Re: [Bioc-devel] [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

[Xiaowen Chen]

Hi Kern,
I am sorry. I ran the following command, I also show the output of the 
corresponding commands.
However the release branch still is not updated.
Could you help me?
Thank you.
Best,
Xiaowen

1.go to https://github.com/TheJacksonLaboratory/epihet/blob/master/DESCRIPTION
update version 1.7.1 of DESCRIPTION FILE to 1.6.1

2.(base) [chenx@helix ~]$ git clone 
https://github.com/TheJacksonLaboratory/epihet.git

Initialized empty Git repository in /home/c-chenx/epihet/.git/
remote: Enumerating objects: 35, done.
remote: Counting objects: 100% (35/35), done.
remote: Compressing objects: 100% (32/32), done.
remote: Total 874 (delta 16), reused 5 (delta 2), pack-reused 839
Receiving objects: 100% (874/874), 4.61 MiB, done.
Resolving deltas: 100% (465/465), done.

3. (base) [chenx@helix ~]$ cd epihet
4. (base) [chenx@helix epihet]$ git remote add upstream 
g...@git.bioconductor.org:packages/epihet.git
(base) [chenx@helix epihet]$ git remote -v

origin https://github.com/TheJacksonLaboratory/epihet.git (fetch)
origin https://github.com/TheJacksonLaboratory/epihet.git (push)
upstream g...@git.bioconductor.org:packages/epihet.git (fetch)
upstream g...@git.bioconductor.org:packages/epihet.git (push)

5.(base) [chenx@helix epihet]$ git fetch --all
Fetching origin
Fetching upstream
Enter passphrase for key '/home/c-chenx/.ssh/id_rsa':
From git.bioconductor.org:packages/epihet
* [new branch]  RELEASE_3_10 -> upstream/RELEASE_3_10
* [new branch]  RELEASE_3_11 -> upstream/RELEASE_3_11
* [new branch]  RELEASE_3_12 -> upstream/RELEASE_3_12
* [new branch]  RELEASE_3_9 -> upstream/RELEASE_3_9
* [new branch]  master -> upstream/master

6.(base) [chenx@helix epihet]$ git checkout RELEASE_3_12
error: pathspec 'RELEASE_3_12' did not match any file(s) known to git.

7. (base) [chenx@helix epihet]$ git checkout -b RELEASE_3_12 
upstream/RELEASE_3_12
Branch RELEASE_3_12 set up to track remote branch RELEASE_3_12 from upstream.
Switched to a new branch 'RELEASE_3_12'

8. (base) [chenx@helix epihet]$ git checkout RELEASE_3_12
Already on 'RELEASE_3_12'

9.(base) [chenx@helix epihet]$ git merge upstream/RELEASE_3_12
Already up-to-date.

(base) [chenx@helix epihet]$ git merge origin/RELEASE_3_12
Already up-to-date.

(base) [chenx@helix epihet]$ git push upstream RELEASE_3_12
Enter passphrase for key '/home/c-chenx/.ssh/id_rsa':
Everything up-to-date
(base) [chenx@helix epihet]$ git push origin RELEASE_3_12
Everything up-to-date


From: "Kern, Lori" 
Date: Friday, December 18, 2020 at 3:24 PM
To: Xiaowen Chen 
Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform 
build/check report for BioC 3.12

If you are on the RELEASE_3_12 branch and made changes, you will need to update 
the version number regardless.  The numbering schema in release and devel are 
different.
of version  x.y.z   the y is even in release and odd in devel...
you could try while you are on the release branch to bump the version to 1.6.1 
and push that up.  but again, I do not see any code changes on the RELEASE_3_12 
branch so you would need to make sure those changes are also there before 
pushing up.




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________
From: Xiaowen Chen 
Sent: Friday, December 18, 2020 3:19 PM
To: Kern, Lori 
Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform 
build/check report for BioC 3.12


I totally understand what you are talking about.

I need to push the latest code to release branch3_12. but I ran the following 
command line several days.



git clone https://github.com/TheJacksonLaboratory/epihet.git

cd epihet

git remote add upstream g...@git.bioconductor.org:packages/epihet.git

git remote -v



git fetch –all

git checkout master

git merge origin/master

git merge upstream/master

git push upstream master

 git push origin master

git checkout RELEASE_3_12

 git merge upstream/RELEASE_3_12

 git merge origin/RELEASE_3_12

 git push upstream RELEASE_3_12

 git push origin RELEASE_3_12





And everything looked fine. No error. But RELEASE_3_12 branch still is not 
updated.



From: "Kern, Lori" 
Date: Friday, December 18, 2020 at 3:15 PM
To: Xiaowen Chen , "bioc-devel@r-project.org" 

Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform 
build/check report for BioC 3.12



That is the code on the devel branch.



You need to make the same code changes you did on devel to fix the ERROR on the 
RELEASE_3_12 branch. It does not get carried over across branches.





Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263



From: Xiaowen Chen 
Sent: 

[Bioc-devel] FW: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

[Xiaowen Chen]

Hi ,
I have follow the website 
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/ 
To push the latest epihet version to release branch.
Why I still to receive the email to complain there are error, seem I did not 
push successfully. 
What should I do, I did not see some error when I run the following commands

git checkout RELEASE_3_6
 git merge upstream/RELEASE_3_6
 git merge origin/RELEASE_3_6
 git push upstream RELEASE_3_6
 git push origin RELEASE_3_6

Best,
Xiaowen



On 12/18/20, 1:00 PM, "bbs-nore...@bioconductor.org" 
 wrote:

[This is an automatically generated email. Please don't reply.]

Hi epihet maintainer,

According to the Multiple platform build/check report for BioC 3.12,
the epihet package has the following problem(s):

  o ERROR for 'R CMD build' on malbec1. See the details here:
  
https://master.bioconductor.org/checkResults/3.12/bioc-LATEST/epihet/malbec1-buildsrc.html

Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org

Notes:

  * This was the status of your package at the time this email was sent to 
you.
Given that the online report is updated daily (in normal conditions) you
could see something different when you visit the URL(s) above, 
especially if
you do so several days after you received this email.

  * It is possible that the problems reported in this report are false 
positives,
either because another package (from CRAN or Bioconductor) breaks your
package (if yours depends on it) or because of a Build System problem.
If this is the case, then you can ignore this email.

  * Please check the report again 24h after you've committed your changes 
to the
package and make sure that all the problems have gone.

  * If you have questions about this report or need help with the
maintenance of your package, please use the Bioc-devel mailing list:

  https://bioconductor.org/help/mailing-list/

(all package maintainers are requested to subscribe to this list)

For immediate notification of package build status, please
subscribe to your package's RSS feed. Information is at:

https://bioconductor.org/developers/rss-feeds/

Thanks for contributing to the Bioconductor project!


