > | > Thanks for the insight. | > | > cheers, | > | > Rolf Turner | > | > -- | > Honorary Research Fellow | > Department of Statistics | > University of Auckland | > Stats. Dep't. (secretaries) phone: | > +64-9-373-7599 ext. 89622 | > Home phone: +64-9-480-4619 | > | > __ | > 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 -- 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] checking CRAN incoming feasibility
Ralf, that check always hangs for me (I don't think it likes NZ ;)), so I just use _R_CHECK_CRAN_INCOMING_REMOTE_=0 R CMD check --as-cran ... Cheers, Simon > On Jan 16, 2024, at 6:49 PM, Rolf Turner wrote: > > > On Tue, 16 Jan 2024 16:24:59 +1100 > Hugh Parsonage wrote: > >>> Surely the software just has to check >> that there is web connection to a CRAN mirror. >> >> Nope! The full code is in tools:::.check_package_CRAN_incoming (the >> body of which filled up my entire console), but to name a few checks >> it has to do: check that the name of the package is not the same as >> any other, including archived packages (which means that it has to >> download the package metadata), make sure the licence is ok, see if >> the version number is ok. 10 minutes is quite a lot though. I suspect >> the initial connection may have been faulty. > > Well, it may not have been 10 minutes, but it was at least 5. The > problem is persistent/repeatable. I don't believe that there is any > faulty connection. > > Thanks for the insight. > > cheers, > > Rolf Turner > > -- > Honorary Research Fellow > Department of Statistics > University of Auckland > Stats. Dep't. (secretaries) phone: > +64-9-373-7599 ext. 89622 > Home phone: +64-9-480-4619 > > __ > 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] checking CRAN incoming feasibility
В Tue, 16 Jan 2024 08:47:07 + David Hugh-Jones пишет: > If I understand correctly, the current procedure is that the client > downloads every package name from CRAN, and then checks its name is > unique. This is not the only check that relies on utils::available.packages(). In particular, strong dependencies are ensured to be present in mainstream repositories, and the whole strong dependency tree is checked for packages with FOSS licenses to ensure that their dependencies do not restrict use. Additional checks require even more files: - src/contrib/PACKAGES.in is checked for CRAN notes on packages - src/contrib/Meta/archive.rds is also checked for potential name collisions, case-insensitively. - src/contrib/Meta/current.rds is checked together with archive.rds for update frequency - web/packages/packages.rds is checked for maintainer changes > Wouldn’t it be faster (for both parties) to check name uniqueness > directly on the server? The current scheme, if somewhat wasteful, makes it possible to run R CMD check with any CRAN mirror without making it run any code server side. (With the small exception of .htaccess to rewrite some paths, but that should be translatable for other servers like nginx too.) It's probably not impossible to transmit only data related to the current package while keeping this property, but recursive dependency checks in particular will not be easy. I think it's not worth the effort. -- Best regards, Ivan __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] checking CRAN incoming feasibility
On 16.01.2024 06:49, Rolf Turner wrote: On Tue, 16 Jan 2024 16:24:59 +1100 Hugh Parsonage wrote: Surely the software just has to check that there is web connection to a CRAN mirror. Nope! The full code is in tools:::.check_package_CRAN_incoming (the body of which filled up my entire console), but to name a few checks it has to do: check that the name of the package is not the same as any other, including archived packages (which means that it has to download the package metadata), make sure the licence is ok, see if the version number is ok. 10 minutes is quite a lot though. I suspect the initial connection may have been faulty. Well, it may not have been 10 minutes, but it was at least 5. The problem is persistent/repeatable. I don't believe that there is any faulty connection. Thanks for the insight. cheers, Rolf Turner I'd suggest to choose a local CRAN mirror for the checks (particularly as you are located at the most opposite side of the world from Vienna) which may help if several requests to CRAN are done. Also, you may want to disable the URL checks, which also take some time for us, but may be way more serious if you point to many URLs that do not resolve to servers in your part of the world. Best, Uwe Ligges __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] checking CRAN incoming feasibility
If I understand correctly, the current procedure is that the client downloads every package name from CRAN, and then checks its name is unique. Wouldn’t it be faster (for both parties) to check name uniqueness directly on the server? Writing: wyclif.substack.com Book: www.wyclifsdust.com On Tue, 16 Jan 2024 at 05:25, Hugh Parsonage wrote: > > Surely the software just has to check > that there is web connection to a CRAN mirror. > > Nope! The full code is in tools:::.check_package_CRAN_incoming (the > body of which filled up my entire console), but to name a few checks > it has to do: check that the name of the package is not the same as > any other, including archived packages (which means that it has to > download the package metadata), make sure the licence is ok, see if > the version number is ok. 10 minutes is quite a lot though. I suspect > the initial connection may have been faulty. > > On Tue, 16 Jan 2024 at 16:15, Rolf Turner wrote: > > > > > > This post essentially amounts to idle curiosity. I don't really expect > > that anything can be done about the problem that I perceive. > > > > When I check a package using --as-cran, the code spits out a line > > > > checking CRAN incoming feasibility ... > > > > and then disappears into a black hole for what seems an eternity (5 or > > 10 minutes). > > > > Why does this step take so long? Surely the software just has to check > > that there is web connection to a CRAN mirror. I would have thought > > that this would be executed virtually instantaneously. > > > > cheers, > > > > Rolf Turner > > > > -- > > Honorary Research Fellow > > Department of Statistics > > University of Auckland > > Stats. Dep't. (secretaries) phone: > > +64-9-373-7599 ext. 89622 > > Home phone: +64-9-480-4619 > > > > __ > > 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 > [[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] checking CRAN incoming feasibility
В Tue, 16 Jan 2024 05:49:01 +
Rolf Turner пишет:
> The problem is persistent/repeatable. I don't believe that there is
> any faulty connection.
