Re: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?
My understanding is that we will not permit dependencies outside of Bioc or
CRAN. If a repository
is created that is at least as rigorous in package admission as CRAN,
perhaps it needs to be
considered. If there are details known about alternate repositories that
we should learn about, please supply.
On Tue, Mar 2, 2021 at 1:20 PM Henrik Bengtsson
wrote:
> Related: Does Bioconductor support 'Additional_repositories'? From RWE:
>
> The ‘Additional_repositories’ field is a comma-separated list of
> repository URLs where the packages named in the other fields may be
> found. It is currently used by R CMD check to check that the packages
> can be found, at least as source packages (which can be installed on
> any platform).
>
> FWIW, CRAN allows/supports them (I've only used them for packages
> under 'Suggests:').
>
> /Henrik
>
> On Tue, Mar 2, 2021 at 4:02 AM Rainer Johannes
> wrote:
> >
> > thanks for the quick reply Lori!
> >
> > OK, so we will have to submit the package to Bioc ASAP.
> >
> > cheers, jo
> >
> > > On 2 Mar 2021, at 12:51, Kern, Lori
> wrote:
> > >
> > > Currently the builders do not allow the user of remotes and you would
> have to wait for it to be submitted to CRAN or Bioconductor. All
> Bioconductor dependencies must be on CRAN or Bioconductor.
> > >
> > > Get Outlook for iOS
> > > From: Bioc-devel on behalf of
> Rainer Johannes
> > > Sent: Tuesday, March 2, 2021 4:36:05 AM
> > > To: bioc-devel
> > > Subject: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?
> > >
> > > Dear All!
> > >
> > > in one of the xcms vignettes we are using a R package which is not yet
> in Bioconductor and I added
> > >
> > > Remotes:
> > > RforMassSpectrometry/MsBackendMgf
> > >
> > > to the DESCRIPTION thinking that on the BioC build machines the
> package might get installed (from github). It does apparently not as we get
> ERROR for this vignette. Is there any way I can use a non-Bioconductor and
> non-CRAN package or do I have to wait until the package is included in
> Bioconductor?
> > >
> > > thanks for any feedback!
> > >
> > > cheers, jo
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > >
> https://secure-web.cisco.com/1H1jWIWyghkLhLM5RAXwwfoWK4PlOlae4Pc1-a_NRbOIOuLSLHtGAyInV-z8t0fCgCfVH0nxURKnBN77cdDWaaKfCoZMnqX4XshZNWoi44Ko2dWmnDvV5BjARxeduRCCmoKigDovJkvgYgbecL-t9v9m2HGULeKeb9va8J3NlYFXnVkCDGyzsNgbeZSN2VlWCKhLL1vQqlJEiglEPQraiCYfRjZdnxkQsRcLPnIkfvjbIHJWHFz0LYJRGav4iCiARcWCn0Uo0qe8ieknAiGloqMR2HJHD6oUNCdG8v7oYy73oVejgIqxYBbvJsrztDawr/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel
> > >
> > >
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Re: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?
Related: Does Bioconductor support 'Additional_repositories'? From RWE: The ‘Additional_repositories’ field is a comma-separated list of repository URLs where the packages named in the other fields may be found. It is currently used by R CMD check to check that the packages can be found, at least as source packages (which can be installed on any platform). FWIW, CRAN allows/supports them (I've only used them for packages under 'Suggests:'). /Henrik On Tue, Mar 2, 2021 at 4:02 AM Rainer Johannes wrote: > > thanks for the quick reply Lori! > > OK, so we will have to submit the package to Bioc ASAP. > > cheers, jo > > > On 2 Mar 2021, at 12:51, Kern, Lori wrote: > > > > Currently the builders do not allow the user of remotes and you would have > > to wait for it to be submitted to CRAN or Bioconductor. All Bioconductor > > dependencies must be on CRAN or Bioconductor. > > > > Get Outlook for iOS > > From: Bioc-devel on behalf of Rainer > > Johannes > > Sent: Tuesday, March 2, 2021 4:36:05 AM > > To: bioc-devel > > Subject: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC? > > > > Dear All! > > > > in one of the xcms vignettes we are using a R package which is not yet in > > Bioconductor and I added > > > > Remotes: > > RforMassSpectrometry/MsBackendMgf > > > > to the DESCRIPTION thinking that on the BioC build machines the package > > might get installed (from github). It does apparently not as we get ERROR > > for this vignette. Is there any way I can use a non-Bioconductor and > > non-CRAN package or do I have to wait until the package is included in > > Bioconductor? > > > > thanks for any feedback! > > > > cheers, jo > > ___ > > Bioc-devel@r-project.org mailing list > > https://secure-web.cisco.com/1H1jWIWyghkLhLM5RAXwwfoWK4PlOlae4Pc1-a_NRbOIOuLSLHtGAyInV-z8t0fCgCfVH0nxURKnBN77cdDWaaKfCoZMnqX4XshZNWoi44Ko2dWmnDvV5BjARxeduRCCmoKigDovJkvgYgbecL-t9v9m2HGULeKeb9va8J3NlYFXnVkCDGyzsNgbeZSN2VlWCKhLL1vQqlJEiglEPQraiCYfRjZdnxkQsRcLPnIkfvjbIHJWHFz0LYJRGav4iCiARcWCn0Uo0qe8ieknAiGloqMR2HJHD6oUNCdG8v7oYy73oVejgIqxYBbvJsrztDawr/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. > > ___ > 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
Re: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?
