Re: [Bioc-devel] UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 234445: ordinal not in range(128)

[Nitesh Turaga]

Hi,

Just to keep the mailing list informed. This has been solved. Please push again.

Nitesh

> On May 18, 2020, at 11:20 AM, Jakob Theorell  
> wrote:
> 
> Dear all,
> I guess this is related to some to me unknown failure on my side to avoid 
> merge conflicts, but I now get the above error when I try to push upstream. I 
> started by pulling upstream changes, had no obvious conflicts, and when 
> pushing I still got this. Puzzled. Have tried to look it up, but all answers 
> to solving this issue seem to relate to python-code, so I got nowhere there. 
> Below is the full message when I tried to push. Very thankful for insights 
> into solving this.
> Best regards
> Jakob
> 
> Enumerating objects: 122, done.
> Counting objects: 100% (122/122), done.
> Delta compression using up to 8 threads
> Compressing objects: 100% (65/65), done.
> Writing objects: 100% (65/65), 26.04 KiB | 5.21 MiB/s, done.
> Total 65 (delta 53), reused 0 (delta 0)
> remote: Traceback (most recent call last):
> remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line 110, 
> in 
> remote: apply_hooks(hooks_dict)
> remote:   File "hooks/pre-receive.h00-pre-receive-hook-software", line 90, in 
> apply_hooks
> remote: prevent_merge_markers(oldrev, newrev, refname)
> remote:   File 
> "/home/git/.gitolite/local/hooks/repo-specific/prevent_merge_markers.py", 
> line 35, in prevent_merge_markers
> remote: conflicts = git_diff_files_with_conflicts(oldrev, newrev)
> remote:   File 
> "/home/git/.gitolite/local/hooks/repo-specific/prevent_merge_markers.py", 
> line 26, in git_diff_files_with_conflicts
> remote: conflicts = pattern.search(diff.decode())
> remote: UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 
> 234445: ordinal not in range(128)
> To git.bioconductor.org:packages/DepecheR.git
> ! [remote rejected] master -> master (pre-receive hook declined)
> error: failed to push some refs to 
> 'g...@git.bioconductor.org:packages/DepecheR.git'
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
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Re: [Bioc-devel] SSH Issues

[Nitesh Turaga]

Hi Chris and Benjamin,

I’m trying to set things in order so that access is resumed back to normal for 
the 7 packages

It seems that there are multiple email address listed for Benjamin --  
‘benjamin.haibe.ka...@utoronto.ca’ and 'bhklab.resea...@gmail.com’.  Can we 
default to only one email address? 'benjamin.haibe.ka...@utoronto.ca’ is 
registered as maintainer on the packages, so choosing this email as the default 
would be easiest for me to fix. But I’ll leave the choice to you.

And I’ve created a new BiocCredentials account for Chris, so that there is no 
crossover of accounts. I’ll share these credentials with Chris in a private 
email. 

Both Chris and Benjamin will have maintainer access to the packages in 
question. 

