Re: [Bioc-devel] Unit tests
There are multiple examples of unit tests for parsers. In your case I would include a small BAM file in /inst/extdata and make a test which parses this file and asserts a number of things about the output. Depending on philosophy, this may not be considered a pure unit test, but it is very useful. If the BAM file gets too big if its going to be "interesting" we have in the past released experiment data packages with testing data; this has usually been done for packages which read multiple different files. Examples are IlluminaDataTestFiles and AffymetrixDataTestFiles (for parsing microarray data) On Thu, Mar 23, 2017 at 10:37 PM, Dan Tenenbaum wrote: > Here's what BiocCheck says: > > Consider adding unit tests. We strongly encourage them. See > http://bioconductor.org/developers/how-to/unitTesting-guidelines/ > > So, unit tests are encouraged but not required. > Dan > > > - Original Message - > > From: "张腾" <2573552...@qq.com> > > To: "bioc-devel" > > Sent: Thursday, March 23, 2017 7:33:22 PM > > Subject: [Bioc-devel] Unit tests > > > Hello all, > > > > I am not sure whether the Unit tests are necessary to release a package > for > > Bioconductor. In my package, only one main function to export and other > > functions are hidden into the main function. In my package, the input > data are > > some files in BAM format and the output is a report in HTML format. So I > want > > to know if the unit tests are very important and necessary for releasing > a > > package. If it is necessary, how can I add these tests to my package in > this > > special input and output situation? > > > > Can anyone help me solve this problem? Thank you very much > > [[alternative HTML version deleted]] > > > > ___ > > Bioc-devel@r-project.org mailing list > > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat. > ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r= > TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo&m=- > y21Sirq2bdhul9Ar8vnDiy_LjASe_ND5ozxWVwudWw&s=Wroy1VJao_ > ttDgKZZY7vOApZkTTauP_S8kAgYTs6jo4&e= > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Unit tests
Here's what BiocCheck says: Consider adding unit tests. We strongly encourage them. See http://bioconductor.org/developers/how-to/unitTesting-guidelines/ So, unit tests are encouraged but not required. Dan - Original Message - > From: "张腾" <2573552...@qq.com> > To: "bioc-devel" > Sent: Thursday, March 23, 2017 7:33:22 PM > Subject: [Bioc-devel] Unit tests > Hello all, > > I am not sure whether the Unit tests are necessary to release a package for > Bioconductor. In my package, only one main function to export and other > functions are hidden into the main function. In my package, the input data are > some files in BAM format and the output is a report in HTML format. So I want > to know if the unit tests are very important and necessary for releasing a > package. If it is necessary, how can I add these tests to my package in this > special input and output situation? > > Can anyone help me solve this problem? Thank you very much > [[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo&m=-y21Sirq2bdhul9Ar8vnDiy_LjASe_ND5ozxWVwudWw&s=Wroy1VJao_ttDgKZZY7vOApZkTTauP_S8kAgYTs6jo4&e= ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Unit tests
Hello all, I am not sure whether the Unit tests are necessary to release a package for Bioconductor. In my package, only one main function to export and other functions are hidden into the main function. In my package, the input data are some files in BAM format and the output is a report in HTML format. So I want to know if the unit tests are very important and necessary for releasing a package. If it is necessary, how can I add these tests to my package in this special input and output situation? Can anyone help me solve this problem? Thank you very much [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] questions about windows build execute permissions and R version dependency
Thanks for the clarification! I will ignore these warnings.
-Alicia
On Thu, Mar 23, 2017 at 7:36 AM Leonardo Collado Torres
wrote:
You can also test your package on R Travis against R 3.4 as shown at
https://travis-ci.org/leekgroup/recount#L518. Just use this on your
.travis.yml file
https://github.com/leekgroup/recount/blob/master/.travis.yml#L3
On Thu, Mar 23, 2017 at 4:26 AM, Martin Morgan
wrote:
> On 03/22/2017 11:08 PM, Alicia Schep wrote:
>>
>> Hi,
>>
>> I have a two questions about the bioconductor build and BiocCheck process
>> when submitting packages.
