Re: [Bioc-devel] Missing link files in Windows (release and devel)

Thanks Martin! I just finished fixing the links in all my packages using the \link[base:cbind]{rbind} syntax. One of them did seem a bit weird to me: Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpqyL54j/R.INSTALL22cc280d642c/derfinder/man/loadCoverage.Rd:15: missing file link 'BamFile'

Re: [Bioc-devel] Missing link files in Windows (release and devel)

Thank you Jim! I changed it to \link[Rsamtools:BamFile-class]{BamFile}. Best, Leo On Wed, Jan 17, 2018 at 11:56 AM, James W. MacDonald wrote: > > On Wed, Jan 17, 2018 at 11:38 AM, Leonardo Collado Torres > wrote: >> >> Thanks Martin! I just finished fixing the

Re: [Bioc-devel] Duplicate commits in Bioconductor commit history

Hi Laurent, After checking your package, it’s very hard to get rid of the duplicate commits at this stage of development. I don’t think it should effect the build process of your package. The only thing it might effect is, when you look back at a later time to specific commit which is

Re: [Bioc-devel] "Duplicate commits" after when pushing change right after doing a clean `git clone g...@git.bioconductor.org:packages/chimeraviz`

The problem is not a separate branch from your primary repository. Its the branch coming from a “remote” which is not the primary repository (i.e Bioconductor). “rebase" is essentially doing what you do in two separate steps, so that does not solve this issue. I would just ask on this forum

Re: [Bioc-devel] Missing link files in Windows (release and devel)

This sentence seems to indicate that the original format \link[base]{rbind} should work: "Because they have been frequently misused, the HTML help system looks for topic foo in package pkg if it does not find file foo.html." On 1/17/18 8:56 AM, James W. MacDonald wrote: On Wed, Jan 17,

Re: [Bioc-devel] Duplicate commits in Bioconductor commit history

On 17 January 2018 17:40, Turaga, Nitesh wrote: > Hi Laurent, > > After checking your package, it’s very hard to get rid of the > duplicate commits at this stage of development. I don’t think it > should effect the build process of your package. > > The only thing it might effect is, when you

Re: [Bioc-devel] "Duplicate commits" after when pushing change right after doing a clean `git clone g...@git.bioconductor.org:packages/chimeraviz`

Hi Stian, I’ve enabled you to push to your repository on Bioconductor. Your duplicate commit history weaves in and out because of merges along the way from your GitHub repository. At this point, there is very little I can do to help unless I spend a lot of time on your package, manually

Re: [Bioc-devel] Duplicate commit error when pushing to annotatr upstream/master

Hi Raymond, I have fixed your repository on Bioconductor, and you are able to push changes again. Duplicate commits are caused because of “merge” commits from remotes. Please make sure that before you push from hence forth, or merge, that the duplicate commit issue doesn’t reoccur. Best,

Re: [Bioc-devel] "Duplicate commits" after when pushing change right after doing a clean `git clone g...@git.bioconductor.org:packages/chimeraviz`

I usually create a seperate branch for work, which I merge into master when I'm happy with the result. Will that be a problem? Should I rebase instead to avoid it? Thank you. On Wed, Jan 17, 2018 at 6:48 PM, Turaga, Nitesh < nitesh.tur...@roswellpark.org> wrote: > Hi Stian, > > I’ve enabled you

Re: [Bioc-devel] "Duplicate commits" after when pushing change right after doing a clean `git clone g...@git.bioconductor.org:packages/chimeraviz`

On 17 January 2018 18:26, Turaga, Nitesh wrote: > The problem is not a separate branch from your primary repository. Its > the branch coming from a “remote” which is not the primary repository > (i.e Bioconductor). > > “rebase" is essentially doing what you do in two separate steps, so > that

[Bioc-devel] git permission denied to synapter repository

Dear Bioconductor admins, I am the (co-)maintainer of the synapter package. I tried to push some changes the first time after the conversion to git and got the following error: ``` > git push upstream master FATAL: W any packages/synapter s.gibb DENIED by fallthru (or you mis-spelled the

Re: [Bioc-devel] Missing link files in Windows (release and devel)

On 01/17/2018 12:02 PM, Stephanie M. Gogarten wrote: This sentence seems to indicate that the original format \link[base]{rbind} should work: "Because they have been frequently misused, the HTML help system looks for topic foo in package pkg if it does not find file foo.html." I looked at

Re: [Bioc-devel] git permission denied to synapter repository

Hi Sebastian, You did not do anything wrong. Laurent is the only one listed on the package so far. I will add you to it. Laurent, just a heads up, I’m adding Sebastian to the “synapter" package. Best, Nitesh > On Jan 17, 2018, at 4:07 PM, Sebastian Gibb wrote: > >

Re: [Bioc-devel] git permission denied to synapter repository

Dear Nitesh, thank you very much. Now it works! Best wishes, Sebastian On 2018-01-17 22:39:17, nitesh.tur...@roswellpark.org wrote: > Hi Sebastian, > > You did not do anything wrong. Laurent is the only one listed on the package > so far. I will add you to it. > > Laurent, just a heads up,

Re: [Bioc-devel] Missing link files in Windows (release and devel)

On Wed, Jan 17, 2018 at 11:38 AM, Leonardo Collado Torres wrote: > Thanks Martin! I just finished fixing the links in all my packages > using the \link[base:cbind]{rbind} syntax. One of them did seem a bit > weird to me: > > Rd warning: