[Bioc-devel] Problem on malbec2 server
Hi everyone, I did a minor update to the package I'm currently developing and the build report shows an error on malbec2 server: * checking for file EventPointer/DESCRIPTION ... OK * preparing EventPointer: * checking DESCRIPTION meta-information ... OK Error in loadVignetteBuilder(pkgdir, TRUE) : vignette builder 'knitr' not found Execution halted Could this be related with a problem in the server? A few hours ago I did a build and it completed without errors and warnings so, I doubt that the version bump (Updated a link on the package vignette) caused this problem. Thank you. Juan Pablo [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Problem on malbec2 server
Thanks Herv�. I will wait to do another version bump until all the servers are updated. Yes, the package suggests knitr. in order to build vignettes correctly. Thanks - Juan Pablo From: Herv� Pag�s Sent: Tuesday, February 14, 2017 11:26 PM To: Romero, Juan Pablo; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Problem on malbec2 server Hi Juan Pablo, We just updated R on malbec2 a couple of hours ago and kintr has not been re-installed yet. Please make sure that your package suggests knitr otherwise the Single Package Builder has no way to know that knitr needs to be installed before trying to run 'R CMD build' or 'R CMD check' on your package. Thanks, H. On 02/14/2017 01:01 PM, Romero, Juan Pablo wrote: > Hi everyone, > > I did a minor update to the package I'm currently developing and the build > report shows an error on malbec2 server: > > * checking for file EventPointer/DESCRIPTION ... OK > * preparing EventPointer: > * checking DESCRIPTION meta-information ... OK > Error in loadVignetteBuilder(pkgdir, TRUE) : > vignette builder 'knitr' not found > Execution halted > > Could this be related with a problem in the server? A few hours ago I did a > build and it completed without errors and warnings so, > I doubt that the version bump (Updated a link on the package vignette) caused > this problem. > > Thank you. > > Juan Pablo > > > >[[alternative HTML version deleted]] > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > -- Herv� Pag�s 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]] ___ 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] Unit Tests & Test Coverage
Hi Hervé, Thanks for all the clarifications related to the tests and the coverage for packages. Yes, I've just checked EventPointer landing page and the coverage bad is working great at this moment. It seems that it was just a matter of time before it was displayed. Again, thanks for all. Best regards, Juan Pablo From: Hervé Pagès Sent: Friday, March 24, 2017 8:29:08 AM To: Romero, Juan Pablo; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Unit Tests & Test Coverage The coverage badge finally got updated: https://bioconductor.org/packages/3.5/bioc/html/EventPointer.html I didn't do anything. Looks like for some reason it took a long time for the coverage result on codecov.io to propagate to the package landing page. Cheers, H. On 03/23/2017 01:32 PM, Hervé Pagès wrote: > 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor-2Dmirror_EventPointer&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=QY4w9Io4Cx1vbUkb-sjYFCC4fp88dTA9tPfm7O_ueSQ&s=O1j0kLptbtmlzKItTODgtPNL9X7OXDteiR7Sn7zCgMg&e= > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor-2Dmirror_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=QY4w9Io4Cx1vbUkb-sjYFCC4fp88dTA9tPfm7O_ueSQ&s=7KRBTOWvXmA76VMkUfMzdWDh-_KsXNXV8K2qWDirx6o&e= > ) 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://urldefense.proofpoint.com/v2/url?u=https-3A__codecov.io_github_Bioconductor-2Dmirror_VariantAnnotation_branch_master&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=QY4w9Io4Cx1vbUkb-sjYFCC4fp88dTA9tPfm7O_ueSQ&s=ANws4fvdvik6ga1hynXgSPss0Jrix_9wdl5_tl_0IIo&e= > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__codecov.io_github_Bioconductor-2Dmirror_EventPointer_branch_master&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=QY4w9Io4Cx1vbUkb-sjYFCC4fp88dTA9tPfm7O_ueSQ&s=dDjRgkJSvMLudzs009l-1rcMyEWa3psee7CK90enRk0&e= > > 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 >>
[Bioc-devel] Error in tokay2
