[Bioc-devel] Version bumps

[Martin Morgan]

On 01/22/2018 07:19 PM, Yuande Tan wrote:
> Dear Martin,
> I have install git and also built github and created public and private 
> keys and built config for automatically loading keys into the ssh-agent 
> and store passphrases in my keychain.  my .ssh has files:
> 
> ~/.ssh/config
> 
> ~/.ssh/id_rsa
> 
> ~/.ssh/id_rsa.pub
> 
> ~/.ssh/known_hosts
> 
> 
> I tried ssh git at github.com <mailto:git at github.com> to automatically load 
> keys into the ssh-agent and store passphrases in my keychain but every 
> time I got bad option:
> 
> /Users/yuandet/.ssh/config: line 4: Bad configuration option: addkeystoagent
> 
> /Users/yuandet/.ssh/config: terminating, 1 bad configuration options
> 
> 
> I used google to try address this problem, but I have not found any 
> answer so far.
> 

Did you follow the simple instructions here?

 
https://help.github.com/articles/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent/

To debug, it would help to see your ./ssh/config file. It is a plain 
text file, and can be edited using a normal text editor. Simply remove 
the AddKeysToAgent line.

This seems likely to be due to differences in macOS versions, as 
summarized here

   https://developer.apple.com/library/content/technotes/tn2449/_index.html

Martin

> 
> Would you like to tell me how to fix this problem for me to update my 
> packages MBttest and GMRP?
> 
> 
> Thank you so much for your great help.
> 
> 
> My best wishes,
> 
> 
> Yuande
> 
> 
> On Fri, Jan 19, 2018 at 6:01 AM, Martin Morgan 
> <martin.morgan at roswellpark.org <mailto:martin.morgan at roswellpark.org>> 
> wrote:
> 
>     Bioc developers!
> 
>     A number of packages in the 'master' branch of their git repository
>     build and check successfully, but do not propagate to the 'devel'
>     repository (red light at the extreme right, e.g., ABSSeq; mouse over
>     for details)
> 
>     https://bioconductor.org/checkResults/3.7/bioc-LATEST/ABSSeq
>     <https://bioconductor.org/checkResults/3.7/bioc-LATEST/ABSSeq>
> 
>     This is because the version of the git repository master branch
>     (1.32.3) is less than the version of the published package in the
>     devel repository (1.33.0).
> 
>     The Bioconductor version scheme is described at
> 
>     https://bioconductor.org/developers/how-to/version-numbering/
>     <https://bioconductor.org/developers/how-to/version-numbering/>
> 
>     Suppose a package has 'devel' version 1.3.1, and release version
>     1.2.0. The middle digit in the devel version is always odd, the
>     middle digit in the release version is even and one less than devel.
>     Best practice would be to introduce bug fixes and new features into
>     the master branch and increment the version to 1.3.2. Bug fixes
>     would then be ported to the RELEASE_3_6 branch and the release
>     branch would be incremented to version 1.2.1.
> 
>     Here are the packages with invalid versions, and a little commentary
> 
>      > versions %>% select(package, published, repo)
>     # A tibble: 9 x 3
>        package        published repo
>        <chr>          <chr>     <chr>
>     1 ABSSeq         1.33.0    1.32.3
> 
>     Looks like this package had bug fixes introduced into the release
>     (even-numbered) branch, and these were ported to the devel branch
>     without changing version number. Introduce bug fixes in devel, and
>     port to release. Remember to increment the appropriate version
>     number in devel, and the appropriate version number in release. The
>     next devel version number is 1.33.1.
> 
>     2 esetVis        1.5.0     1.3.2
> 
>     Looks like this package had bug fixes introduced into the devel
>     branch, but did not pull the version bump from Biocoductor after the
>     last release. The next devel version number is 1.5.1.
> 
>     3 Logolas        1.3.0     1.2.1
>     4 microbiome     1.1.10006 1.1.2
> 
>     It's true that .2 > .10006, but the number after the '.' is treated
>     as an integer, and 2 < 10006. The correct version number for this
>     package is 1.1.10007.
> 
>     5 multiClust     1.9.0     1.8.1
>     6 nucleR         2.11.0    2.2.0
> 
>     It looks perhaps like the nucleR author is incrementing the middle
>     version field, rather than the last. The package does not propagate
>     for the same reason as microbiome, 2 < 11. The rule is that the
>     'devel' version have odd-numbered middle digits, so the correct
>     version in the repo would be 2.11.1.
> 
>     7 QuaternaryProd 1.7.0     1.6.1
>     8 rDGIdb         1.5.0     1.4.2
>     9 Rnits          1.13.0    1.11.2
> 
>     Please respond to the bioc-devel mailing list with any questions; I
>     look forward to fewer red lights!
> 
>     Martin
> 
> 
>     This email message may contain legally privileged and/or...{{dropped:2}}
> 
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> 
> 


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