---

The information in this email, including attachments, may be confidential and 
is intended solely for the addressee(s). If you believe you received this email 
by mistake, please notify the sender by return email as soon as possible.
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

[Xiaowen Chen]

Hi Bioconductor,
Yes, I have updated epihet because the issue
“ 'x' is NULL so the result will be NULL
Quitting from lines 483-495 (/Users/ma38727/b/git/epihet/vignettes/epihet.Rnw)
Error in ans[ypos] <- rep(yes, length.out = len)[ypos] :”

Now before to push bioconductor, I would like to build and check,
Now,
I uninstrall tinytex, and used the conda to install texlive  “conda install -c 
conda-forge texlive-core”

And build again, now it complained no epihet.log file.

So I  built epihet without vigenttes, then using Rstudio on my MAC, NOT hpc, 
installed epihet, and compile epihet.Rnw, it can successfully transform Rnw to 
PDF.

Any suggestion?
I will appreciate it.
Thanks.
Best,
Xiaowen
From: "Kern, Lori" 
Date: Monday, November 23, 2020 at 4:05 PM
To: Xiaowen Chen 
Cc: "bioc-devel@r-project.org" 
Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform 
build/check report for BioC 3.12

And For What Its Worth -  I can reproduce the ERROR locally using a git clone 
from
g...@git.bioconductor.org:packages/epihet.git


(base) shepherd@jbcj433:~/BioconductorPackages/Software$ R CMD build epihet
Bioconductor version 3.13 (BiocManager 1.30.10), ?BiocManager::install for help
* checking for file 'epihet/DESCRIPTION' ... OK
* preparing 'epihet':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘epihet.Rnw’ using knitr
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'AnnotationDbi'

The following object is masked from 'package:clusterProfiler':

select


'select()' returned 1:1 mapping between keys and columns
Warning in rep(yes, length.out = len) :
  'x' is NULL so the result will be NULL
Quitting from lines 484-496 (epihet.Rnw)
Error: processing vignette 'epihet.Rnw' failed with diagnostics:
replacement has length zero
--- failed re-building ‘epihet.Rnw’

SUMMARY: processing the following file failed:
  ‘epihet.Rnw’

Error: Vignette re-building failed.
Execution halted




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Kern, Lori 

Sent: Monday, November 23, 2020 4:01 PM
To: Xiaowen Chen 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] [EXTERNAL]epihet problems reported in the Multiple 
platform build/check report for BioC 3.12

Please make sure your github repositories are up-to-date with the 
git.bioconductor.org repositories.  On quick glance, I can see you have not 
pulled the changes on the bioconductor server since the version numbers are not 
up-to-date for relesae and devel.  The version we have at git.bioconductor.org 
is the version of the package we are building and checking. not a github 
repository.  Perhaps you forgot to push changes to the git.bioconductor.org 
repository?
I suggest you check out the git help pages especially for

Syncing with Bioconductor:
http://secure-web.cisco.com/1_ed4MO3wzGEv9vtahMGt3EjH_fRdxuy-Ggwfv072LHMg33gJDq6NJ-O4j8ElxPP6icz-SAKtYbg7YAb7NdXVsKWMH8rsoXdimZDOKZDL7d1c-Mb6cggFxH5YKCjkmj08UrH5at6XPatjaa6_LPY4cOVXz-hkOZCdt7p7octVbhxBusXEUQExxebo1-rsrzBqvFppOI8qnlYv5hosKQk6izKY5rjKG_JhkfAIfazaOWJBSZXxxE9Ml4V8YhYZOEZXt470d1XSlY8F-lsYsPTTiaLRveK0RbPuwODtpKAm609JGxKZmcpOUNeXoX8TTLMg/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F

Pushing to Bioconductor release and devel:
http://secure-web.cisco.com/1Xg3LpZwFnSWhmcDJ_Cyy7XvU1VQn3SiYLwUSqjNAoFWlNnuYj0VmoRb53jBGHdlG73IPrxMQlsLZyP0hBmOi9kVhS2yTbZMs5OWxmyWWW-6f_i_lklGJ5LmzPDeW7bYBmZ4NqRPdQenUdQ460VyVO9wcXxyHHv0wpPEs8YAV4BlRDIXRA7Y6QeuDZbInXsw0YnL0ba7Swify49bnp-OyHs4gvC8p11paPMo_w07Zk0dbcexLbs9reMtR-lWRvGV9NGtSycUHQNNZlkYay03mW_eCIAthyAYaaxxFYg8GBD1srNlOD8qKFcL954Spxjp_/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fbug-fix-in-release-and-devel%2F



Other things to consider:

Make sure you are using the latest version of R and that all package 
dependencies are up to date.

For Release you should be using R 4.0.3 with Bioconductor 3.12.  Make sure all 
packages are up-to-date by running
BiocManager::install(version="3.12")
BiocManager::valid()   and/or   BiocManager::install()


For Devel you should be using R-devel  (what will be  R 4.1.0)  and 
Bioconductor 3.13. Again make sure packages are updated for this version
BiocManager::install(version="devel")
BiocManager::valid()   and/or   BiocManager::install()





Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostat

Re: [Bioc-devel] [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

[Xiaowen Chen]

Hi Kern,
I followed your suggestion and updated my Bioconductor version and epihet,
Then when I build epihet, it complained that

The following object is masked from 'package:clusterProfiler':

select


'select()' returned 1:1 mapping between keys and columns
Error: processing vignette 'epihet.Rnw' failed with diagnostics:
pdflatex is not available
--- failed re-building ‘epihet.Rnw’

SUMMARY: processing the following file failed:
  ‘epihet.Rnw’

Error: Vignette re-building failed.

I check my HPC has not pdflatex, so I installed tinytex from the website 
https://yihui.org/tinytex/ using following command lines:

remotes::install_github('yihui/tinytex')
tinytex::install_tinytex()

but another error occurred :

Error: processing vignette 'epihet.Rnw' failed with diagnostics:
unable to run pdflatex on 'epihet.tex'
LaTeX errors:
! LaTeX Error: File `mathptmx.sty' not found.

I tried it :
tlmgr install mathptmx.sty
tlmgr: package repository http://ctan.mirrors.hoobly.com/systems/texlive/tlnet 
(verified)
tlmgr install: package mathptmx.sty not present in repository.
tlmgr: action install returned an error; continuing.
tlmgr: An error has occurred. See above messages. Exiting.