Hello all, I know that today is the deadline for passing R CMD build and R CMD check without errors and warnings, and my package EventPointer has been working perfectly for the last weeks. Today the build report in tokay2 shows an error in one of the examples: ** running examples for arch 'x64' ... ERROR Make the TxDb object ... Error in if (file.exists(dest) && file.mtime(dest) > file.mtime(lib) && : missing value where TRUE/FALSE needed The error is coming from the function makeTxDbFromGFF and the error does not come from functions from my package. Is anybody having a similar error? I will appreciate any help on this to avoid problems related with adding the package to the new release. Thanks! Best regards, Juan Pablo [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Error in tokay2
Thanks to both Valerie and Herv� for all the comments with this problem. Just to let you know, I encountered with this problem while developing the algorithm, initially. In both windows and mac, I wasn't able to run R CMD Check locally due to the same error. In both machines I did a new installation of R and all the packages again and that solved the problem for Mac but not for Windows. Thanks Again! Best, Juan Pablo > but not GenomicFeatures, which is another victim of this > install.packages bug: > > > https://bioconductor.org/checkResults/3.5/bioc-LATEST/GenomicFeatures/tokay2-checksrc.html > > AFAICS we've been seeing this problem on tokay2 (Windows) almost every > day for the last few weeks. I guess it started after we updated R to a > more recent R 3.4 on this machine. So I suspect a change in R somehow > triggered this. > > H. > > On 04/15/2017 08:02 PM, Obenchain, Valerie wrote: > EventPointer 0.99.36 built clean today: > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bioconductor.org_checkResults_devel_bioc-2DLATEST_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=auvr-W1IWGGZ6bEm2_E4MMb1dYZxyOJiJEHxw8ffrPk&s=ZxAUJxS48UK2FAs1mcQeAC2XXy0-eiv9SW4OyyOUZDs&e= > > Valerie > On 04/14/2017 09:16 AM, Obenchain, Valerie wrote: >> Hi Juan Pablo, >> >> We think this is a problem related to installed.packages(), see >> discussion here: >> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2017-2DApril_010819.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=auvr-W1IWGGZ6bEm2_E4MMb1dYZxyOJiJEHxw8ffrPk&s=bSGL5D0ea0jkhT_HDTBTWVccTXfXi-E7uYm4ZCy4VuY&e= >> >> You can ignore this for now. Thanks for keeping an eye on the build report. >> >> Valerie >> On 04/14/2017 12:41 AM, Romero, Juan Pablo wrote: >>> Hello all, >>> >>> >>> I know that today is the deadline for passing R CMD build and R CMD check >>> without errors and warnings, and my package EventPointer has been working >>> perfectly for the last weeks. >>> >>> >>> Today the build report in tokay2 shows an error in one of the examples: >>> >>> >>> ** running examples for arch 'x64' ... ERROR >>> >>> >>> Make the TxDb object ... Error in if (file.exists(dest) && file.mtime(dest) >>> > file.mtime(lib) && : >>> missing value where TRUE/FALSE needed >>> >>> >>> The error is coming from the function makeTxDbFromGFF and the error does >>> not come from functions from >>> >>> my package. >>> >>> >>> Is anybody having a similar error? >>> >>> >>> I will appreciate any help on this to avoid problems related with adding >>> the package to the new release. >>> >>> >>> Thanks! >>> >>> >>> Best regards, >>> >>> >>> Juan Pablo >>> From: Herv� Pag�s Sent: Monday, April 17, 2017 1:51:48 AM To: Obenchain, Valerie; Romero, Juan Pablo; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Error in tokay2 but not GenomicFeatures, which is another victim of this install.packages bug: https://bioconductor.org/checkResults/3.5/bioc-LATEST/GenomicFeatures/tokay2-checksrc.html AFAICS we've been seeing this problem on tokay2 (Windows) almost every day for the last few weeks. I guess it started after we updated R to a more recent R 3.4 on this machine. So I suspect a change in R somehow triggered this. H. On 04/15/2017 08:02 PM, Obenchain, Valerie wrote: > EventPointer 0.99.36 built clean today: > > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bioconductor.org_checkResults_devel_bioc-2DLATEST_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=auvr-W1IWGGZ6bEm2_E4MMb1dYZxyOJiJEHxw8ffrPk&s=ZxAUJxS48UK2FAs1mcQeAC2XXy0-eiv9SW4OyyOUZDs&e= > > Valerie > > > > On 04/14/2017 09:16 AM, Obenchain, Valerie wrote: >> Hi Juan Pablo, >> >> We think this is a problem related to installed.packages(), see >> discussion here: >> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_pipermail_bioc-2Ddevel_2017-2DApril_010819.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=auvr-W1IWGGZ6bEm2_E4MMb1dYZxyOJiJEHxw8ffrPk&s=bSGL5D0ea0jkhT_HDTBTWVccTXfXi-E7uYm4ZCy4VuY&e= >> >> You can