One of the things done by R CMD check --as-cran at this point is
sending a HEAD request to every Web link mentioned in the package
documentation and DESCRIPTION. One of the hosts may be slow to respond,
either by accident or due to misguided anti-robot countermeasures.
(Most website protection systems would say that R CMD check counts as a
robot because there's no human behind it to look at the ads.)
Here's what you could try. Unpack your built source package. If you
have a fresh .Rcheck directory from an R CMD check, use
YOURPACKAGE.Rcheck/00_pkg_src/YOURPACKAGE. Then profile the check
function, using the subdirectory from the source package archive as the
argument:
Rprof(); tools:::.check_package_CRAN_incoming(dir); Rprof('NULL')
Does any one function stand out in the subsequent summaryRprof()
output? For me, it's readRDS (not very helpful), but by reading
Rprof.out I can see that it's used by CRAN_package_db and
CRAN_archive_db to download web/packages/packages.rds and
src/contrib/Meta/archive.rds from the chosen CRAN mirror, which for me
takes a few seconds for both files.
Do you have a CRAN mirror set up in ~/.Rprofile? It could be having a
slow day.
--
Best regards,
Ivan
__
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Re: [R-pkg-devel] checking CRAN incoming feasibility
On Tue, 16 Jan 2024 16:24:59 +1100 Hugh Parsonage wrote: > > Surely the software just has to check > that there is web connection to a CRAN mirror. > > Nope! The full code is in tools:::.check_package_CRAN_incoming (the > body of which filled up my entire console), but to name a few checks > it has to do: check that the name of the package is not the same as > any other, including archived packages (which means that it has to > download the package metadata), make sure the licence is ok, see if > the version number is ok. 10 minutes is quite a lot though. I suspect > the initial connection may have been faulty. Well, it may not have been 10 minutes, but it was at least 5. The problem is persistent/repeatable. I don't believe that there is any faulty connection. Thanks for the insight. cheers, Rolf Turner -- Honorary Research Fellow Department of Statistics University of Auckland Stats. Dep't. (secretaries) phone: +64-9-373-7599 ext. 89622 Home phone: +64-9-480-4619 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] checking CRAN incoming feasibility
> Surely the software just has to check that there is web connection to a CRAN mirror. Nope! The full code is in tools:::.check_package_CRAN_incoming (the body of which filled up my entire console), but to name a few checks it has to do: check that the name of the package is not the same as any other, including archived packages (which means that it has to download the package metadata), make sure the licence is ok, see if the version number is ok. 10 minutes is quite a lot though. I suspect the initial connection may have been faulty. On Tue, 16 Jan 2024 at 16:15, Rolf Turner wrote: > > > This post essentially amounts to idle curiosity. I don't really expect > that anything can be done about the problem that I perceive. > > When I check a package using --as-cran, the code spits out a line > > checking CRAN incoming feasibility ... > > and then disappears into a black hole for what seems an eternity (5 or > 10 minutes). > > Why does this step take so long? Surely the software just has to check > that there is web connection to a CRAN mirror. I would have thought > that this would be executed virtually instantaneously. > > cheers, > > Rolf Turner > > -- > Honorary Research Fellow > Department of Statistics > University of Auckland > Stats. Dep't. (secretaries) phone: > +64-9-373-7599 ext. 89622 > Home phone: +64-9-480-4619 > > __ > 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-pkg-devel] checking CRAN incoming feasibility
This post essentially amounts to idle curiosity. I don't really expect that anything can be done about the problem that I perceive. When I check a package using --as-cran, the code spits out a line checking CRAN incoming feasibility ... and then disappears into a black hole for what seems an eternity (5 or 10 minutes). Why does this step take so long? Surely the software just has to check that there is web connection to a CRAN mirror. I would have thought that this would be executed virtually instantaneously. cheers, Rolf Turner -- Honorary Research Fellow Department of Statistics University of Auckland Stats. Dep't. (secretaries) phone: +64-9-373-7599 ext. 89622 Home phone: +64-9-480-4619 __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] checking CRAN incoming feasibility NOTE