>>
>> 1) My submitted package ('motifmatchr') returns the following warning on
>> the Windows computer:
>>
>> Warning: file 'motifmatchr/cleanup' did not have execute permissions:
>> corrected
>>
>> How can this warning be averted? How to give the file permission? I
tried
>> fixing this issue by making the file executable on my computer-- on
GitHub
>> it shows up as marked as "Executable File". This did not prevent the
>> warning though.
>
>
> It seems like you've done the right thing and R is mistaken. It's also
> irrelevant, since you have a cleanup.win file that supersedes cleanup.
> Ignore the warning.
>
>> 2) The same package also gives a warning in BiocCheck related to the
>> version of R required in DESCRIPTION. As the package is currently hosted
>> on GitHub and tested against the current release of R using travis, I
>> would
>> like the github version to have a dependency of only R 3.3 rather than R
>> 3.4. Is it possible to have a different dependency for the R version on
>> GitHub versus on Bioconductor?
>
>
> Certainly anything is possible, e.g., creating a release branch on github
> with a different dependency, but again I'd suggest evaluating whether the
> warning is relevant in your situation, and if not ignoring it.
>
> From the Bioconductor perspective, the fact that your package builds on
> travis under an earlier version of R is unknown, so the assertion that it
> only requires R-3.3 is not supportable -- the warning tries to bring your
> version requirements into line with what we know to be true. Of course the
> assertion that it depends on a version of R > 3.4 is also not supportable.
>
> Martin
>
>>
>> Appreciate any guidance on these question. Thanks,
>>
>> Alicia
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> This email message may contain legally privileged and/or...{{dropped:2}}
>
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] xps build problem on veracruz2
- Original Message - > From: "Hervé Pagès" > To: "cstrato" , "bioc-devel" > Sent: Thursday, March 23, 2017 12:14:38 PM > Subject: Re: [Bioc-devel] xps build problem on veracruz2 > On 03/23/2017 11:09 AM, cstrato wrote: >> Dear Herve, >> >> Thank you for your explanation. >> >> The reason that xps does not work with ROOT 6 is that I have tried it >> but there seem to be so many changes, that I did not succeed. >> Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5 >> was still supported, I have decided to stay with ROOT 5. > > OK > >> >> BTW, I have also one question: >> Why did you decide to set up a new Mac with El Capitan instead of using >> the newest OS Sierra? (I have the impression that most Mac users are >> either happy to stay with their old OS or they upgrade to the newest one.) > > Same reason as for the choice of compilers: that's what the R folks > decided to use for producing the Mac binaries of R and CRAN packages. > We're just following their lead on that. > Also, it's always good not to require users to upgrade if they don't have to. Building on El Capitan means users will not have to upgrade to macOS Sierra if they don't want to. Building on Sierra would mean R and packages would not be backwards-compatible with El Capitan. But it's a tradeoff that also involves the difficulty of maintaining build machines with old OSes, and wanting to take advantage of newer compiler technology. Otherwise R/Bioc would still be building on Mavericks, or Snow Leopard... Dan > Cheers, > H. > >> >> Best regards, >> Christian >> >> >> On 03/23/17 17:47, Hervé Pagès wrote: >>> Hi Christian, >>> >>> The CRAN folks are currently experimenting with clang 4.0.0 for >>> producing the Mac binaries of R and CRAN packages so we are using >>> the same on veracruz2. This is a version of clang that is ahead of >>> what's in XCode 8.x or XCode 7.x. So I guess that means we'll have >>> to compile ROOT from source on veracruz2. >>> >>> BTW any reason not to make xps work with ROOT 6? >>> >>> Cheers, >>> H. >>> >>> On 03/23/2017 07:28 AM, cstrato wrote: Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw&e= The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l:cstrato at aon.at _._._._._._._._._._._._._._._._._._ ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=0bNMm-aoHuwWs9yBRjyGHTxT0y3UceNADHgMjtosTWU&e= >>> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax:(206) 667-1319 > > ___ > Bioc-devel@r-project.org mailing list > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=TF6f93hjWmgMzjqP9F3thRifibmFvfjc5Ae-bzNwDGo&m=WB1ofcLb-W4SN6VNAgoSRdgRXQRPaelptAH2g0Ur7q8&s=IDfsJGqV_D7hzqLryd27eoZNIuiAIfSNATUnxMy61oo&e= ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Incorrect order of installing dependencies on OS X in bioc-devel in travis
