Re: [R-pkg-devel] Failed CRAN tar.gz upload to CRAN
Hi Ivan, The submit button has worked You are right that it is counterintuitive and I have been well trained not to submit things to CRAN that contain errors :-) I agree that something like "Package uploaded" would be better than "No file chosen" in Stage 2, afterall I have chosen a file. Thanks very much for your help. All's well that ends well. Cheers, Chris > -Original Message- > From: Ivan Krylov > Sent: Saturday, 14 January 2023 8:45 AM > To: Chris Brien > Cc: r-package-devel@r-project.org > Subject: Re: [R-pkg-devel] Failed CRAN tar.gz upload to CRAN > > CAUTION: External email. Only click on links or open attachments from > trusted senders. > > On Fri, 13 Jan 2023 21:51:01 + > Chris Brien wrote: > > > the package files is being dropped as well. It replaces my file name > > with "No file chosen". Consequently I cannot continue submit the > > package. > > I understand that this behaviour is counter-intuitive, but that seems to be > the way it's supposed to work. Package submission is a multi-step > process: > > Step 1 involves providing your name, your e-mail address and the package > file. Once uploaded, the package file stays somewhere at CRAN, at least for a > while. > > Step 2 involves making sure that you've uploaded the right package. > You're shown your name, e-mail address, the optional comment and the > fields from the DESCRIPTION file. The "Package:" file upload field should be > empty because CRAN already has a copy of the file. > > Pressing the "Re-upload the package/Edit information" will repeat the step 1 > and take you back to the same place, just before the step 2. In order to > progress, you need to press the "Submit package" button below the form, > despite the "Package:" file upload field is empty. > > Do the "Title:", "Description:", "Authors(s):" fields contain the information > for > your package? Does the "Submit package" button work for you? Are there > any other messages there? > > Perhaps the CRAN submission form should show some indication that the file > has been uploaded near the file entry field during step 2? > > -- > Best regards, > Ivan __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Failed CRAN tar.gz upload to CRAN
On Fri, 13 Jan 2023 21:51:01 + Chris Brien wrote: > the package files is being dropped as well. It replaces my file name > with "No file chosen". Consequently I cannot continue submit the > package. I understand that this behaviour is counter-intuitive, but that seems to be the way it's supposed to work. Package submission is a multi-step process: Step 1 involves providing your name, your e-mail address and the package file. Once uploaded, the package file stays somewhere at CRAN, at least for a while. Step 2 involves making sure that you've uploaded the right package. You're shown your name, e-mail address, the optional comment and the fields from the DESCRIPTION file. The "Package:" file upload field should be empty because CRAN already has a copy of the file. Pressing the "Re-upload the package/Edit information" will repeat the step 1 and take you back to the same place, just before the step 2. In order to progress, you need to press the "Submit package" button below the form, despite the "Package:" file upload field is empty. Do the "Title:", "Description:", "Authors(s):" fields contain the information for your package? Does the "Submit package" button work for you? Are there any other messages there? Perhaps the CRAN submission form should show some indication that the file has been uploaded near the file entry field during step 2? -- Best regards, Ivan __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Failed CRAN tar.gz upload to CRAN
Hi Ivan, Thanks for taking up my query. I realized after I sent the message that I should have added that the package files is being dropped as well. It replaces my file name with "No file chosen". Consequently I cannot continue submit the package. I saw it as an error message because it is not a message that I have seen in the many times that I have uploaded a package to CRAN. My interpretation of the message was that there is some "non-editable" material in the package information, most likely the DESCRIPTION file. However, I doubted that this could be the case because the only changes in the DESCRIPTION file since I uploaded Version 2.1.16 two months ago are in the Version, Date, Packaged and Suggests, the latter having writeXLS removed because it is no longer needed. I have verified that these are the only changed by extracting the DESCRIPTION file from both growthPheno_2.1.16 and 2.1.17 and doing a file comparison on them. This led me to think that the problem must be in other than the DESCRIPTION file. Unfortunately, I remain unable to upload the package. Cheers, Chris > -Original Message- > From: Ivan Krylov > Sent: Saturday, 14 January 2023 12:37 AM > To: Chris Brien > Cc: r-package-devel@r-project.org > Subject: Re: [R-pkg-devel] Failed CRAN tar.gz upload to CRAN > > CAUTION: External email. Only click on links or open attachments from > trusted senders. > > В Fri, 13 Jan 2023 08:54:50 + > Chris Brien пишет: > > > I am getting the following response when I try to upload > > growthPheno_2.1.17.tar.gz: > > > > Detected package information [non-editable] In case of errors reupload > > the package or contact cran team > > That's not an error. This message is to inform you that the following fields > have been extracted from your DESCRIPTION file and aren't supposed to be > edited by hand. Is there a better way to phrase that? > > Do you see anything out of place in the form? If the form content seems OK, > click the "Submit package" button near the bottom of the page to continue. > > -- > Best regards, > Ivan __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [Rd] Combinations and Permutations
On 1/13/23 4:11 AM, Serguei Sokol via R-devel wrote:
Le 13/01/2023 à 09:00, Dario Strbenac via R-devel a écrit :
Good day,
In utils, there is a function named combn. It would seem complementary
for utils to also offer permutations because of how closely
mathematically related they are to each other. Could permutations be
added to save on a package dependency if developing a package?