Could you give me some suggestions?
Thank you!
Best,
Xiaowen
From: "Kern, Lori" 
Date: Monday, November 23, 2020 at 4:05 PM
To: Xiaowen Chen 
Cc: "bioc-devel@r-project.org" 
Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform 
build/check report for BioC 3.12

And For What Its Worth -  I can reproduce the ERROR locally using a git clone 
from
g...@git.bioconductor.org:packages/epihet.git


(base) shepherd@jbcj433:~/BioconductorPackages/Software$ R CMD build epihet
Bioconductor version 3.13 (BiocManager 1.30.10), ?BiocManager::install for help
* checking for file 'epihet/DESCRIPTION' ... OK
* preparing 'epihet':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘epihet.Rnw’ using knitr
Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'AnnotationDbi'

The following object is masked from 'package:clusterProfiler':

select


'select()' returned 1:1 mapping between keys and columns
Warning in rep(yes, length.out = len) :
  'x' is NULL so the result will be NULL
Quitting from lines 484-496 (epihet.Rnw)
Error: processing vignette 'epihet.Rnw' failed with diagnostics:
replacement has length zero
--- failed re-building ‘epihet.Rnw’

SUMMARY: processing the following file failed:
  ‘epihet.Rnw’

Error: Vignette re-building failed.
Execution halted




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Kern, Lori 

Sent: Monday, November 23, 2020 4:01 PM
To: Xiaowen Chen 
Cc: bioc-devel@r-project.org 
Subject: Re: [Bioc-devel] [EXTERNAL]epihet problems reported in the Multiple 
platform build/check report for BioC 3.12

Please make sure your github repositories are up-to-date with the 
git.bioconductor.org repositories.  On quick glance, I can see you have not 
pulled the changes on the bioconductor server since the version numbers are not 
up-to-date for relesae and devel.  The version we have at git.bioconductor.org 
is the version of the package we are building and checking. not a github 
repository.  Perhaps you forgot to push changes to the git.bioconductor.org 
repository?
I suggest you check out the git help pages especially for

Syncing with Bioconductor:
http://secure-web.cisco.com/1_ed4MO3wzGEv9vtahMGt3EjH_fRdxuy-Ggwfv072LHMg33gJDq6NJ-O4j8ElxPP6icz-SAKtYbg7YAb7NdXVsKWMH8rsoXdimZDOKZDL7d1c-Mb6cggFxH5YKCjkmj08UrH5at6XPatjaa6_LPY4cOVXz-hkOZCdt7p7octVbhxBusXEUQExxebo1-rsrzBqvFppOI8qnlYv5hosKQk6izKY5rjKG_JhkfAIfazaOWJBSZXxxE9Ml4V8YhYZOEZXt470d1XSlY8F-lsYsPTTiaLRveK0RbPuwODtpKAm609JGxKZmcpOUNeXoX8TTLMg/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F

Pushing to Bioconductor release and devel:
http://secure-web.cisco.com/1Xg3LpZwFnSWhmcDJ_Cyy7XvU1VQn3SiYLwUSqjNAoFWlNnuYj0VmoRb53jBGHdlG73IPrxMQlsLZyP0hBmOi9kVhS2yTbZMs5OWxmyWWW-6f_i_lklGJ5LmzPDeW7bYBmZ4NqRPdQenUdQ460VyVO9wcXxyHHv0wpPEs8YAV4BlRDIXRA7Y6QeuDZbInXsw0YnL0ba7Swify49bnp-OyHs4gvC8p11paPMo_w07Zk0dbcexLbs9reMtR-lWRvGV9NGtSycUHQNNZlkYay03mW_eCIAthyAYaaxxFYg8GBD1srNlOD8qKFcL954Spxjp_/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fbug-fix-in-release-and-devel%2F



Other things to consider:

Make sure you are using the latest version of R and that all package 
dependencies are up to date.

For Release you shoul

Re: [Bioc-devel] [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

[Xiaowen Chen]

Hi Kern,
I built epihet in my linux system, did not see anything wrong.
 Could you help me?thanks

First, download epihet, and build

(base) [chenx@helix ~]$ git clone 
https://github.com/TheJacksonLaboratory/epihet.git
Initialized empty Git repository in /home/c-chenx/epihet/.git/
remote: Enumerating objects: 839, done.
remote: Total 839 (delta 0), reused 0 (delta 0), pack-reused 839
Receiving objects: 100% (839/839), 4.59 MiB, done.
Resolving deltas: 100% (449/449), done.
(base) [chenx@helix ~]$ R CMD build epihet
* checking for file ‘epihet/DESCRIPTION’ ... OK
* preparing ‘epihet’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘epihet_1.5.5.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'

Please check the time, I indeed built it again today

(base) [chenx@helix ~]$ ll -a
-rw-r--r--   1 chenx jaxuser 798104 Nov 23 13:34 epihet_1.5.5.tar.gz

AND CHECK IT, ONLY WARINGS , just COMPLAIN THE Compile version,please see 
attached file for complete check result

R CMD check epihet_1.5.5.tar.gz
WARNINGs: program compiled against libxml 209 using older 207



From: "Kern, Lori" 
Date: Monday, November 23, 2020 at 12:42 PM
To: Xiaowen Chen , "bioc-devel@r-project.org" 

Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform 
build/check report for BioC 3.12

Your packages is failing in both release and devel of Bioconductor.  You need 
to fix the package.  You can see the ERROR on the build reports

bioconductor.org/checkResults/devel/bioc-LATEST/epihet

and

bioconductor.org/checkResults/release/bioc-LATEST/epihet
If you click on the ERROR on either one of those pages for any of the operating 
systems it will give more information on how the package is failing.




Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Xiaowen Chen 

Sent: Monday, November 23, 2020 12:19 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] FW: [EXTERNAL]epihet problems reported in the Multiple 
platform build/check report for BioC 3.12

Hi Bioconductor,
Recently I received the next email, but I used the website you sent me, version 
1.7 looks fine after three days when I submitted :
 bioconductor.org/checkResults/devel/bioc-LATEST/epihet/.
 And I can find my package on the following website.

bioconductor.org/packages/devel/bioc/html/epihet.html

but, I checked bioconductor.org/checkResults/devel/bioc-LATEST/epihet/ again 
today, why it told me build is wrong. I am confused.


Best,
Xiaowen

On 11/20/20, 1:00 PM, "bbs-nore...@bioconductor.org" 
 wrote:

[This is an automatically generated email. Please don't reply.]