Herve, thanks! It seems I got it: there are no r-devel binaries for RSQLite (https://cran.r-project.org/web/packages/RSQLite/index.html) so it's installed from the sources as reactome.db, but not as AnnotationDbi. That's why the installer doesn't know about dependency between reactome.db and RSQLite. And this doesn't happen in bioc-release, because there is the corresponding binary RSQLite package. I understand that it's not specific to Bioconductor and is more appropriate for r-devel list, right? -- Alexey On Fri, Mar 24, 2017 at 1:14 AM, Hervé Pagès wrote: > Hi Alexey, > > Based on the Travis build report, it looks like Travis used > install.packages() to install reactome.db. > What makes you think it used biocLite()? > > The problem seems to be related to the fact that reactome.db > deps are divided in 2 groups: binary packages on one side and > source packages on the other side. The installation procedure > seems to treat each group separately and independently: binary > packages first, and then source packages. This is flawed design > to me, even if the "testing if installed package can be loaded" > step is skipped when installing a binary package, which seems > like an ostrich strategy to ignore possibly missing deps during > the process. > > What's also puzzling with this Travis build report is that > it looks like the binary packages were downloaded but not > installed! This would explain why installation of reactome.db > (source package) fails later (AnnotationDbi binary was downloaded > but not installed). Flawed design "binaries first, then source > packages" should actually work as long as (1) there is no attempt > to load binary packages immediately after their installation and > (2) the source packages are installed in topological order after > all the binary packages have been installed. > > Cheers, > H. > > > On 03/23/2017 02:14 PM, Alexey Sergushichev wrote: > >> Hello all, >> >> I'm using travis for checking my project build and found something that >> looks like a bug in how biocLite installs package dependencies. It appears >> that at some point biocLite started to install them in an alphabet order, >> not topological, and specifically on OS X. >> >> I've made a small dummy package to illustrate this: see >> https://urldefense.proofpoint.com/v2/url?u=https-3A__github. >> com_assaron_travis-2Dtest&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ& >> r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECGVqk534I_z >> BnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=aNFQogh-gU_9sSF80iI9ROXy70 >> ayZvLrkPoKYiqGPQE&e= and corresponding travis build >> https://urldefense.proofpoint.com/v2/url?u=https-3A__travis- >> 2Dci.org_assaron_travis-2Dtest&d=DwICAg&c=eRAMFD45gAfqt84VtB >> cfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECGVqk5 >> 34I_zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=Pf3mEHAtHZHCN4WlB3cb3 >> 7Y2Wf_p2v_7mT2oBQGSIow&e= . >> >> There reactome.db package should be installed but fails on osx platform in >> bioc-devel version. What happens there is reactome.db is installed before >> RSQLite, while reactome.db dependes on RSQLite via AnnotationDbi ( >> https://urldefense.proofpoint.com/v2/url?u=https-3A__travis- >> 2Dci.org_assaron_travis-2Dtest_jobs_214404313-23L630&d= >> DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0W >> YiZvSXAJJKaaPhzWA&m=ECGVqk534I_zBnZd1EBIrNR6efOzyEjt8YnPElhR >> 1DU&s=369SlWBQZQV3iA3lfRmQ2DuAuMOuMtdbMzZaB9o9LV0&e= ). Compare it >> with bioc-release version: >> https://urldefense.proofpoint.com/v2/url?u=https-3A__travis- >> 2Dci.org_assaron_travis-2Dtest_jobs_214404316-23L543&d= >> DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0W >> YiZvSXAJJKaaPhzWA&m=ECGVqk534I_zBnZd1EBIrNR6efOzyEjt8YnPElhR >> 1DU&s=chGtEiWkCYtswsgsZLMArKK67TI_MiX6sTgzLsc-v_c&e= or bioc-devel >> but on linux: https://urldefense.proofpoint. >> com/v2/url?u=https-3A__travis-2Dci.org_assaron_travis-2Dtest >> _jobs_214389446-23L928&d=DwICAg&c=eRAMFD45gAfqt84VtBcfh >> Q&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECGVqk534I >> _zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=6REbwOP9lyEopleeq2Em9yxa >> hQF6vA7iVVCkGw73Ick&e= >> >> Can anyone reproduce this behavior at their OS X machine? Is this bug in >> biocLite or Travis? >> >> Best, >> Alexey >> >> [[alternative HTML version deleted]] >> >> ___ >> Bioc-devel@r-project.org mailing list >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.et >> hz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt >> 84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=EC >> GVqk534I_zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=HC5qJ-IF0Lmc4Qob >> gJA8rfOpOHR9bWaF4MtFchvQma0&e= >> >> > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax:(206) 667-1319 > [[alternative HTML version deleted
Re: [Bioc-devel] Incorrect order of installing dependencies on OS X in bioc-devel in travis
Hi Alexey, Based on the Travis build report, it looks like Travis used install.packages() to install reactome.db. What makes you think it used biocLite()? The problem seems to be related to the fact that reactome.db deps are divided in 2 groups: binary packages on one side and source packages on the other side. The installation procedure seems to treat each group separately and independently: binary packages first, and then source packages. This is flawed design to me, even if the "testing if installed package can be loaded" step is skipped when installing a binary package, which seems like an ostrich strategy to ignore possibly missing deps during the process. What's also puzzling with this Travis build report is that it looks like the binary packages were downloaded but not installed! This would explain why installation of reactome.db (source package) fails later (AnnotationDbi binary was downloaded but not installed). Flawed design "binaries first, then source packages" should actually work as long as (1) there is no attempt to load binary packages immediately after their installation and (2) the source packages are installed in topological order after all the binary packages have been installed. Cheers, H. On 03/23/2017 02:14 PM, Alexey Sergushichev wrote: Hello all, I'm using travis for checking my project build and found something that looks like a bug in how biocLite installs package dependencies. It appears that at some point biocLite started to install them in an alphabet order, not topological, and specifically on OS X. I've made a small dummy package to illustrate this: see https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_assaron_travis-2Dtest&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECGVqk534I_zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=aNFQogh-gU_9sSF80iI9ROXy70ayZvLrkPoKYiqGPQE&e= and corresponding travis build https://urldefense.proofpoint.com/v2/url?u=https-3A__travis-2Dci.org_assaron_travis-2Dtest&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECGVqk534I_zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=Pf3mEHAtHZHCN4WlB3cb37Y2Wf_p2v_7mT2oBQGSIow&e= . There reactome.db package should be installed but fails on osx platform in bioc-devel version. What happens there is reactome.db is installed before RSQLite, while reactome.db dependes on RSQLite via AnnotationDbi ( https://urldefense.proofpoint.com/v2/url?u=https-3A__travis-2Dci.org_assaron_travis-2Dtest_jobs_214404313-23L630&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECGVqk534I_zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=369SlWBQZQV3iA3lfRmQ2DuAuMOuMtdbMzZaB9o9LV0&e= ). Compare it with bioc-release version: https://urldefense.proofpoint.com/v2/url?u=https-3A__travis-2Dci.org_assaron_travis-2Dtest_jobs_214404316-23L543&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECGVqk534I_zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=chGtEiWkCYtswsgsZLMArKK67TI_MiX6sTgzLsc-v_c&e= or bioc-devel but on linux: https://urldefense.proofpoint.com/v2/url?u=https-3A__travis-2Dci.org_assaron_travis-2Dtest_jobs_214389446-23L928&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECGVqk534I_zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=6REbwOP9lyEopleeq2Em9yxahQF6vA7iVVCkGw73Ick&e= Can anyone reproduce this behavior at their OS X machine? Is this bug in biocLite or Travis? Best, Alexey [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECGVqk534I_zBnZd1EBIrNR6efOzyEjt8YnPElhR1DU&s=HC5qJ-IF0Lmc4QobgJA8rfOpOHR9bWaF4MtFchvQma0&e= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Incorrect order of installing dependencies on OS X in bioc-devel in travis