If you need a function returning a matrix with all permutations of a
vector x in its columns, a simple recursive one-liner can be sufficient,
no need for a whole package dependency for this:
perm=function(x) {n=length(x); f=factorial(n); if (n>1)
structure(vapply(seq_along(x), function(i) rbind(x[i], perm(x[-i])),
x[rep(1L, f)]), dim=c(n, f)) else x}
It works for all king of vectors (integer, numeric, character, ...):
perm(1:3)
perm(pi*1:3)
perm(letters[1:3])
Obviously, a particular attention should be brought to the size of x
(referred here as n) as the column number in the returned matrix growths
as n!.. E.g. 8!=40320. So growths the cpu time too.
What about "combinat::permn"?
Spencer Graves
Hoping it helps,
Serguei.
--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
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Re: [R-pkg-devel] Failed CRAN tar.gz upload to CRAN
В Fri, 13 Jan 2023 08:54:50 + Chris Brien пишет: > I am getting the following response when I try to upload > growthPheno_2.1.17.tar.gz: > > Detected package information [non-editable] > In case of errors reupload the package or contact cran team That's not an error. This message is to inform you that the following fields have been extracted from your DESCRIPTION file and aren't supposed to be edited by hand. Is there a better way to phrase that? Do you see anything out of place in the form? If the form content seems OK, click the "Submit package" button near the bottom of the page to continue. -- Best regards, Ivan __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
[R-pkg-devel] Failed CRAN tar.gz upload to CRAN
Dear list members, I am getting the following response when I try to upload growthPheno_2.1.17.tar.gz: Detected package information [non-editable] In case of errors reupload the package or contact cran team The package was successfully uploaded on 2022-11-15. It is available on https://github.com/briencj/growthPheno. I have scoured the DESCRIPTION file and compared it with the DESCRIPTION file for dae, another of my packages that has been successfully uploaded in the last 12 hours. I have run R CMD --as-cran growthPheno_2.1.17.tar.gz with the final status being OK. I am stumped as to what is causing the problem. Can anyone throw any lot on what the problem might be? Thanks in advance, Cheers, Chris Chris Brien | Senior Biostatistician Australian Plant Phenomics Facility __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [Bioc-devel] BiocCredentials Account Activation
Generally Bioconductor does not allow more than one maintainer. Please consider the need for multiple maintainers. Since the change has been pushed up and I see it in the Bioconductor git repository we can assist with allowing access. Simply updating the DESCRIPTION file for a maintainer does not automatically give a maintainer push access to the repository. It must be requested here so we can map the access to a BiocCredentials account. We will need to create a BiocCredentials account for you to manage ssh keys. I will contact you off list to obtain necessary information. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Quirin Manz Sent: Friday, January 13, 2023 2:52 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] BiocCredentials Account Activation Dear Bioconductor Team, Recently, I have been added to the DeepBlueR Bioconductor package as a maintainer. Unfortunately, I still cannot activate my account at https://secure-web.cisco.com/1kgMs1L1h7uEhy2ZwsViFeR2nGZ1GwBf8URN10Rv71eI1ny4oMBe47MpRw120gYLY1ydbuw8YyqMQof3nMGYd2cZlWk2piR1ZWlSbivmd6F0ezN0G8p1bEuNYwTUXnvvQwu1RGZ8r6nHIIFRhFYp62SLXtYDQT1lZPzjTRq83W9cWWdN1kN3-17fJTuNazjBcWaTGW9aKVIgi3DxJefdLOVx0SWdLmZq5GtToVRT6dcY2vHpeOd0TCI7BLeMgYPGq27HltazyfrLNQvSnbUJjAYI9KdZPhZiuIK0aB3r6kRq6V2aDrokWcPGktHPK1QCl/https%3A%2F%2Fgit.bioconductor.org%2FBiocCredentials%2Faccount_activation%2F It gives the following error message: quirin.m...