On Sat, 5 Oct 2019 16:52:16 -0500 "R. Mark Sharp" wrote: > MIT + file LICENSE > File 'LICENSE': > Copyright 2017-2019 R. Mark Sharp > > Permission is hereby granted, <...> Note that for packages licensed under MIT license, the LICENSE file should only contain the lines: >> YEAR: 2019 >> COPYRIGHT HOLDER: R. Mark Sharp and not the actual text of MIT license. See [*] for more info. -- Best regards, Ivan [*] https://www.r-project.org/Licenses/MIT __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] checking CRAN incoming feasibility NOTE
Roy, Thank you for your guidance and advice. I ran usethis::use_cran_comments() shown below. > usethis::use_cran_comments() ✔ Setting active project to '/Users/msharp/Documents/Development/R/r_workspace/library/nprcmanager' ✔ Writing 'cran-comments.md' ✔ Adding '^cran-comments\\.md$' to '.Rbuildignore' ● Modify 'cran-comments.md’ The text of “cran-comments.md” follows and also makes me think it was a clean inspection: ## Test environments * local OS X install, R 3.6.1 * ubuntu 14.04 (on travis-ci), R 3.6.1 * win-builder (devel and release) ## R CMD check results 0 errors | 0 warnings | 1 note * This is a new release. R. Mark Sharp, Ph.D. Data Scientist and Biomedical Statistical Consultant 7526 Meadow Green St. San Antonio, TX 78251 mobile: 210-218-2868 rmsh...@me.com > On Oct 5, 2019, at 5:10 PM, Roy Mendelssohn - NOAA Federal > wrote: > > use this::use_cran_comments() > > There is a place to put that it is a new submission > > I would recommend also testing using: > > devtools::check_win_release() > devtools::check_win_devel() > > You should only have the one note that it is a new submission. When you > submit, you may or may not get a note that it was rejected by the automatic > checker. Sit tight, someone from CRAN will see that it is a new submission. > A new submission is given a much more thorough review, so it can take a > coupe days or more for CRAN to get back to you. You can check the status of > CRAN submissions at: > > https://cransays.itsalocke.com/articles/dashboard.html > > HTH, > > -Roy > > >> On Oct 5, 2019, at 2:52 PM, R. Mark Sharp wrote: >> >> I getting ready to submit a package to CRAN for the first time. I have run >> cran_prep <- check_for_cran() using the rhub package. I understand that as a >> new package it will generate a NOTE. As a novice, I do not know what is to >> be expected within that NOTE and want to make sure the NOTEs I have received >> are satisfactory. I have not found an example of a minimal first submission >> NOTE. Below is what I am getting from the above test on rhub. I have three >> test environments but only two NOTEs. Do these results indicate a problem to >> be addressed? >> >>> cran_prep$cran_summary() >> For a CRAN submission we recommend that you fix all NOTEs, WARNINGs and >> ERRORs. >> ## Test environments >> - R-hub windows-x86_64-devel (r-devel) >> - R-hub ubuntu-gcc-release (r-release) >> - R-hub fedora-clang-devel (r-devel) >> >> ## R CMD check results >> ❯ On windows-x86_64-devel (r-devel), ubuntu-gcc-release (r-release) >> checking CRAN incoming feasibility ... NOTE >> Maintainer: 'R. Mark Sharp ' >> >> New submission >> >> License components with restrictions and base license permitting such: >> MIT + file LICENSE >> File 'LICENSE': >> Copyright 2017-2019 R. Mark Sharp >> >> Permission is hereby granted, free of charge, to any person obtaining a >> copy of this software and associated documentation files (the "Software"), >> to deal in the Software without restriction, including without limitation >> the rights to use, copy, modify, merge, publish, distribute, sublicense, >> and/or sell copies of the Software, and to permit persons to whom the >> Software is furnished to do so, subject to the following conditions: >> >> The above copyright notice and this permission notice shall be included in >> all copies or substantial portions of the Software. >> >> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR >> IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, >> FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE >> AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER >> LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING >> FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS >> IN THE SOFTWARE. >> >> ❯ On fedora-clang-devel (r-devel) >> checking CRAN incoming feasibility ...NB: need Internet access to use CRAN >> incoming checks >> NOTE >> Maintainer: ‘R. Mark Sharp ’ >> >> License components with restrictions and base license permitting such: >> MIT + file LICENSE >> File 'LICENSE': >> Copyright 2017-2019 R. Mark Sharp >> >> Permission is hereby granted, free of charge, to any person obtaining a >> copy of this software and associated documentation files (the "Software"), >> to deal in the Software without restriction, including without limitation >> the rights to use, copy, modify, merge, publish, distribute, sublicense, >> and/or sell copies of the Software, and to permit persons to whom the >> Software is furnished to do so, subject to the following conditions: >> >> The above copyright notice and this permission notice shall be included in >> all copies or substantial portions of the Software. >> >> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR >> IMPLIED, INCLUDING BUT NOT LIMITED TO