Hi epihet maintainer,

According to the Multiple platform build/check report for BioC 3.12,
the epihet package has the following problem(s):

  o ERROR for 'R CMD build' on malbec1. See the details here:
  
https://secure-web.cisco.com/1fRXgUrwUkGrlrUDBrAssYtjnWZ-Ei1qmcSwfCkNOpPfQsZvTKlMKAUwIM0Ag_-qE1zFpBvCdNihAlCt6_fYWYphCHVxFB5wyxcQqR0gzMNayDOvQwTmufIBoA8d2RwGmEFUvgggpZAVFxwNP0Zbu_89smQJZwjII5_ag8UQkhFvdtphCVpQfyHdDVfUMGS-Rm24LeQn3HMPHMMGV6yy4Eov__WPpc-wmnktd6BeAnZ4bUWfezkpiFvyqLcwiq_9noR4g9avJtIL8Nnx9OPq7KkClUOvoOsgkAerycbIhZ0iraZJYEcV9qF3Zi8-Q-lxf/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.12%2Fbioc-LATEST%2Fepihet%2Fmalbec1-buildsrc.html

Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org

Notes:

  * This was the status of your package at the time this email was sent to 
you.
Given that the online report is updated daily (in normal conditions) you
could see something different when you visit the URL(s) above, 
especially if
you do so several days after you received this email.

  * It is possible that the problems reported in this report are false 
positives,
either because another package (from CRAN or Bioconductor) breaks your
package (if yours depends on it) or because of a Build System problem.
If this is the case, then you can ignore this email.

  * Please check the report again 24h after you've committed your changes 
to the
package and make sure that all the problems have gone.

  * If you have questions about this report or need help with the
maintenance of your package, please use the Bioc-devel mailing list:

  
https://secure-web.cisco.com/1_7E5OlJQt1L6CDez_cje5Rll39xYbr1dzA_gY80oK0T7QPCCw_NrsmbHec-DGJbKBlUO-Icx-P31S8j3TV_kxeXELPzefr_cBmzKwXYr_TvNrZXPFutuo_wS2tVkJDEcxkg7ZipWs

[Bioc-devel] FW: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

[Xiaowen Chen]

Hi Bioconductor,
Recently I received the next email, but I used the website you sent me, version 
1.7 looks fine after three days when I submitted :
 bioconductor.org/checkResults/devel/bioc-LATEST/epihet/. 
 And I can find my package on the following website.

bioconductor.org/packages/devel/bioc/html/epihet.html

but, I checked bioconductor.org/checkResults/devel/bioc-LATEST/epihet/ again 
today, why it told me build is wrong. I am confused.


Best,
Xiaowen

On 11/20/20, 1:00 PM, "bbs-nore...@bioconductor.org" 
 wrote:

[This is an automatically generated email. Please don't reply.]

Hi epihet maintainer,

According to the Multiple platform build/check report for BioC 3.12,
the epihet package has the following problem(s):

  o ERROR for 'R CMD build' on malbec1. See the details here:
  
https://master.bioconductor.org/checkResults/3.12/bioc-LATEST/epihet/malbec1-buildsrc.html

Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org

Notes:

  * This was the status of your package at the time this email was sent to 
you.
Given that the online report is updated daily (in normal conditions) you
could see something different when you visit the URL(s) above, 
especially if
you do so several days after you received this email.

  * It is possible that the problems reported in this report are false 
positives,
either because another package (from CRAN or Bioconductor) breaks your
package (if yours depends on it) or because of a Build System problem.
If this is the case, then you can ignore this email.

  * Please check the report again 24h after you've committed your changes 
to the
package and make sure that all the problems have gone.

  * If you have questions about this report or need help with the
maintenance of your package, please use the Bioc-devel mailing list:

  https://bioconductor.org/help/mailing-list/

(all package maintainers are requested to subscribe to this list)

For immediate notification of package build status, please
subscribe to your package's RSS feed. Information is at:

https://bioconductor.org/developers/rss-feeds/

Thanks for contributing to the Bioconductor project!


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Re: [Bioc-devel] [EXTERNAL]Re: A question about r package update

[Xiaowen Chen]

Yes, the check report is the one I lately push, 
But the epihet on the website" 
bioconductor.org/packages/devel/bioc/html/epihet.html " is not the one latest 
through check the vignettes.

So now I updated the version in DESCRIPTION to 1.5.3, and push again and hope I 
can see the latest version on the website " 
bioconductor.org/packages/devel/bioc/html/epihet.html "

Thank you.
Best,
Xiaowen

On 10/17/20, 10:26 AM, "Martin Morgan"  wrote:

Packages are built nightly, so you must usually wait ~24 - 48 hours for 
your commits to be reflected in the build report. 

Sometimes issues prevent the build report from being processed, so on the 
build overview page such as

  http://bioconductor.org/checkResults/devel/bioc-LATEST/

compare

  - 'This page generated on...'
  - 'Approx snapshot date...'

and on individual package pages such as

  http://bioconductor.org/checkResults/devel/bioc-LATEST/epihet/

look for

  - 'Snapshot date...'
  - 'Last commit...' 

If your last commit (`git log --oneline`) was after the snapshot date, then 
changes you made will not be reflected in the build report.

Because of the delay in the nightly builds, it makes sense to do your best 
to ensure that commits are correct, ensuring that your R and Bioconductor 
packages are current for the version that you are committing to, and running

  R CMD build 
  R CMD check 

locally before pushing changes.

Martin



On 10/16/20, 5:08 PM, "Bioc-devel on behalf of Xiaowen Chen" 
 wrote:

Hi Kern,
I checked the epihet on the website 
“bioconductor.org/packages/devel/bioc/html/epihet.html”.
I saw its version is 1.5.2
Unfortunately, it is not the one I push this morning. It is not the 
latest one.
Could you help me check what’s wrong here? I am so sorry about that.

Best,
Xiaowen
From: "Kern, Lori" 
Date: Friday, October 16, 2020 at 9:54 AM
To: Xiaowen Chen , "bioc-devel@r-project.org" 

Subject: [EXTERNAL]Re: A question about r package update

We apologize.  It was announced on the Bioconductor slack but we forgot 
to post on the bioc-devel mailing list. There was an issue with the builders 
and there was no report generated yesterday Thursday October 15.  The issue 
should be resolved and we expect a build report today.
I do see 1.5.2 in our git repository so it should be reflected in the 
report today.
We apologize for the confusion and the inconvenience


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________
From: Bioc-devel  on behalf of 
Xiaowen Chen 
Sent: Friday, October 16, 2020 9:49 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] A question about r package update

Hi bioc-devel,
I am sorry for email you so often, this morning I checked the check 
report website, it did not change.
And I noticed that the data is “This page was generated on 2020-10-14 
11:07:41 -0400 (Wed, 14 Oct 2020).”

Indeed I pushed my package on 2020-10-14. But its version is 1.5.2, not 
1.5.1 shown in the website.
Even it is not the one I pushed, now it have been two days.