Hello all, I'm using travis for checking my project build and found something that looks like a bug in how biocLite installs package dependencies. It appears that at some point biocLite started to install them in an alphabet order, not topological, and specifically on OS X. I've made a small dummy package to illustrate this: see https://github.com/assaron/travis-test and corresponding travis build https://travis-ci.org/assaron/travis-test. There reactome.db package should be installed but fails on osx platform in bioc-devel version. What happens there is reactome.db is installed before RSQLite, while reactome.db dependes on RSQLite via AnnotationDbi ( https://travis-ci.org/assaron/travis-test/jobs/214404313#L630). Compare it with bioc-release version: https://travis-ci.org/assaron/travis-test/jobs/214404316#L543 or bioc-devel but on linux: https://travis-ci.org/assaron/travis-test/jobs/214389446#L928 Can anyone reproduce this behavior at their OS X machine? Is this bug in biocLite or Travis? Best, Alexey [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Unit Tests & Test Coverage
Hi Juan Pablo, Thanks for adding unit tests to your package. We really encourage developers to do this. I'm sorry that this is not reflected on EventPointer's landing page. I investigated this a bit (I'm not familiar with how the coverage badges are generated on the package landing pages) and here is what I found so far. One possible reason for this is that some packages on Bioconductor-mirror are lagging behind their latest svn revision. This is actually the case right now for EventPointer. Latest svn commit is 127626: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/EventPointer but the package is still at commit 127616 on Bioconductor-mirror: https://github.com/Bioconductor-mirror/EventPointer This is a known issue. We'll try to remedy this ASAP. This can be a reason why coverage is not updated on a package landing page. That's because the script we use for computing the coverage interacts with our svn repo (on hedgehog.fhcrc.org) in order to get the latest revision of the package, but also with the Bioconductor-mirror account on github (https://github.com/Bioconductor-mirror/) in order to map the latest svn revision of a package to the corresponding git commit on Bioconductor-mirror. This seems to be needed in order to upload the coverage results to codecov.io where the coverage history is kept e.g. https://codecov.io/github/Bioconductor-mirror/VariantAnnotation/branch/master The coverage information displayed on a package landing page is coming from there. When a package is lagging behind on Bioconductor-mirror, the mapping between last svn revision and git commit fails and so uploading the coverage results to codecov.io also fails. However, in the case of EventPointer, there seems to be already 1 point in the coverage history at codecov.io: https://codecov.io/github/Bioconductor-mirror/EventPointer/branch/master It shows a coverage of about 30%. For some reason, this doesn't show up on EventPointer's landing page. I'll investigate more and will let you know. H. On 03/23/2017 04:58 AM, Romero, Juan Pablo wrote: Hi, I'm currently doing the last updates to my package EventPointer before the deadline for next BioC release. I've added unit tests according to the guide lines in https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_developers_unitTesting-2Dguidelines_&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=4xEe7s13qw8OtBMzGMqJ0vk6PIoU68FR0RJ88otY0yg&s=47DUypCrCnkcv9C1Mlybb0QHi3RLMZh57Q35XoIXkBU&e= and the package build report shows no problems for both build and check in all systems. However, the test coverage tab at top of the package page still displays "unknown" and im not sure if there is any problem with the tests or how to find possible errors. Here is what the build report shows in all OS: * checking examples ... OK * checking for unstated dependencies in �tests� ... OK * checking tests ... Running �runTests.R� OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in �inst/doc� ... OK Thanks! Best regards, Juan Pablo Romero [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=4xEe7s13qw8OtBMzGMqJ0vk6PIoU68FR0RJ88otY0yg&s=cT2EjT9BIxY3Q8Nmikk0rGfWteNuwuaDEpwNFwpjL2g&e= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] xps build problem on veracruz2
