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theislab / destiny

R package for single cell and other data analysis using diffusion maps
https://theislab.github.io/destiny/
GNU General Public License v3.0
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package ‘destiny’ is not available for Bioconductor version '3.13' #49

Closed madalenamrp closed 2 years ago

madalenamrp commented 3 years ago

Hi,

I am experiencing issues with installing the package 'destiny' using the most current version of Bioconductor. The error message is reported below:

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing package(s) 'destiny' Installation paths not writeable, unable to update packages path: /Library/Frameworks/R.framework/Versions/4.1/Resources/library packages: Matrix, mgcv Warning message: In .inet_warning(msg) : package ‘destiny’ is not available for Bioconductor version '3.13'

A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

So far I could not figure out an alternative. Do you have any suggestions for overcoming this issue?

With best regards and thanks for your time and help, Madalena

SONGDONGYUAN1994 commented 3 years ago

Hi, I have the exact same problem. Any solutions? Thanks!

kullrich commented 3 years ago

Hi, for me this worked:

library(devtools)
install_github("https://github.com/theislab/destiny", build_vignettes = FALSE, dependencies = TRUE)
jpcartailler commented 3 years ago

For reference, it doesn't build properly as per http://bioconductor.org/checkResults/release/bioc-LATEST/destiny/.

rargelaguet commented 2 years ago

Please fix this, such a useful package needs to be available from the latest Bioconductor branch :)

flying-sheep commented 2 years ago

@vjcitn from bioconductor wrote me about it but isn’t replying.

I‘m trying to update it, but I get:

$ git push upstream master
FATAL: W any packages/destiny p.angerer DENIED by fallthru

“p.angerer” indicates that it recognizes me, but still doesn’t allow me to push commits.

vjcitn commented 2 years ago

thanks for writing this is an faq in developer git pages plz use bioc-devel mailing list for such concerns if doc does not foster solution at your end deprecation can be avoided if u get it running in bioc 3.14

On Mon, Nov 8, 2021 at 4:55 AM Philipp A. @.***> wrote:

@vjcitn https://github.com/vjcitn from bioconductor wrote me about it but isn’t replying.

I‘m trying to update it, but I get:

$ git push upstream master FATAL: W any packages/destiny p.angerer DENIED by fallthru

“p.angerer” indicates that it recognizes me, but still doesn’t allow me to push commits.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/theislab/destiny/issues/49#issuecomment-962984301, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABDI5QQYUKQFDGO3QJR6KFLUK6M7LANCNFSM5BEHYREQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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flying-sheep commented 2 years ago

I did that, but please read fully: The FAQ covers the case “I’m not authenticated properly”. It doesn’t cover the case “I’m authenticated and recognized, but denied access to my own package”

flying-sheep commented 2 years ago

I posted to the mailing list and got no response so far: https://stat.ethz.ch/pipermail/bioc-devel/2021-November/018658.html

vjcitn commented 2 years ago

Noted. Your issue will be addressed as schedules permit. We appreciate your contributions to the Bioconductor ecosystem. If you have a modification to the FAQ that you think will be helpful, please let us know.

flying-sheep commented 2 years ago

Fixed now for bioconductor 3.14

vjcitn commented 2 years ago

Please bump the version for your RELEASE_3_14. Merge the changes to master branch at git.bioconductor.org and the package will re-enter the devel build stream. @lshep

flying-sheep commented 2 years ago

Done, see #59