So this morning I push epihet again. The command is as following
(base) [chenx@helix epihet]$ git remote add upstream 
g...@git.bioconductor.org:packages/epihet.git
(base) [chenx@helix epihet]$ git fetch --all
Fetching origin
Fetching upstream
Enter passphrase for key '/home/c-chenx/.ssh/id_rsa':
From git.bioconductor.org:packages/epihet
* [new branch]  RELEASE_3_10 -> upstream/RELEASE_3_10
* [new branch]  RELEASE_3_11 -> upstream/RELEASE_3_11
* [new branch]  RELEASE_3_9 -> upstream/RELEASE_3_9
* [new branch]  master -> upstream/master
(base) [chenx@helix epihet]$ git checkout master
Already on 'master'
(base) [chenx@helix epihet]$ git merge origin/master
Already up-to-date.
(base) [chenx@helix epihet]$ git merge upstream/master
Already up-to-date.
(base) [chenx@helix epihet]$ git push upstream master
Enter passphrase for key '/home/c-chenx/.ssh/id_rsa':
Everything up-to-date
(base) [chenx@helix epihet]$ git push origin master
Everything up-to-date


Previously, when I typed “git merge upstream/master”, it returned 
something like this
Merge made by recursive.
DESCRIPTION |2 +-
NEWS|7 +--
2 files changed, 6 insertions(+), 3 deletions(-)
mode change 100755 =>

Re: [Bioc-devel] [EXTERNAL]Re: A question about r package update

[Xiaowen Chen]

Hi Kern,
I checked the epihet on the website 
“bioconductor.org/packages/devel/bioc/html/epihet.html”.
I saw its version is 1.5.2
Unfortunately, it is not the one I push this morning. It is not the latest one.
Could you help me check what’s wrong here? I am so sorry about that.

Best,
Xiaowen
From: "Kern, Lori" 
Date: Friday, October 16, 2020 at 9:54 AM
To: Xiaowen Chen , "bioc-devel@r-project.org" 

Subject: [EXTERNAL]Re: A question about r package update

We apologize.  It was announced on the Bioconductor slack but we forgot to post 
on the bioc-devel mailing list. There was an issue with the builders and there 
was no report generated yesterday Thursday October 15.  The issue should be 
resolved and we expect a build report today.
I do see 1.5.2 in our git repository so it should be reflected in the report 
today.
We apologize for the confusion and the inconvenience


Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: Bioc-devel  on behalf of Xiaowen Chen 

Sent: Friday, October 16, 2020 9:49 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] A question about r package update

Hi bioc-devel,
I am sorry for email you so often, this morning I checked the check report 
website, it did not change.
And I noticed that the data is “This page was generated on 2020-10-14 11:07:41 
-0400 (Wed, 14 Oct 2020).”

Indeed I pushed my package on 2020-10-14. But its version is 1.5.2, not 1.5.1 
shown in the website.
Even it is not the one I pushed, now it have been two days.

So this morning I push epihet again. The command is as following
(base) [chenx@helix epihet]$ git remote add upstream 
g...@git.bioconductor.org:packages/epihet.git
(base) [chenx@helix epihet]$ git fetch --all
Fetching origin
Fetching upstream
Enter passphrase for key '/home/c-chenx/.ssh/id_rsa':
From git.bioconductor.org:packages/epihet
* [new branch]  RELEASE_3_10 -> upstream/RELEASE_3_10
* [new branch]  RELEASE_3_11 -> upstream/RELEASE_3_11
* [new branch]  RELEASE_3_9 -> upstream/RELEASE_3_9
* [new branch]  master -> upstream/master
(base) [chenx@helix epihet]$ git checkout master
Already on 'master'
(base) [chenx@helix epihet]$ git merge origin/master
Already up-to-date.
(base) [chenx@helix epihet]$ git merge upstream/master
Already up-to-date.
(base) [chenx@helix epihet]$ git push upstream master
Enter passphrase for key '/home/c-chenx/.ssh/id_rsa':
Everything up-to-date
(base) [chenx@helix epihet]$ git push origin master
Everything up-to-date


Previously, when I typed “git merge upstream/master”, it returned something 
like this
Merge made by recursive.
DESCRIPTION |2 +-
NEWS|7 +--
2 files changed, 6 insertions(+), 3 deletions(-)
mode change 100755 => 100644 DESCRIPTION

So I am curious whether epihet1.5.2 successfully push to upstream?
Could you help me to check? Since tomorrow is weekend.
Thank you pretty much.
Best,
Xiaowen
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[Bioc-devel] A question about r package update

[Xiaowen Chen]

Hi bioc-devel,
I am sorry for email you so often, this morning I checked the check report 
website, it did not change.
And I noticed that the data is “This page was generated on 2020-10-14 11:07:41 
-0400 (Wed, 14 Oct 2020).”

Indeed I pushed my package on 2020-10-14. But its version is 1.5.2, not 1.5.1 
shown in the website.
Even it is not the one I pushed, now it have been two days.

So this morning I push epihet again. The command is as following
(base) [chenx@helix epihet]$ git remote add upstream 
g...@git.bioconductor.org:packages/epihet.git
(base) [chenx@helix epihet]$ git fetch --all
Fetching origin
Fetching upstream
Enter passphrase for key '/home/c-chenx/.ssh/id_rsa':
From git.bioconductor.org:packages/epihet
* [new branch]  RELEASE_3_10 -> upstream/RELEASE_3_10
* [new branch]  RELEASE_3_11 -> upstream/RELEASE_3_11
* [new branch]  RELEASE_3_9 -> upstream/RELEASE_3_9
* [new branch]  master -> upstream/master
(base) [chenx@helix epihet]$ git checkout master
Already on 'master'
(base) [chenx@helix epihet]$ git merge origin/master
Already up-to-date.
(base) [chenx@helix epihet]$ git merge upstream/master
Already up-to-date.
(base) [chenx@helix epihet]$ git push upstream master
Enter passphrase for key '/home/c-chenx/.ssh/id_rsa':
Everything up-to-date
(base) [chenx@helix epihet]$ git push origin master
Everything up-to-date


Previously, when I typed “git merge upstream/master”, it returned something 
like this
Merge made by recursive.
DESCRIPTION |2 +-
NEWS|7 +--
2 files changed, 6 insertions(+), 3 deletions(-)
mode change 100755 => 100644 DESCRIPTION

So I am curious whether epihet1.5.2 successfully push to upstream?
Could you help me to check? Since tomorrow is weekend.
Thank you pretty much.
Best,
Xiaowen
---

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[Bioc-devel] Help for R package check

[Xiaowen Chen]

Hi bioc-devel,
I pushed the epihet to Bioconductor on Wen. And this morning I checked the 
result on the website “bioconductor.org/checkResults/devel/bioc-LATEST/epihet/. 
“

And I found the window environment there are error

“ERROR: dependency 'ReactomePA' is not available for package 'epihet'”

But this error is not from epihet package. Could you help me to fix it? And 
also I found epihet version still 1.5.1 even I update

DESCRIPTION document to 1.5.2, I don’t know why.