On 03/23/2017 11:09 AM, cstrato wrote: Dear Herve, Thank you for your explanation. The reason that xps does not work with ROOT 6 is that I have tried it but there seem to be so many changes, that I did not succeed. Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5 was still supported, I have decided to stay with ROOT 5. OK BTW, I have also one question: Why did you decide to set up a new Mac with El Capitan instead of using the newest OS Sierra? (I have the impression that most Mac users are either happy to stay with their old OS or they upgrade to the newest one.) Same reason as for the choice of compilers: that's what the R folks decided to use for producing the Mac binaries of R and CRAN packages. We're just following their lead on that. Cheers, H. Best regards, Christian On 03/23/17 17:47, Hervé Pagès wrote: Hi Christian, The CRAN folks are currently experimenting with clang 4.0.0 for producing the Mac binaries of R and CRAN packages so we are using the same on veracruz2. This is a version of clang that is ahead of what's in XCode 8.x or XCode 7.x. So I guess that means we'll have to compile ROOT from source on veracruz2. BTW any reason not to make xps work with ROOT 6? Cheers, H. On 03/23/2017 07:28 AM, cstrato wrote: Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw&e= The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l:cstrato at aon.at _._._._._._._._._._._._._._._._._._ ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=0bNMm-aoHuwWs9yBRjyGHTxT0y3UceNADHgMjtosTWU&e= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Bioconductor 3.5 release: deprecated packages
Sorry, xcms was a mistake on my part. This package is not deprecated. Valerie On 03/23/2017 10:06 AM, Obenchain, Valerie wrote: > Just a heads up about deprecated packages. > > These have been 'deprecated' in Biocondcutor 3.4 and will be 'defunct' > in Bioconductor 3.5. The 'defunct' status means they are removed from > the nightly builds, don't have a landing page and aren't available via > biocLite(). > > Software: > betr > > Experimental Data: > encoDnasel > ggtut > > These have been 'deprecated' in devel at some point over the past 6 > months and will appear 'deprecated' the 3.5 release. They will be > 'defunct' in the new devel, Bioconductor 3.6. > > Software: > coRNAi > networkBMA > xcms > AtlasRDF > GEOsearch > saps > mmnet > CopyNumber450k > MeSHSim > GENE.E > > Experimental Data: > CopyNumber450kData > > Feel free to contact me with any questions. > > Valerie > > > 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. > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] xps build problem on veracruz2
Dear Herve, Thank you for your explanation. The reason that xps does not work with ROOT 6 is that I have tried it but there seem to be so many changes, that I did not succeed. Since for xps there is no advantage using ROOT 6 vs ROOT 5, and ROOT 5 was still supported, I have decided to stay with ROOT 5. BTW, I have also one question: Why did you decide to set up a new Mac with El Capitan instead of using the newest OS Sierra? (I have the impression that most Mac users are either happy to stay with their old OS or they upgrade to the newest one.) Best regards, Christian On 03/23/17 17:47, Hervé Pagès wrote: Hi Christian, The CRAN folks are currently experimenting with clang 4.0.0 for producing the Mac binaries of R and CRAN packages so we are using the same on veracruz2. This is a version of clang that is ahead of what's in XCode 8.x or XCode 7.x. So I guess that means we'll have to compile ROOT from source on veracruz2. BTW any reason not to make xps work with ROOT 6? Cheers, H. On 03/23/2017 07:28 AM, cstrato wrote: Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw&e= The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l:cstrato at aon.at _._._._._._._._._._._._._._._._._._ ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=0bNMm-aoHuwWs9yBRjyGHTxT0y3UceNADHgMjtosTWU&e= ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Bioconductor 3.5 release: deprecated packages