Best,

Nitesh 




> On Jun 3, 2020, at 1:27 PM, Nitesh Turaga  wrote:
> 
> Hi Chris,
> 
> Thanks for that list. I’ll give you and Benjamin access all those packages. 
> That is what you need right? 
> 
> I’ll contact you when it’s done. Don’t do anything from your end just yet.
> 
> Best,
> 
> Nitesh 
> 
>> On Jun 3, 2020, at 1:26 PM, Chris Eeles > > wrote:
>> 
>> Hi Nitesh,
>> 
>> I did not change the username on purpose, maybe it happened because I 
>> submitted CoreGx under my GitHub account with Benjamin listed as the 
>> maintainer?
>> 
>> Anyway, all of our package on Bioconductor are:
>> genefu
>> PharmacoGx
>> predictionnet
>> survcomp
>> Xeva
>> consensusOV
>> CoreGx
>>  
>> Benjamin’s GitHub username is bhaibeka, if I just change the username back 
>> will that work?
>> 
>> Sorry for an inconvenience.
>>  
>> Best,
>> Chris
>>  
>> From: Nitesh Turaga mailto:nturaga.b...@gmail.com>> 
>> Sent: June 3, 2020 1:15 PM
>> To: Chris Eeles > >
>> Cc: bioc-devel@r-project.org ; Haibe-Kains, 
>> Benjamin > >
>> Subject: Re: [Bioc-devel] SSH Issues
>>  
>> Hi Chris,
>>  
>> I just checked and it seems you have changed the username in Benjamin’s 
>> account. Is that correct? 
>>  
>> So, the mapping is lost for all the packages Benjamin had, and your username 
>> as well has lost all of it’s mapping on Git repo. 
>>  
>> Can you tell me what packages you need access to? We should keep Benjamin’s 
>> account at his ‘utoronto.ca 
>> ’
>>  separate from yours. 
>>  
>> I’ll create an account for you and give you access. I’ll have to fix 
>> benjamin’s account and yours as well/
>>  
>> Best,
>>  
>> Nitesh 
>>  
>> 
>> 
>> On Jun 3, 2020, at 12:56 PM, Chris Eeles > > wrote:
>>  
>> Hi Nitesh,
>> 
>> I had a look at the packages I have access to and it seems that the 
>> Bioconductor credentials account I logged into only has access to the Xeva 
>> repo. I am using ‘benjamin.haibe.ka...@utoronto.ca 
>> ', the email listed as maintainer 
>> for all of the BHKLAB Bioconductor submissions.
>> 
>> 
>> Which email would the credentials be managed if not the maintainers’?
>> 
>> I tried activating an account using my GitHub email but it says I am not the 
>> maintainer of any packages.
>> 
>> Are you able to see which email the credentials for PharmacoGx and CoreGx 
>> are managed under? If not how can I manage access to these repos?
>> 
>> Thanks for your support.
>> 
>> Best,
>> Chris
>>  
>> From: Nitesh Turaga mailto:nturaga.b...@gmail.com>> 
>> Sent: June 3, 2020 11:05 AM
>> To: Chris Eeles > >
>> Cc: Bioc-devel@r-project.org 
>> Subject: Re: [Bioc-devel] SSH Issues
>>  
>> Hi Chris,
>>  
>> http://bioconductor.org/developers/how-to/git/faq/ 
>> 
>>  Take a look at #13 and #14. 
>>  
>> I’ll be able to better help you with more information.
>>  
>> Best,
>>  
>> Nitesh 
>> 
>> 
>> 
>> On Jun 3, 2020, at 10:49 AM, Chris Eeles > > wrote:
>>  
>> Hello Bioconductor team,
>> 
>> I am having issues pushing updates to the development branch of the CoreGx 
>> package.
>> 
>> When I try to push to upstream I get:
>> "FATAL: W any packages/CoreGx gangeshberiuhn DENIED by fallthru
>> (or you mis-spelled the reponame)
>> Fatal: Could not read from remote repository.
>> 
>> Please make sure you have the correct access rights
>> on the repository and the repository exists."
>> 
>> I have access to our Bioconductor 

Re: [Bioc-devel] Bioconductor package tidybulk

[Shepherd, Lori]

The master branch is the development branch (Bioc 3.12) .  The version  of  
x.y.z   The y is always odd in devel  and even in release.  This is the very 
first section on the page you referenced.  
http://bioconductor.org/developers/how-to/version-numbering/

We do not jump full y versions in the middle of a release.

The current RELEASE_3_11  version is  1.0.0  =  the appropriate version bump on 
this branch is  1.0.1

The current master version is 1.1.0  = the appropriate version bump on this 
branch is  1.1.1


If you are unfamiliar with git and github branches I encourage you to read more 
documentation about it.  There are many helpful tutorials.
You can have as many branches on your local github repository as you like. We 
recommend creating unique branches for bioconductor releases to mimic our 
branch structure.   In general, and to make it less confusing we would highly 
recommend using the master branch as the development branch and link that to 
the master (development version) of Bioconductor.   This would be consistent 
and then you can following the guides and tutorials listed on the Bioconductor 
help pages

http://bioconductor.org/developers/how-to/git/


The release branch is designed to always be a stable branch and should only be 
updated for bug corrections.
The master branch should be for development and new features.