Re: [R-pkg-devel] checking CRAN incoming feasibility NOTE
use this::use_cran_comments() There is a place to put that it is a new submission I would recommend also testing using: devtools::check_win_release() devtools::check_win_devel() You should only have the one note that it is a new submission. When you submit, you may or may not get a note that it was rejected by the automatic checker. Sit tight, someone from CRAN will see that it is a new submission. A new submission is given a much more thorough review, so it can take a coupe days or more for CRAN to get back to you. You can check the status of CRAN submissions at: https://cransays.itsalocke.com/articles/dashboard.html HTH, -Roy > On Oct 5, 2019, at 2:52 PM, R. Mark Sharp wrote: > > I getting ready to submit a package to CRAN for the first time. I have run > cran_prep <- check_for_cran() using the rhub package. I understand that as a > new package it will generate a NOTE. As a novice, I do not know what is to be > expected within that NOTE and want to make sure the NOTEs I have received are > satisfactory. I have not found an example of a minimal first submission NOTE. > Below is what I am getting from the above test on rhub. I have three test > environments but only two NOTEs. Do these results indicate a problem to be > addressed? > >> cran_prep$cran_summary() > For a CRAN submission we recommend that you fix all NOTEs, WARNINGs and > ERRORs. > ## Test environments > - R-hub windows-x86_64-devel (r-devel) > - R-hub ubuntu-gcc-release (r-release) > - R-hub fedora-clang-devel (r-devel) > > ## R CMD check results > ❯ On windows-x86_64-devel (r-devel), ubuntu-gcc-release (r-release) > checking CRAN incoming feasibility ... NOTE > Maintainer: 'R. Mark Sharp ' > > New submission > > License components with restrictions and base license permitting such: >MIT + file LICENSE > File 'LICENSE': >Copyright 2017-2019 R. Mark Sharp > >Permission is hereby granted, free of charge, to any person obtaining a > copy of this software and associated documentation files (the "Software"), to > deal in the Software without restriction, including without limitation the > rights to use, copy, modify, merge, publish, distribute, sublicense, and/or > sell copies of the Software, and to permit persons to whom the Software is > furnished to do so, subject to the following conditions: > >The above copyright notice and this permission notice shall be included in > all copies or substantial portions of the Software. > >THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE > SOFTWARE. > > ❯ On fedora-clang-devel (r-devel) > checking CRAN incoming feasibility ...NB: need Internet access to use CRAN > incoming checks > NOTE > Maintainer: ‘R. Mark Sharp ’ > > License components with restrictions and base license permitting such: >MIT + file LICENSE > File 'LICENSE': >Copyright 2017-2019 R. Mark Sharp > >Permission is hereby granted, free of charge, to any person obtaining a > copy of this software and associated documentation files (the "Software"), to > deal in the Software without restriction, including without limitation the > rights to use, copy, modify, merge, publish, distribute, sublicense, and/or > sell copies of the Software, and to permit persons to whom the Software is > furnished to do so, subject to the following conditions: > >The above copyright notice and this permission notice shall be included in > all copies or substantial portions of the Software. > >THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR > IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, > FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE > AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE > SOFTWARE. > > 0 errors ✔ | 0 warnings ✔ | 2 notes ✖ >> > R. Mark Sharp, Ph.D. > Data Scientist and Biomedical Statistical Consultant > 7526 Meadow Green St. > San Antonio, TX 78251 > mobile: 210-218-2868 > rmsh...@me.com > > __ > R-package-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-package-devel ** "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