Just a heads up about deprecated packages. These have been 'deprecated' in Biocondcutor 3.4 and will be 'defunct' in Bioconductor 3.5. The 'defunct' status means they are removed from the nightly builds, don't have a landing page and aren't available via biocLite(). Software: betr Experimental Data: encoDnasel ggtut These have been 'deprecated' in devel at some point over the past 6 months and will appear 'deprecated' the 3.5 release. They will be 'defunct' in the new devel, Bioconductor 3.6. Software: coRNAi networkBMA xcms AtlasRDF GEOsearch saps mmnet CopyNumber450k MeSHSim GENE.E Experimental Data: CopyNumber450kData Feel free to contact me with any questions. Valerie 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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] xps build problem on veracruz2
Hi Christian, The CRAN folks are currently experimenting with clang 4.0.0 for producing the Mac binaries of R and CRAN packages so we are using the same on veracruz2. This is a version of clang that is ahead of what's in XCode 8.x or XCode 7.x. So I guess that means we'll have to compile ROOT from source on veracruz2. BTW any reason not to make xps work with ROOT 6? Cheers, H. On 03/23/2017 07:28 AM, cstrato wrote: Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://urldefense.proofpoint.com/v2/url?u=https-3A__root.cern.ch_download_root-5Fv5.34.36.source.tar.gz&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=Lz7YkqZ3XwjRsYIXVTbSvbDvTM-jTyoWvoVSa1PdBDw&e= The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l:cstrato at aon.at _._._._._._._._._._._._._._._._._._ ___ Bioc-devel@r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=q9mk6yIytaNZlSdiLX_dFwchX8Tb7ra6x3WBBNIcs2o&s=0bNMm-aoHuwWs9yBRjyGHTxT0y3UceNADHgMjtosTWU&e= -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] xps build problem on veracruz2
Hi, veracruz2 is in testing / setup stage and is not the official Mac devel builder. See my post here: https://stat.ethz.ch/pipermail/bioc-devel/2017-March/010629.html Currently there are more pressing issues than the ROOT system dependency. Rest assured that ROOT will be correctly installed on veracruz2 when it becomes the official builder, as it was on toluca2 when that machine replaced oaxaca. Valerie On 03/23/2017 07:28 AM, cstrato wrote: > Dear Valerie, > > I have seen that you have set up a new Mac server, veracruz2, running El > Capitan. > > Although the development version of xps does even run on Mac OS Sierra, > one issue still remains the same: > > You need to install the latest ROOT version 5, since xps does not run > with ROOT 6! > > So you need to install on veracruz2 the same root version that you have > installed on toluca2 running Maverics, i.e. > root_v5.34.36.macosx64-10.11-clang70.dmg > > However, if you have installed on El Capitan XCode 8.x instead of XCode > 7.x, then you need to compile ROOT from source, i.e.: > https://root.cern.ch/download/root_v5.34.36.source.tar.gz > > The README file of xps does explain how to compile ROOT for Sierra. This > should also be valid for El Capitan running XCode 8.x. > > Thank you in advance. > Best regards, > Christian > _._._._._._._._._._._._._._._._._._ > C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a > V.i.e.n.n.a A.u.s.t.r.i.a > e.m.a.i.l:cstrato at aon.at > _._._._._._._._._._._._._._._._._._ > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] questions about windows build execute permissions and R version dependency
You can also test your package on R Travis against R 3.4 as shown at
https://travis-ci.org/leekgroup/recount#L518. Just use this on your
.travis.yml file
https://github.com/leekgroup/recount/blob/master/.travis.yml#L3
On Thu, Mar 23, 2017 at 4:26 AM, Martin Morgan
wrote:
> On 03/22/2017 11:08 PM, Alicia Schep wrote:
>>
>> Hi,
>>
>> I have a two questions about the bioconductor build and BiocCheck process
>> when submitting packages.
>>
>> 1) My submitted package ('motifmatchr') returns the following warning on
>> the Windows computer:
>>
>> Warning: file 'motifmatchr/cleanup' did not have execute permissions:
>> corrected
>>
>> How can this warning be averted? How to give the file permission? I tried
>> fixing this issue by making the file executable on my computer-- on GitHub
>> it shows up as marked as "Executable File". This did not prevent the
>> warning though.
>
>
> It seems like you've done the right thing and R is mistaken. It's also
> irrelevant, since you have a cleanup.win file that supersedes cleanup.
> Ignore the warning.