We will assume you ran the following to set up your remotes as recommended:
git remote add upstream g...@git.bioconductor.org:packages/tidybulk.git


if you do
git remote -v

you should see something similar:
origin   (fetch)
origin   (push)
upstream g...@git.bioconductor.org:packages/tidybulk.git (fetch)
upstream g...@git.bioconductor.org:packages/tidybulk.git (push)


To create and work on a release branch:

git fetch --all
# this gets all branches from all remotes


# The following would only need to be run once EVER!
git checkout -b RELEASE_3_11  upstream/RELEASE_3_11

# this says checkout  a branch (-b)  call it RELEASE_3_11  and have it 
copied/link to the code at  upstream/RELEASE_3_11 (the #bioconductor upstream 
remote branch of RELEASE_3_11)

After it is created, to switch to this branch on a daily basis you can simply:
git checkout RELEASE_3_11



git pull upstream RELEASE_3_11
# pulls changes from the upstream RELEASE_3_11 remote


# The following would only need to be run once EVER!   It creates a branch on 
your local github called RELEASE_3_11
git push -u origin RELEASE_3_11



Make your code changes to fix bugs! Make sure to do a valid version bump by 
bumping the  z  of version  x.y.z

git add 
git commit# give an informative commit message


git push upstream RELEASE_3_11
# This should push to the Bioconductor git repository

git push origin RELEASE_3_11
# This should push to your github local git repository


git checkout master
# Switch back to your master branch for development and code changes


If you are ever confused on what branch you are on you can do
git branch


To work on the devel master branch the commands would be similar to above but 
using master

git pull upstream master  # pulls from git bioconductor
git pull origin master# pull from your individual github

# make changes, commit changes

git push upstream master  # pushes to git Bioconductor
git push origin master   # push to your github


Hopefully that helped clarified and will get you started.



Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


From: stefano 
Sent: Thursday, June 4, 2020 12:56 AM
To: Shepherd, Lori 
Cc: bioc-devel@r-project.org 
Subject: Re: Bioconductor package tidybulk

Thanks Lori,

I have to questions

1)
I got versioning error


```

rstudio-1 267 % git push upstream master
Counting objects: 372, done.
Delta compression using up to 32 threads.
Compressing objects: 100% (276/276), done.
Writing objects: 100% (290/290), 1.13 MiB | 0 bytes/s, done.
Total 290 (delta 208), reused 21 (delta 13)
remote: Resolving deltas: 100% (208/208), completed with 41 local objects.
remote: Error: Illegal version bump from '1.1.0' to '1.2.1'. Check
remote: 
http://bioconductor.org/developers/how-to/version-numbering/
remote: for details
To g...@git.bioconductor.org:packages/tidybulk.git

```

Even reading the guide 
http://bioconductor.org/developers/how-to/version-numbering/

Re: [Bioc-devel] How I hide non-exported function from the manual

[Martin Morgan]

None of the items below are \Sexp{}. Only \Sexp{} are \Sexp{}.

I built your package from github 

  git clone https://github.com/stemangiola/tidybulk
  R CMD build tidybulk
  R CMD BiocCheck tidybulk

and saw many (easily fixable) problems, but I did not see a line

You have  initialised objects"

so you must tell us exactly what you are doing to produce this.

Martin

On 6/4/20, 4:04 AM, "Bioc-devel on behalf of stefano" 
 wrote:

Thanks to Both,

since I cannot find any exhaustive documentation about  \Sexpr{} I will ask
here.

- is \examples{} an  \Sexpr{}
- is \value{} an  \Sexpr{}
- is \arguments{} an  \Sexpr{}
- is \item{} an  \Sexpr{}

Because although all my functions in the manual have, for example \value{},
non of them have  \Sexpr{} in the man. (only rowwise from dplyr, for which
I deleted the \Sexpr{} from the header).



Best wishes.

*Stefano *



Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544


Il giorno gio 4 giu 2020 alle ore 16:09 Henrik Bengtsson <
henrik.bengts...@gmail.com> ha scritto:

> On Wed, Jun 3, 2020 at 10:40 PM Vincent Carey
>  wrote:
> >
> > On Wed, Jun 3, 2020 at 11:48 PM stefano 
> wrote:
> >
> > > Hello Community,
> > >
> > > I am used to document function although hey are not exported
> > >
> > >
> > I suppose you are talking about tidybulk?  I am somewhat mystified by 
the
> > behavior
> > of
> >
> > %vjcair> R CMD build tidybulk
> >
> > * checking for file ‘tidybulk/DESCRIPTION’ ... OK
> >
> > * preparing ‘tidybulk’:
> >
> > * checking DESCRIPTION meta-information ... OK
> >
> > * installing the package to process help pages
> >
> > * building the PDF package manual
> >
> > Hmm ... looks like a package
> >
> > Converting Rd files to LaTeX .
> >
> > Creating pdf output from LaTeX ...
> >
> >
> > which produces a 147 page manual, and as you note many
> >
> > non-user-visible symbols are documented in manual.  I've
> >
> > never seen the "process help pages" phase in any
> >)
> > of my packages, and I don't know why.
>
> This step happens iff you have \Sexpr{} macros in your man/*.Rd files
> (see
> 
https://github.com/wch/r-source/blob/5bd6e3ce1430374105ebf02101f9d55173496cfe/src/library/tools/R/build.R#L582-L586
> )
>
> /Henrik
>
> >
> >
> > I don't have experience with the RdMacros setting in
> >
> > DESCRIPTION, and the way S3 methods are being handled
> >
> > in the package leads, I think, to an excess of Rd
> >
> > files relative to what you have as visible symbols
> >
> > in the package namespace.
> >
> >
> > Perhaps some tidyverse experts can comment.
> >
> >
> > > ```
> > > #' Get differential transcription information to a tibble using edgeR.
> > > #'
> > > #' @import dplyr
> > > #' @import tidyr
> > > #' @import tibble
> > > #' @importFrom magrittr set_colnames
> > > #' @importFrom stats model.matrix
> > > #' @importFrom utils installed.packages
> > > #' @importFrom utils install.packages
> > > #' @importFrom purrr when
> > > #'
> > > #'
> > > #' @param .data A tibble
> > > #' @param .formula a formula with no response variable, referring only
> to
> > > numeric variables
> > > #' @param .sample The name of the sample column
> > > #' @param .transcript The name of the transcript/gene column
> > > #' @param .abundance The name of the transcript/gene abundance column
> > > #' @param .contrasts A character vector. See edgeR makeContrasts
> > > specification for the parameter `contrasts`. If contrasts are not
> present
> > > the first covariate is the one the model is tested against (e.g., ~
> > > factor_of_interest)
> > > #' @param method A string character. Either "edgeR_quasi_likelihood"
> (i.e.,
> > > QLF), "edgeR_likelihood_ratio" (i.e., LRT)
> > > #' @param significance_threshold A real between 0 and 1
> > > #' @param minimum_counts A positive integer. Minimum counts required
> for at
> > > least some samples.
> > > #' @param minimum_proportion A real positive number between 0 and 1.
> It is
> > > the threshold of proportion of samples for each transcripts/genes that
> have
> > > to be characterised by a cmp bigger than the threshold to be included
> for
> > > scaling procedure.
> > > #' @param fill_missing_values A boolean. Whether to fill missing
> > > sample/transcript values with the median of the transcript. This is
> rarely
> > > needed.
> > > #' @param scaling_method A character string. The scaling method passed
> to
> > > the backend function

Re: [Bioc-devel] How I hide non-exported function from the manual

[Lluís Revilla]

Hi Stefano,

About 1) you can document internal functions but remove them from the index
if you use #' @keywords internal tag.
See the vignette of roxygen2
https://cran.r-project.org/web/packages/roxygen2/vignettes/rd.html under
Other tags.
About 2) perhaps you have too many/long examples?

Hope this helps,

Lluís



On Thu, 4 Jun 2020 at 05:48, stefano  wrote:

> Hello Community,
>
> I am used to document function although hey are not exported
>
> ```
> #' Get differential transcription information to a tibble using edgeR.
> #'
> #' @import dplyr
> #' @import tidyr
> #' @import tibble
> #' @importFrom magrittr set_colnames
> #' @importFrom stats model.matrix
> #' @importFrom utils installed.packages
> #' @importFrom utils install.packages
> #' @importFrom purrr when
> #'
> #'
> #' @param .data A tibble
> #' @param .formula a formula with no response variable, referring only to
> numeric variables
> #' @param .sample The name of the sample column
> #' @param .transcript The name of the transcript/gene column
> #' @param .abundance The name of the transcript/gene abundance column
> #' @param .contrasts A character vector. See edgeR makeContrasts
> specification for the parameter `contrasts`. If contrasts are not present
> the first covariate is the one the model is tested against (e.g., ~
> factor_of_interest)
> #' @param method A string character. Either "edgeR_quasi_likelihood" (i.e.,
> QLF), "edgeR_likelihood_ratio" (i.e., LRT)
> #' @param significance_threshold A real between 0 and 1
> #' @param minimum_counts A positive integer. Minimum counts required for at
> least some samples.
> #' @param minimum_proportion A real positive number between 0 and 1. It is
> the threshold of proportion of samples for each transcripts/genes that have
> to be characterised by a cmp bigger than the threshold to be included for
> scaling procedure.
> #' @param fill_missing_values A boolean. Whether to fill missing
> sample/transcript values with the median of the transcript. This is rarely
> needed.
> #' @param scaling_method A character string. The scaling method passed to
> the backend function (i.e., edgeR::calcNormFactors;
> "TMM","TMMwsp","RLE","upperquartile")
> #' @param omit_contrast_in_colnames If just one contrast is specified you
> can choose to omit the contrast label in the colnames.
> #'
> #' @return A tibble with edgeR results
> #'
> get_differential_transcript_abundance_bulk <- function
> [...]
> ```
>
> However this leads to 2 problems
>
> 1) The PDF manual includes many function that are not accessible to the
> user. How can I hide documented non-exported function from the manual
> 2) I receive the Biocheck note. "You have  initialised objects".
> Again how can I document an object without initialising it?
>
> Thanks a lot.
>
> Best wishes.
>
> *Stefano *
>
>
>
> Stefano Mangiola | Postdoctoral fellow
>
> Papenfuss Laboratory
>
> The Walter Eliza Hall Institute of Medical Research
>
> +61 (0)466452544
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] How I hide non-exported function from the manual