Thanks.

Best,

Xiaowen
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[Bioc-devel] Help me check if I push my package to git bioconductor

[Xiaowen Chen]

Hi there,
I have followed 
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/ to 
push to both Bioconductor and GitHub repositories.

However, I went to the website https://github.com/Bioconductor, I did not find 
my R package “epihet”,

  1.  Could you help me to check it?
  2.  When the epihet can be updated on the website 
https://bioconductor.riken.jp/packages/3.9/bioc/html/epihet.html, since it is 
related with paper revision, the reviewer will check if I updated R document 
based on her/his comments
  3.  If I update my epihet later, how can I update Bioconductor?

Still performed the following command?

3.1  git fetch –all

3.2  git checkout master

3.3  git merge origin/master

3.4  git merge upstream/master

3.5  git push upstream master

3.6   git push origin master

Thank you! I will appreciate it.
Best,
Xiaowen
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[Bioc-devel] An issue about submitting my SSH key to Bioconductor

[Xiaowen Chen]

Hi,
I would like to submit my SSH key to Bioconductor, so I went to the website 
https://git.bioconductor.org/BiocCredentials/account_activation/

When I input my email in my description file of my package ‘epihet’, I got the 
error like this

xiaowen.c...@jax.org is not associated with a maintainer of a Bioconductor 
package. Please check the spelling or contact bioc-devel@r-project.org for help.

Also try the my github email

hrbmu...@163.com is not associated with a maintainer of a Bioconductor package. 
Please check the spelling or contact bioc-devel@r-project.org for help.

Could you help to check why both of emails do not work? Or tell me what I 
should do?

I will appreciate it.
Thank you pretty much.

Best,
Xiaowen
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Re: [Bioc-devel] [EXTERNAL]Re: Update R package I developed which has been released by bioconductor

[Xiaowen Chen]

Hi Shepherd,

I tried to activate my account on 
https://git.bioconductor.org/BiocCredentials/account_activation/

xiaowen.c...@jax.org<mailto:xiaowen.c...@jax.org> which is shown in description 
file, but it told me:
xiaowen.c...@jax.org<mailto:xiaowen.c...@jax.org> is not associated with a 
maintainer of a Bioconductor package. Please check the spelling or contact 
bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> for help.
 This is my epihet link: 
https://bioconductor.riken.jp/packages/3.9/bioc/html/epihet.html
Could you help me?
Best,
Xiaowen

From: "Shepherd, Lori" 
Date: Friday, September 25, 2020 at 7:33 AM
To: Xiaowen Chen , "bioc-devel@r-project.org" 

Subject: Re: [EXTERNAL]Re: Update R package I developed which has been released 
by bioconductor

The remote set up you have is correct.  Based on your previous email and your 
new email to bioc-devel it looks like the issue is your access 
credentials/public key  and activating your git credentials account so you can 
manage keys.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

____
From: Xiaowen Chen 
Sent: Thursday, September 24, 2020 10:04 PM
To: Shepherd, Lori ; bioc-devel@r-project.org 

Subject: Re: [EXTERNAL]Re: Update R package I developed which has been released 
by bioconductor


By the way, when I performed “git remote -v”

It is different with yours, I have a “.git” for upstream



origin https://github.com/TheJacksonLaboratory/epihet.git (fetch)

origin https://github.com/TheJacksonLaboratory/epihet.git (push)

upstream g...@git.bioconductor.org:packages/epihet.git (fetch)

upstream g...@git.bioconductor.org:packages/epihet.git (push)



Is it right?

Best,

Xiaowen



From: "Shepherd, Lori" 
Date: Monday, September 21, 2020 at 9:22 AM
To: Xiaowen Chen , "bioc-devel@r-project.org" 

Subject: [EXTERNAL]Re: Update R package I developed which has been released by 
bioconductor



Bioconductor would not have your package on github.  Bioconductor has your 
repository in a git server.   If you already have a clone of your github 
repository you could follow the instructions here to add the remote to the 
Bioconductor repository you referenced here:

http://bioconductor.org/developers/how-to/git/sync-existing-repositories/<http://secure-web.cisco.com/1CGgZFviZNHf_PzBZoDIbYfrWRtCAwE3cXN_Br4oaRqMG09TfgkuIPaaxMorCSWOA2I-xG9LPFz8HvmW0DJCUsryRqjDpMlCCP8YGR-HE6UHUyiBMtcTmAA0Hv_au5qFFBiqwEtqSc9J3USTWIxrc2P3gDVByHH5nd1KeU-vuxvjj0iZWdcn6vjPhFCKcPkoYhIm8P5XMBNhJ9DFKM75lukyg2L4We-JZRzv--Rty7SvM78FRQOJ_2eTDHZeFm35Jr4nNl9tWOsEAUQNqBYKSxN4FmxewdWNw66l2EV-6qsKNUzbO1QV8_cEUZTvco2jt/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F>



so :

git clone  

cd epihet





Make sure you do the

git fetch --all

git pull upstream master before making any changes!! This will make sure you 
get the release version bumps the core team performed and that everything is 
up-to-date with our version of your repository at git.bioconductor.org



Once you add the remote upstream if you do git remote -v

origin should point to your github

upstream should point to Bioconductor

It would be something similar to



origin 
https://github.com/https://secure-web.cisco.com/1jto4PqGAETGWWrZg1lJy8YTYiLxiUl6gMitOiLT-D9gFgHHJkw_50iAKfQD_Y8E-yvcvsQstFNjcCTuG0KbQi7vAxa3T_mSjpQJyFClUmFsBZrjmkvqRRxT7EXwChsNl-Hey6xDhuuoav2gXJqN8ogSDyK5oa3ZuPgiYMyctBxAd8NlrTcgj9CztmC__ziIZOaq4GKOHK8zzkngrqfKqbd9UqMtEVhpy93WVveVYXbzNZT72inuxFJSEAfyaD_pGEreCH1Ve-6JSCfxspTiqV9518XeNfXDIYzL_wVd_qG3nYj9_Xy0Kiop6kFuVXh5-/https%3A%2F%2Fgithub.com%2F%253cYour>
 github> .git (fetch)

origin 
https://github.com/https://secure-web.cisco.com/1jto4PqGAETGWWrZg1lJy8YTYiLxiUl6gMitOiLT-D9gFgHHJkw_50iAKfQD_Y8E-yvcvsQstFNjcCTuG0KbQi7vAxa3T_mSjpQJyFClUmFsBZrjmkvqRRxT7EXwChsNl-Hey6xDhuuoav2gXJqN8ogSDyK5oa3ZuPgiYMyctBxAd8NlrTcgj9CztmC__ziIZOaq4GKOHK8zzkngrqfKqbd9UqMtEVhpy93WVveVYXbzNZT72inuxFJSEAfyaD_pGEreCH1Ve-6JSCfxspTiqV9518XeNfXDIYzL_wVd_qG3nYj9_Xy0Kiop6kFuVXh5-/https%3A%2F%2Fgithub.com%2F%253cYour>
 github>.git (push)

upstream g...@git.bioconductor.org:packages/epihet (fetch)

upstream g...@git.bioconductor.org:packages/epihet (push)