>
>> 2) The same package also gives a warning in BiocCheck related to the
>> version of R required in DESCRIPTION. As the package is currently hosted
>> on GitHub and tested against the current release of R using travis, I
>> would
>> like the github version to have a dependency of only R 3.3 rather than R
>> 3.4. Is it possible to have a different dependency for the R version on
>> GitHub versus on Bioconductor?
>
>
> Certainly anything is possible, e.g., creating a release branch on github
> with a different dependency, but again I'd suggest evaluating whether the
> warning is relevant in your situation, and if not ignoring it.
>
> From the Bioconductor perspective, the fact that your package builds on
> travis under an earlier version of R is unknown, so the assertion that it
> only requires R-3.3 is not supportable -- the warning tries to bring your
> version requirements into line with what we know to be true. Of course the
> assertion that it depends on a version of R > 3.4 is also not supportable.
>
> Martin
>
>>
>> Appreciate any guidance on these question. Thanks,
>>
>> Alicia
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
> This email message may contain legally privileged and/or...{{dropped:2}}
>
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] xps build problem on veracruz2
Dear Valerie, I have seen that you have set up a new Mac server, veracruz2, running El Capitan. Although the development version of xps does even run on Mac OS Sierra, one issue still remains the same: You need to install the latest ROOT version 5, since xps does not run with ROOT 6! So you need to install on veracruz2 the same root version that you have installed on toluca2 running Maverics, i.e. root_v5.34.36.macosx64-10.11-clang70.dmg However, if you have installed on El Capitan XCode 8.x instead of XCode 7.x, then you need to compile ROOT from source, i.e.: https://root.cern.ch/download/root_v5.34.36.source.tar.gz The README file of xps does explain how to compile ROOT for Sierra. This should also be valid for El Capitan running XCode 8.x. Thank you in advance. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l:cstrato at aon.at _._._._._._._._._._._._._._._._._._ ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] Unit Tests & Test Coverage
Hi, I'm currently doing the last updates to my package EventPointer before the deadline for next BioC release. I've added unit tests according to the guide lines in http://bioconductor.org/developers/unitTesting-guidelines/ and the package build report shows no problems for both build and check in all systems. However, the test coverage tab at top of the package page still displays "unknown" and im not sure if there is any problem with the tests or how to find possible errors. Here is what the build report shows in all OS: * checking examples ... OK * checking for unstated dependencies in �tests� ... OK * checking tests ... Running �runTests.R� OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in �inst/doc� ... OK Thanks! Best regards, Juan Pablo Romero [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] questions about windows build execute permissions and R version dependency
On 03/22/2017 11:08 PM, Alicia Schep wrote:
Hi,
I have a two questions about the bioconductor build and BiocCheck process
when submitting packages.
1) My submitted package ('motifmatchr') returns the following warning on
the Windows computer:
Warning: file 'motifmatchr/cleanup' did not have execute permissions: corrected
How can this warning be averted? How to give the file permission? I tried
fixing this issue by making the file executable on my computer-- on GitHub
it shows up as marked as "Executable File". This did not prevent the
warning though.
It seems like you've done the right thing and R is mistaken. It's also
irrelevant, since you have a cleanup.win file that supersedes cleanup.
Ignore the warning.
2) The same package also gives a warning in BiocCheck related to the
version of R required in DESCRIPTION. As the package is currently hosted
on GitHub and tested against the current release of R using travis, I would
like the github version to have a dependency of only R 3.3 rather than R
3.4. Is it possible to have a different dependency for the R version on
GitHub versus on Bioconductor?
Certainly anything is possible, e.g., creating a release branch on
github with a different dependency, but again I'd suggest evaluating
whether the warning is relevant in your situation, and if not ignoring it.
From the Bioconductor perspective, the fact that your package builds on
travis under an earlier version of R is unknown, so the assertion that
it only requires R-3.3 is not supportable -- the warning tries to bring
your version requirements into line with what we know to be true. Of
course the assertion that it depends on a version of R > 3.4 is also not
supportable.
Martin
Appreciate any guidance on these question. Thanks,
Alicia
[[alternative HTML version deleted]]
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