[stefano]

Thanks to Both,

since I cannot find any exhaustive documentation about  \Sexpr{} I will ask
here.

- is \examples{} an  \Sexpr{}
- is \value{} an  \Sexpr{}
- is \arguments{} an  \Sexpr{}
- is \item{} an  \Sexpr{}

Because although all my functions in the manual have, for example \value{},
non of them have  \Sexpr{} in the man. (only rowwise from dplyr, for which
I deleted the \Sexpr{} from the header).



Best wishes.

*Stefano *



Stefano Mangiola | Postdoctoral fellow

Papenfuss Laboratory

The Walter Eliza Hall Institute of Medical Research

+61 (0)466452544


Il giorno gio 4 giu 2020 alle ore 16:09 Henrik Bengtsson <
henrik.bengts...@gmail.com> ha scritto:

> On Wed, Jun 3, 2020 at 10:40 PM Vincent Carey
>  wrote:
> >
> > On Wed, Jun 3, 2020 at 11:48 PM stefano 
> wrote:
> >
> > > Hello Community,
> > >
> > > I am used to document function although hey are not exported
> > >
> > >
> > I suppose you are talking about tidybulk?  I am somewhat mystified by the
> > behavior
> > of
> >
> > %vjcair> R CMD build tidybulk
> >
> > * checking for file ‘tidybulk/DESCRIPTION’ ... OK
> >
> > * preparing ‘tidybulk’:
> >
> > * checking DESCRIPTION meta-information ... OK
> >
> > * installing the package to process help pages
> >
> > * building the PDF package manual
> >
> > Hmm ... looks like a package
> >
> > Converting Rd files to LaTeX .
> >
> > Creating pdf output from LaTeX ...
> >
> >
> > which produces a 147 page manual, and as you note many
> >
> > non-user-visible symbols are documented in manual.  I've
> >
> > never seen the "process help pages" phase in any
> >)
> > of my packages, and I don't know why.
>
> This step happens iff you have \Sexpr{} macros in your man/*.Rd files
> (see
> https://github.com/wch/r-source/blob/5bd6e3ce1430374105ebf02101f9d55173496cfe/src/library/tools/R/build.R#L582-L586
> )
>
> /Henrik
>
> >
> >
> > I don't have experience with the RdMacros setting in
> >
> > DESCRIPTION, and the way S3 methods are being handled
> >
> > in the package leads, I think, to an excess of Rd
> >
> > files relative to what you have as visible symbols
> >
> > in the package namespace.
> >
> >
> > Perhaps some tidyverse experts can comment.
> >
> >
> > > ```
> > > #' Get differential transcription information to a tibble using edgeR.
> > > #'
> > > #' @import dplyr
> > > #' @import tidyr
> > > #' @import tibble
> > > #' @importFrom magrittr set_colnames
> > > #' @importFrom stats model.matrix
> > > #' @importFrom utils installed.packages
> > > #' @importFrom utils install.packages
> > > #' @importFrom purrr when
> > > #'
> > > #'
> > > #' @param .data A tibble
> > > #' @param .formula a formula with no response variable, referring only
> to
> > > numeric variables
> > > #' @param .sample The name of the sample column
> > > #' @param .transcript The name of the transcript/gene column
> > > #' @param .abundance The name of the transcript/gene abundance column
> > > #' @param .contrasts A character vector. See edgeR makeContrasts
> > > specification for the parameter `contrasts`. If contrasts are not
> present
> > > the first covariate is the one the model is tested against (e.g., ~
> > > factor_of_interest)
> > > #' @param method A string character. Either "edgeR_quasi_likelihood"
> (i.e.,
> > > QLF), "edgeR_likelihood_ratio" (i.e., LRT)
> > > #' @param significance_threshold A real between 0 and 1
> > > #' @param minimum_counts A positive integer. Minimum counts required
> for at
> > > least some samples.
> > > #' @param minimum_proportion A real positive number between 0 and 1.
> It is
> > > the threshold of proportion of samples for each transcripts/genes that
> have
> > > to be characterised by a cmp bigger than the threshold to be included
> for
> > > scaling procedure.
> > > #' @param fill_missing_values A boolean. Whether to fill missing
> > > sample/transcript values with the median of the transcript. This is
> rarely
> > > needed.
> > > #' @param scaling_method A character string. The scaling method passed
> to
> > > the backend function (i.e., edgeR::calcNormFactors;
> > > "TMM","TMMwsp","RLE","upperquartile")
> > > #' @param omit_contrast_in_colnames If just one contrast is specified
> you
> > > can choose to omit the contrast label in the colnames.
> > > #'
> > > #' @return A tibble with edgeR results
> > > #'
> > > get_differential_transcript_abundance_bulk <- function
> > > [...]
> > > ```
> > >
> > > However this leads to 2 problems
> > >
> > > 1) The PDF manual includes many function that are not accessible to the
> > > user. How can I hide documented non-exported function from the manual
> > > 2) I receive the Biocheck note. "You have  initialised
> objects".
> > > Again how can I document an object without initialising it?
> > >
> > > Thanks a lot.
> > >
> > > Best wishes.
> > >
> > > *Stefano *
> > >
> > >
> > >
> > > Stefano Mangiola | Postdoctoral fellow
> > >
> > > Papenfuss Laboratory
> > >
> > > The Walter Eliza Hall Institute of Medical Research
> > >
> > > +61 (