So when you push changes:



git push origin master

would update YOUR github

it is saying git push  to the origin which is your github on the master branch



To update on Bioconductor

git push upstream master

it is saying git push changes to the upstream with is the bioconductor remote 
master branch (devel)



Make sure the version number has a version bump!  Our version is at 1.5.0  so 
you would have to bump the z of version x.y.z for it to register on 
Bioconductor (>=  1.5.1  )



Hope that helps clarify.





Lori Shepherd

Bioconductor Core Team

Rosw

[Bioc-devel] Bioconductor Git Credentials

[Xiaowen Chen]

Hi there,
I have a R package ‘epihet’ published by Bioconductor, I would like to activate 
my account on https://git.bioconductor.org/BiocCredentials/account_activation/

xiaowen.c...@jax.org which is shown in description 
file, but it told me:
xiaowen.c...@jax.org is not associated with a maintainer of a Bioconductor 
package. Please check the spelling or contact bioc-devel@r-project.org for help.

Could you help me?
Thanks.

---

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is intended solely for the addressee(s). If you believe you received this email 
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Re: [Bioc-devel] [EXTERNAL]Re: Update R package I developed which has been released by bioconductor

[Xiaowen Chen]

By the way, when I performed “git remote -v”
It is different with yours, I have a “.git” for upstream

origin https://github.com/TheJacksonLaboratory/epihet.git (fetch)
origin https://github.com/TheJacksonLaboratory/epihet.git (push)
upstream g...@git.bioconductor.org:packages/epihet.git (fetch)
upstream g...@git.bioconductor.org:packages/epihet.git (push)

Is it right?
Best,
Xiaowen

From: "Shepherd, Lori" 
Date: Monday, September 21, 2020 at 9:22 AM
To: Xiaowen Chen , "bioc-devel@r-project.org" 

Subject: [EXTERNAL]Re: Update R package I developed which has been released by 
bioconductor

Bioconductor would not have your package on github.  Bioconductor has your 
repository in a git server.   If you already have a clone of your github 
repository you could follow the instructions here to add the remote to the 
Bioconductor repository you referenced here:
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/

so :
git clone  
cd epihet


Make sure you do the
git fetch --all
git pull upstream master before making any changes!! This will make sure you 
get the release version bumps the core team performed and that everything is 
up-to-date with our version of your repository at git.bioconductor.org

Once you add the remote upstream if you do git remote -v
origin should point to your github
upstream should point to Bioconductor
It would be something similar to

origin https://github.com/https://github.com/%3cYour> github> .git (fetch)
origin https://github.com/https://github.com/%3cYour> github>.git (push)
upstream g...@git.bioconductor.org:packages/epihet (fetch)
upstream g...@git.bioconductor.org:packages/epihet (push)


So when you push changes:

git push origin master
would update YOUR github
it is saying git push  to the origin which is your github on the master branch

To update on Bioconductor
git push upstream master
it is saying git push changes to the upstream with is the bioconductor remote 
master branch (devel)

Make sure the version number has a version bump!  Our version is at 1.5.0  so 
you would have to bump the z of version x.y.z for it to register on 
Bioconductor (>=  1.5.1  )

Hope that helps clarify.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________
From: Bioc-devel  on behalf of Xiaowen Chen 

Sent: Monday, September 21, 2020 8:57 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Update R package I developed which has been released by 
bioconductor

Hi,
I submit R package called epihet on 2018. It has been accepted and released on 
Bioconductor.
Recently, we received the reviewers’ comments about the corresponding paper for 
epihet, and the reviewer need us to add more parameters for some function in 
epihet,
Could you tell me what I should do step-by-step? Now I know the link

  1.  
http://secure-web.cisco.com/1-EVvVLIafjMbq01E8DqEQNgmvkKvvnjD-0pOAg6fnFQJZO7UJhpm74hsFevQdnOceH8Ueh2BWTT9kb9bsdL13IqIS93SOktOTaRvzl88vZQIjyKpVvpYcasFBguMZ539EF4nnf-yJhgY9ZqzCEecd6Lt5PcT0r6hY6iwYo-kRFbGTZgQvUYbiv4RVLCB0aMNRwNiL_faHaysCM-N9aMnkF0QCtDVuYHDOpwzG0F5eCLtvMhWpKTH29P3I5RfQgzRralE_Wz3O-tYENZrRrhyzlXMEbSEmVj6BtcGZ5p0YdkUaFJ_5NswJT984xe0R4_R/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F
 for sync an existing GitHub repository with Bioconductor
  2.  
http://secure-web.cisco.com/1a15GjCpVQyP3eF8WecbERPx8u0-Q3oUVwuRg9flwlizP3Dc6jfSdhF4CRMxd0I4M7S6UAfWCIbVnl67rKj6PsgIKMl5dppsGvqDKq8rf66Cm3qOq2JthrZCWEmdK4xZxV60M5gelNAIlZgVx1Q4HRDN_N4xilgDKIOy5WaMqWYc-57D0HIplyKyzL7xcmCZRnrdmYTfuxIAtS9KhxTHXcp1dfY6CZmW00wMdYPUWfUCkFjSe4_DancgDyMQkmB6EZ4S-PO5qKEdtIAkAEscewyygalAfrQEpiFigAz2iRvFjnDKvTOw5mBH4gvd0eGkb/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fbug-fix-in-release-and-devel%2F
 for fix bugs in devel and release
but I still not sure which github repository I need to git clone on my local 
machine, my own github or Bioconductor github, but I did not found my package 
“epihet” on Bioconductor github

Thank you.
Best,
Xiaowen

---

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Re: [Bioc-devel] [EXTERNAL]Re: Update R package I developed which has been released by bioconductor

[Xiaowen Chen]

Hi Shepherd,

I updated epihet in my github, then, I perform the following code:
git clone https://github.com/TheJacksonLaboratory/epihet.git
cd epihet
git remote add upstream g...@git.bioconductor.org:packages/epihet.git
git remote -v

git fetch –all

Fetching origin
Fetching upstream
The authenticity of host 'git.bioconductor.org (34.192.48.227)' can't be 
established.
RSA key fingerprint is 8b:f5:32:b4:a1:bb:94:d2:a3:8c:1a:35:90:98:f6:4e.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'git.bioconductor.org,34.192.48.227' (RSA) to the 
list of known hosts.
Permission denied (publickey).
fatal: The remote end hung up unexpectedly
error: Could not fetch upstream

I got the above error, could you give me some suggestion, I am not familiar 
git, I will appreciate it.

