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 g...@github.com <mailto:g...@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.mor...@roswellpark.org <mailto:martin.mor...@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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