@tum.de is not associated with a maintainer of a Bioconductor package. Please check the spelling or contact bioc-devel@r-project.org for help. On https://secure-web.cisco.com/1oUNSHikR2DayopPHrfvt6gSrEvK46jJo0VdQtrwTyke-fkIsSVZy0cr-xZqRSeU9mOJTs2KTRhDoOZPXGtIh9mdOYdw94s1MhrM1AZKdLufLraI2fGtOLIMWS761Q4Qze1am1R_LZggWfUkcqjm14AHtZjcYAhJyZujZLREpo53XQ-u7K9g4bRTJ0r8MwqWKIyIs8A4AYG5ubbJpSw7C1Zx4IyV5fr7y6maxx72xuPcFQs6z17GYizXeOakotaa4wOLW--D1WReYigWxsKeeghgStQQwQK9b47wGGZaQMKTDnYJbsTHtIdA62bkzE_0g/https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.16%2Fbioc%2Fhtml%2FDeepBlueR.html, my name and e-mail address is listed, so I assumed it should work. I appreciate any information you could give me. Best regards, Quirin Manz [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1ybwtl0vioRrZHYECg6woLQSDfeS_WgaK3SjZTFECSltgVTdCrOQPU2aAkWFLN5vJhhyol1KXLDvQ65PWXORDHpX7DCKOZL9rWL0-Q831mznCFVPIsEoWG-IwHjkB-KUq-KwniHuImsivBP97rWMm9m-kJWMUWy2T-3uCbVMQ1p42GRrFmTWk9VGjqgkD3gfr8ptU9qqdzO8L5npOHDjOXD6ICv0e3X0_IjBbB6U7Y3zvjsRIZh4nBFOgw1-QAt_YLjTK5FAQPXrPuqR7G7qVM0VDuoybwxFnANOwUgqAxuLY1e0hJDzbL7YZ5797ZV_-/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] BiocCredentials Account Activation
Dear Bioconductor Team, Recently, I have been added to the DeepBlueR Bioconductor package as a maintainer. Unfortunately, I still cannot activate my account at https://git.bioconductor.org/BiocCredentials/account_activation/. It gives the following error message: quirin.m...@tum.de is not associated with a maintainer of a Bioconductor package. Please check the spelling or contact bioc-devel@r-project.org for help. On https://bioconductor.org/packages/3.16/bioc/html/DeepBlueR.html, my name and e-mail address is listed, so I assumed it should work. I appreciate any information you could give me. Best regards, Quirin Manz [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Rd] Combinations and Permutations
Le 13/01/2023 à 09:00, Dario Strbenac via R-devel a écrit :
Good day,
In utils, there is a function named combn. It would seem complementary for
utils to also offer permutations because of how closely mathematically related
they are to each other. Could permutations be added to save on a package
dependency if developing a package?
If you need a function returning a matrix with all permutations of a
vector x in its columns, a simple recursive one-liner can be sufficient,
no need for a whole package dependency for this:
perm=function(x) {n=length(x); f=factorial(n); if (n>1)
structure(vapply(seq_along(x), function(i) rbind(x[i], perm(x[-i])),
x[rep(1L, f)]), dim=c(n, f)) else x}
It works for all king of vectors (integer, numeric, character, ...):
perm(1:3)
perm(pi*1:3)
perm(letters[1:3])
Obviously, a particular attention should be brought to the size of x
(referred here as n) as the column number in the returned matrix growths
as n!.. E.g. 8!=40320. So growths the cpu time too.
Hoping it helps,
Serguei.
--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
__
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__
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Re: [Rd] rhub vs. CRAN fedora-*-devel, using armadillo & slapack
The CRAN check on fedora gives me more detailed results now:
https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/rlibkriging-00check.html
.
It points a fairly strange issue (possibly due to recursive programming, that
remains to investigate), but anyway I can now circumvent the problem for CRAN.
In next "true" release, I will try to switch back to a testthat suitable
reporter instead of the enumerated tests in tests/, as you suggested.
So, thank you very much to all of you for your kind help and suggestions.
Yann & libKriging team.