thanks for the quick reply Lori! OK, so we will have to submit the package to Bioc ASAP. cheers, jo > On 2 Mar 2021, at 12:51, Kern, Lori wrote: > > Currently the builders do not allow the user of remotes and you would have to > wait for it to be submitted to CRAN or Bioconductor. All Bioconductor > dependencies must be on CRAN or Bioconductor. > > Get Outlook for iOS > From: Bioc-devel on behalf of Rainer > Johannes > Sent: Tuesday, March 2, 2021 4:36:05 AM > To: bioc-devel > Subject: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC? > > Dear All! > > in one of the xcms vignettes we are using a R package which is not yet in > Bioconductor and I added > > Remotes: > RforMassSpectrometry/MsBackendMgf > > to the DESCRIPTION thinking that on the BioC build machines the package might > get installed (from github). It does apparently not as we get ERROR for this > vignette. Is there any way I can use a non-Bioconductor and non-CRAN package > or do I have to wait until the package is included in Bioconductor? > > thanks for any feedback! > > cheers, jo > ___ > Bioc-devel@r-project.org mailing list > https://secure-web.cisco.com/1H1jWIWyghkLhLM5RAXwwfoWK4PlOlae4Pc1-a_NRbOIOuLSLHtGAyInV-z8t0fCgCfVH0nxURKnBN77cdDWaaKfCoZMnqX4XshZNWoi44Ko2dWmnDvV5BjARxeduRCCmoKigDovJkvgYgbecL-t9v9m2HGULeKeb9va8J3NlYFXnVkCDGyzsNgbeZSN2VlWCKhLL1vQqlJEiglEPQraiCYfRjZdnxkQsRcLPnIkfvjbIHJWHFz0LYJRGav4iCiARcWCn0Uo0qe8ieknAiGloqMR2HJHD6oUNCdG8v7oYy73oVejgIqxYBbvJsrztDawr/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. ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?
Currently the builders do not allow the user of remotes and you would have to wait for it to be submitted to CRAN or Bioconductor. All Bioconductor dependencies must be on CRAN or Bioconductor. Get Outlook for iOS<https://aka.ms/o0ukef> From: Bioc-devel on behalf of Rainer Johannes Sent: Tuesday, March 2, 2021 4:36:05 AM To: bioc-devel Subject: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC? Dear All! in one of the xcms vignettes we are using a R package which is not yet in Bioconductor and I added Remotes: RforMassSpectrometry/MsBackendMgf to the DESCRIPTION thinking that on the BioC build machines the package might get installed (from github). It does apparently not as we get ERROR for this vignette. Is there any way I can use a non-Bioconductor and non-CRAN package or do I have to wait until the package is included in Bioconductor? thanks for any feedback! cheers, jo ___ Bioc-devel@r-project.org mailing list https://secure-web.cisco.com/1H1jWIWyghkLhLM5RAXwwfoWK4PlOlae4Pc1-a_NRbOIOuLSLHtGAyInV-z8t0fCgCfVH0nxURKnBN77cdDWaaKfCoZMnqX4XshZNWoi44Ko2dWmnDvV5BjARxeduRCCmoKigDovJkvgYgbecL-t9v9m2HGULeKeb9va8J3NlYFXnVkCDGyzsNgbeZSN2VlWCKhLL1vQqlJEiglEPQraiCYfRjZdnxkQsRcLPnIkfvjbIHJWHFz0LYJRGav4iCiARcWCn0Uo0qe8ieknAiGloqMR2HJHD6oUNCdG8v7oYy73oVejgIqxYBbvJsrztDawr/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] Remotes in DESCRIPTION not supported for BioC?
Dear All! in one of the xcms vignettes we are using a R package which is not yet in Bioconductor and I added Remotes: RforMassSpectrometry/MsBackendMgf to the DESCRIPTION thinking that on the BioC build machines the package might get installed (from github). It does apparently not as we get ERROR for this vignette. Is there any way I can use a non-Bioconductor and non-CRAN package or do I have to wait until the package is included in Bioconductor? thanks for any feedback! cheers, jo ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
