package ‘destiny’ is not available for Bioconductor version '3.13'

[madalenamrp]

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]

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

[kullrich]

Hi, for me this worked:

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

[jpcartailler]

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

[rargelaguet]

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

[flying-sheep]

@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]

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 <#49 (comment)>, 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]

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]

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

[vjcitn]

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]

Fixed now for bioconductor 3.14

• https://bioconductor.org/packages/release/bioc/src/contrib/destiny_3.8.0.tar.gz
• https://bioconductor.org/packages/release/bioc/bin/windows/contrib/4.1/destiny_3.8.0.zip
• https://bioconductor.org/packages/release/bioc/bin/macosx/contrib/4.1/destiny_3.8.0.tgz

[vjcitn]

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]

Done, see #59