-Message d'origine-
De : Duncan Murdoch
Envoyé : jeudi 12 janvier 2023 10:07
À : RICHET Yann ; Sebastian Meyer ; Ivan
Krylov
Cc : Pascal Havé ; R-devel@r-project.org
Objet : Re: [Rd] rhub vs. CRAN fedora-*-devel, using armadillo & slapack
On 12/01/2023 2:51 a.m., RICHET Yann wrote:
> Well, I tried to move the tests outside testthat.R logic, because I expect
> that CRAN output will not give me the reporter results... and as I
> re-submitted the package, I wanted to ensure readable result. But maybe I am
> wrong about that... ?
I think CRAN output will only show you the reporter results if there's an
error. If it's a regular error, you get the last 13 lines. From your earlier
posting, it looks as though a timeout might give more. But even the last 13
lines should identify exactly which test was running when the timeout happened.
I probably wouldn't use the location reporter for routine runs, because it will
give a lot of output, and conceivably this will slow things down.
Duncan Murdoch
>
>
> -Message d'origine-
> De : Duncan Murdoch Envoyé : mercredi 11
> janvier 2023 19:09 À : RICHET Yann ; Sebastian
> Meyer ; Ivan Krylov Cc :
> Pascal Havé ; R-devel@r-project.org Objet : Re:
> [Rd] rhub vs. CRAN fedora-*-devel, using armadillo & slapack
>
> On 11/01/2023 12:35 p.m., RICHET Yann wrote:
>> Thank you all, for these advices.
>>
>> So I try to fix OMP_THREADS, cleanup tests, and display explicitly what test
>> is running by moving in tests/ instead of tests/testthat/...
>> Next step should be to investigate blocking test using a reporter (maybe
>> "list").
>> For now, waiting for CRAN results...
>
> I think Sebastian or my suggestion is easier than redoing all of your tests.
> They are each one line changes.
>
> Duncan Murdoch
>
>>
>> Yann
>>
>> -Message d'origine-
>> De : Duncan Murdoch Envoyé : mercredi 11
>> janvier 2023 00:36 À : Sebastian Meyer ; Ivan
>> Krylov ; RICHET Yann Cc
>> : Pascal Havé ; R-devel@r-project.org Objet :
>> Re: [Rd] rhub vs. CRAN fedora-*-devel, using armadillo & slapack
>>
>> On 10/01/2023 4:07 p.m., Sebastian Meyer wrote:
>>> Am 10.01.23 um 21:28 schrieb Duncan Murdoch:
On 10/01/2023 2:05 p.m., Ivan Krylov wrote:
> On Tue, 10 Jan 2023 16:27:53 + RICHET Yann
> wrote:
>
>> In facts, 10 threads are asked by armadillo for some LinAlg,
>> which backs to two threads as warned.
>
> I think you're right about your tests de-facto using two threads,
> but it might be a good idea to _default_ to up to two threads in
> tests and examples. This is especially valuable for third-party
> developers who have to mass-test packages (one of which could be
> rlibkriging) in parallel.
>
>> - is there any reason that could explain that fedora-*-devel is
>> so slow for this package or compilation of Rcpp/testthat ?
>
> Compilation time is definitely not the reason. Something in
> tests/* actually runs for 30 minutes by itself.
>
>> - is there any chance that I can get a deeper log of what happened ?
>
> If you split your tests into separate files under tests/*.R
> instead of using a single tests/testthat.R calling the rest of the
> tests, R will be able to show you the individual test file that
> hung and maybe the line where it happened. (Also, you'll get
> per-file
> timing.) But that is potentially a huge investment: you may have
> to rewrite the tests to work outside the testthat harness, and
> you'd also have to prepare another CRAN submission just to have
> those tests run. It's also against CRAN policy to knowingly submit a
> package with unfixed ERRORs.
>
> (Currently, R can only tell you that the tests hung in the
> test_check('rlibkriging') call in the tests/testthat.R, which
> isn't precise enough.)
You can specify a different "reporter" in the test_check() call,
and it will print more useful information. I don't think there's a
perfect one, but
test_check('rlibkriging', reporter = "progress")
should at least show you the tests that finished running before the
timeout.
>>>
>>> I had similar problems with testthat and timeouts when mass-checking
>>> packages on patched R versions. My notes say
>>>
## testthat's 'LocationReporter' does cat() after each
[Rd] Combinations and Permutations
Good day, In utils, there is a function named combn. It would seem complementary for utils to also offer permutations because of how closely mathematically related they are to each other. Could permutations be added to save on a package dependency if developing a package? -- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