Re: [Bioc-devel] git push permission denied

[Christian Mertes]

Dear Nitesh,

thank you for resolving this so quickly! 

Best,
Christian

On Tue, 2020-06-02 at 11:53 -0400, Nitesh Turaga wrote:
> Hi,
> 
> This is because you don’t have access to FRASER package. Only Ines
> Scheller seems to have access to it. 
> 
> I’ve made the change and you should have access to it now. 
> 
> Best,
> 
> Nitesh 
> 
> 
> 
> > On Jun 2, 2020, at 12:34 AM, Christian Mertes 
> > wrote:
> > 
> > Dear Bioc team,
> > 
> > I tried to push an update to my FRASER package, but was not
> > successful.
> > Are the permissions correct? Maybe the problem comes from the fact
> > that
> > Ines Scheller did submit the package but I'm stated as maintainer
> > in
> > the DESCRIPTION. 
> > 
> > Here are some details: 
> > 
> > $ git remote --verbose
> > biocg...@git.bioconductor.org:packages/FRASER.git (fetch)
> > biocg...@git.bioconductor.org:packages/FRASER.git (push)
> > origin  g...@github.com:gagneurlab/FRASER (fetch)
> > origin  g...@github.com:gagneurlab/FRASER (push)
> > 
> > $ git push bioc master 
> > FATAL: W any packages/FRASER c-mertes DENIED by fallthru
> > (or you mis-spelled the reponame)
> > fatal: Could not read from remote repository.
> > 
> > Please make sure you have the correct access rights
> > and the repository exists.
> > 
> > I'm able to push to my other package OUTRIDER with no issues.
> > 
> > Let me know if you need more infos on this.
> > 
> > Best,
> > Christian
> > 
> > -- 
> > Christian Mertes | PhD Student / Lab Administrator
> > 
> > Gagneur Lab - Computational Genomics
> > I12 - Department of Informatics
> > Technical University of Munich
> > Boltzmannstr. 3, 85748 Garching, Germany
> > 
> > mer...@in.tum.de | https://in.tum.de/gagneurlab
> > 
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> 
-- 
Christian Mertes | PhD Student / Lab Administrator

Gagneur Lab - Computational Genomics
I12 - Department of Informatics
Technical University of Munich
Boltzmannstr. 3, 85748 Garching, Germany

mer...@in.tum.de | https://in.tum.de/gagneurlab

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