[Bioc-devel] Version bumps
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 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. 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> 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 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/ 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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