[Bioc-devel] Version bumps

[Martin Morgan]

On 01/23/2018 10:15 AM, Martin Morgan wrote:
> 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

Have you made any progress? Your packages MBttest and GMRP have been 
failing for quite some time and are now deprecated.

Martin

> 
> 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
>>
>>
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>>
>>     _______________________________________________
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>>
>>
> 
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