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ccagc / QDNAseq

QDNAseq package for Bioconductor
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Prepare for update in matrixStats where colMedians() is no longer an S4 method #41

Closed HenrikBengtsson closed 8 years ago

HenrikBengtsson commented 8 years ago

I'm planning to (finally) turn col-/rowMedians() for matrixStats into a plain function - for historical reasons they're currently S4 methods, but that will change. In order for QDNAseq not to break when that happens, this patch needs to be applied.

For more details on the matrixStats update, see HenrikBengtsson/matrixStats#80

HenrikBengtsson commented 8 years ago

Forgot to say that this update is backward compatible with previous versions of matrixStats.

HenrikBengtsson commented 8 years ago

Thanks. Seems to pass Travis CI tests too. Would you mind pushing this up to Bioconductor SVN (and then master) too?

HenrikBengtsson commented 8 years ago

Just a heads up; I'll soon update matrixStats such that rowMedians() is no longer an S4 method. This will cause QDNAseq to break in Bioconductor. This is why this update needs to be pushed up to the Bioconductor SVN.

ilarischeinin commented 8 years ago

@daoud-sie is the only one who can do that, so tagging him here in case he hasn't seen this.

ilarischeinin commented 8 years ago

Branch master is ready to be pushed to the development version of Bioconductor. But for the current release version, I think we need:

HenrikBengtsson commented 8 years ago

FYI, Bioconductor 3.4 will be released on 2016-10-18, cf. http://bioconductor.org/developers/release-schedule/. There is a freeze on Friday 2016-10-07. I highly recommend that you get this PR in before then.

I will submit the next version of matrixStats to CRAN around 2016-10-07 so that it will be used part of the Bioconductor devel / 3.4 testing. This make sure that any remaining Bioconductor packages assuming matrixStats S4 methods will break before the new release.

daoud-sie commented 8 years ago

Hi Henrik,

Thanx for the heads up. I was expecting the release somewhere in October, I will make sure everything gets in somewhere next week.

Grtz,

Daoud

From: Henrik Bengtsson notifications@github.com Reply-To: ccagc/QDNAseq reply@reply.github.com Date: Tuesday 13 September 2016 at 22:09 To: ccagc/QDNAseq QDNAseq@noreply.github.com Cc: Daoud Sie d.sie@vumc.nl, Mention mention@noreply.github.com Subject: Re: [ccagc/QDNAseq] Prepare for update in matrixStats where colMedians() is no longer an S4 method (#41)

FYI, Bioconductor 3.4 will be released on 2016-10-18, cf. http://bioconductor.org/developers/release-schedule/. There is a freeze on Friday 2016-10-07. I highly recommend that you get this PR in before then.

I will submit the next version of matrixStats to CRAN around 2016-10-07 so that it will be used part of the Bioconductor devel / 3.4 testing. This make sure that any remaining Bioconductor packages assuming matrixStats S4 methods will break before the new release.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/ccagc/QDNAseq/pull/41#issuecomment-246807696, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AD-17tbd-d9zkO7RDDduM_DZcxXnl556ks5qpwL7gaJpZM4JKCZm.

ilarischeinin commented 8 years ago

Just a reminder that this still needs the push to SVN. (And nothing but the push.)

daoud-sie commented 8 years ago

Thanx for the reminder. First thing in the morning.

Van: Ilari Scheinin [mailto:notifications@github.com] Verzonden: maandag 3 oktober 2016 16:03 Aan: ccagc/QDNAseq CC: Sie, Daud; Mention Onderwerp: Re: [ccagc/QDNAseq] Prepare for update in matrixStats where colMedians() is no longer an S4 method (#41)

Just a reminder that this still needs the push to SVN. (And nothing but the push.)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/ccagc/QDNAseq/pull/41#issuecomment-251113823, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AD-17vUdIkOT-pJScmHowFvMxhgpDT-5ks5qwQsXgaJpZM4JKCZm.

daoud-sie commented 8 years ago

Even though it doesn’t yet show on the Bioconductor website, the changes have been pushed:

https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/QDNAseq/NAMESPACE https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/QDNAseq/DESCRIPTION

Sorry for the long wait.

Grtz,

Daoud

From: Ilari Scheinin notifications@github.com Reply-To: ccagc/QDNAseq reply@reply.github.com Date: Monday, 3 October 2016 at 16:03 To: ccagc/QDNAseq QDNAseq@noreply.github.com Cc: Daud Sie d.sie@vumc.nl, Mention mention@noreply.github.com Subject: Re: [ccagc/QDNAseq] Prepare for update in matrixStats where colMedians() is no longer an S4 method (#41)

Just a reminder that this still needs the push to SVN. (And nothing but the push.)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/ccagc/QDNAseq/pull/41#issuecomment-251113823, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AD-17vUdIkOT-pJScmHowFvMxhgpDT-5ks5qwQsXgaJpZM4JKCZm.

HenrikBengtsson commented 8 years ago

Thxs. FYI

For #Bioconductor devels: SVN snapshots every Mon/Wed/Sat @ 19:15 PT. Then builds/checks take ~2 days for results/pkgs to appear online

https://twitter.com/henrikbengtsson/status/783744785404145664

HenrikBengtsson commented 8 years ago

Just an update and a note for the records: matrixStats 0.51.0 is on CRAN since a few days and everything works fine with QDNAseq 1.9.2.

I realized that current version in Bioc release, which several people will still be using for a while, would also break if not updated. I took the freedom to do an SVN commit (I've got super-user rights there) fixing also that branch now holding QDNAseq 1.8.1. That has now also be build and tested against the new matrixStats and everything went well. For completness, but probably not necessary, you might wanna pull in that branch to Git as well. I'm not sure what you're setup is these days.