Thank you.
Best,
Xiaowen

From: "Shepherd, Lori" 
Date: Monday, September 21, 2020 at 9:22 AM
To: Xiaowen Chen , "bioc-devel@r-project.org" 

Subject: [EXTERNAL]Re: Update R package I developed which has been released by 
bioconductor

Bioconductor would not have your package on github.  Bioconductor has your 
repository in a git server.   If you already have a clone of your github 
repository you could follow the instructions here to add the remote to the 
Bioconductor repository you referenced here:
http://bioconductor.org/developers/how-to/git/sync-existing-repositories/

so :
git clone  
cd epihet


Make sure you do the
git fetch --all
git pull upstream master before making any changes!! This will make sure you 
get the release version bumps the core team performed and that everything is 
up-to-date with our version of your repository at git.bioconductor.org

Once you add the remote upstream if you do git remote -v
origin should point to your github
upstream should point to Bioconductor
It would be something similar to

origin https://github.com/https://github.com/%3cYour> github> .git (fetch)
origin https://github.com/https://github.com/%3cYour> github>.git (push)
upstream g...@git.bioconductor.org:packages/epihet (fetch)
upstream g...@git.bioconductor.org:packages/epihet (push)


So when you push changes:

git push origin master
would update YOUR github
it is saying git push  to the origin which is your github on the master branch

To update on Bioconductor
git push upstream master
it is saying git push changes to the upstream with is the bioconductor remote 
master branch (devel)

Make sure the version number has a version bump!  Our version is at 1.5.0  so 
you would have to bump the z of version x.y.z for it to register on 
Bioconductor (>=  1.5.1  )

Hope that helps clarify.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________
From: Bioc-devel  on behalf of Xiaowen Chen 

Sent: Monday, September 21, 2020 8:57 AM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Update R package I developed which has been released by 
bioconductor

Hi,
I submit R package called epihet on 2018. It has been accepted and released on 
Bioconductor.
Recently, we received the reviewers’ comments about the corresponding paper for 
epihet, and the reviewer need us to add more parameters for some function in 
epihet,
Could you tell me what I should do step-by-step? Now I know the link

  1.  
http://secure-web.cisco.com/1-EVvVLIafjMbq01E8DqEQNgmvkKvvnjD-0pOAg6fnFQJZO7UJhpm74hsFevQdnOceH8Ueh2BWTT9kb9bsdL13IqIS93SOktOTaRvzl88vZQIjyKpVvpYcasFBguMZ539EF4nnf-yJhgY9ZqzCEecd6Lt5PcT0r6hY6iwYo-kRFbGTZgQvUYbiv4RVLCB0aMNRwNiL_faHaysCM-N9aMnkF0QCtDVuYHDOpwzG0F5eCLtvMhWpKTH29P3I5RfQgzRralE_Wz3O-tYENZrRrhyzlXMEbSEmVj6BtcGZ5p0YdkUaFJ_5NswJT984xe0R4_R/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fsync-existing-repositories%2F
 for sync an existing GitHub repository with Bioconductor
  2.  
http://secure-web.cisco.com/1a15GjCpVQyP3eF8WecbERPx8u0-Q3oUVwuRg9flwlizP3Dc6jfSdhF4CRMxd0I4M7S6UAfWCIbVnl67rKj6PsgIKMl5dppsGvqDKq8rf66Cm3qOq2JthrZCWEmdK4xZxV60M5gelNAIlZgVx1Q4HRDN_N4xilgDKIOy5WaMqWYc-57D0HIplyKyzL7xcmCZRnrdmYTfuxIAtS9KhxTHXcp1dfY6CZmW00wMdYPUWfUCkFjSe4_DancgDyMQkmB6EZ4S-PO5qKEdtIAkAEscewyygalAfrQEpiFigAz2iRvFjnDKvTOw5mBH4gvd0eGkb/http%3A%2F%2Fbioconductor.org%2Fdevelopers%2Fhow-to%2Fgit%2Fbug-fix-in-release-and-devel%2F
 for fix bugs in devel and release
but I still not sure which github repository I need to git clone on my local 
machine, my own github or Bioconductor github, but I did not found my package 
“epihet” on Bioconductor github

Thank you.
Best,
Xiaowen

---

The information in this email, including attachments, may be confidential and 
is intended solely for the addressee(s). If you believe you received this email 
by mistake, please notify the sender by return email as soon as possible.

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.or

[Bioc-devel] Update R package I developed which has been released by bioconductor

[Xiaowen Chen]

Hi,
I submit R package called epihet on 2018. It has been accepted and released on 
Bioconductor.
Recently, we received the reviewers’ comments about the corresponding paper for 
epihet, and the reviewer need us to add more parameters for some function in 
epihet,
Could you tell me what I should do step-by-step? Now I know the link

  1.  http://bioconductor.org/developers/how-to/git/sync-existing-repositories/ 
for sync an existing GitHub repository with Bioconductor
  2.  
http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ for 
fix bugs in devel and release
but I still not sure which github repository I need to git clone on my local 
machine, my own github or Bioconductor github, but I did not found my package 
“epihet” on Bioconductor github

Thank you.
Best,
Xiaowen

---

The information in this email, including attachments, may be confidential and 
is intended solely for the addressee(s). If you believe you received this email 
by mistake, please notify the sender by return email as soon as possible.

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

[Bioc-devel] Update R package I developed which has been released by bioconductor

[Xiaowen Chen]

Hi,
I submit R package called epihet on 2018. It has been accepted and released on 
Bioconductor.
Recently, we received the reviewers’ comments about the corresponding paper for 
epihet, and the reviewer need us to add more parameters for some function in 
epihet,
Could you tell me what I should do step-by-step?
Thank you.
Best,
Xiaowen



---

The information in this email, including attachments, may be confidential and 
is intended solely for the addressee(s). If you believe you received this email 
by mistake, please notify the sender by return email as soon as possible.

[[alternative HTML version deleted]]

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel