[Bioc-devel] git permissions

2021-03-01 Thread Michael Lawrence via Bioc-devel 
Just got this when trying to push a change to IRanges:

Pushing to g...@git.bioconductor.org:packages/IRanges.git
FATAL: W any packages/IRanges m.lawrence DENIED by fallthru
(or you mis-spelled the reponame)
fatal: Could not read from remote repository.

Have git permissions changed?

Thanks,
Michael

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Senior Scientist, Director of Data Science and Statistical Computing
Genentech, A Member of the Roche Group
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Re: [Bioc-devel] Error on BiocCheckGitClone and Windows build

2021-03-01 Thread Kern, Lori 
Please feel free to also comment directly on your issue for your reviewer to 
assist.

The packages not being available on windows is likely on our end and you can 
ignore for now.

System files should not be git tracked. They should be remove using git remove 
and then committed up.
git rm 
git commit -a

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 Oluwafemi 
OLUSOJI 
Sent: Monday, March 1, 2021 12:12 PM
To: bioc-devel@r-project.org 
Subject: [Bioc-devel] Error on BiocCheckGitClone and Windows build

Dear All,

I recently submitted a package to Bioconductor and got this error message
as part of the reply email. I am not sure what to do about it.

The two files are git tracked,  but they are also named in .Rbuildignore so
I felt they should have been avoided. This is my first experience with
Bioconductor so any help would be appreciated.

Furthermore, there are errors related to dependencies on the windows build.
Should I worry about these?

Regards,
Olusoji Oluwafemi Daniel

## Error Related to Windows test build 

===

 R CMD BUILD

===

* checking for file 'cyanoFilter/DESCRIPTION' ... OK
* preparing 'cyanoFilter':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
  ---
ERROR: dependencies 'flowCore', 'flowDensity' are not available for
package 'cyanoFilter'
* removing 
'C:/Users/pkgbuild/AppData/Local/Temp/Rtmp0gaTHW/Rinst8fd05a8549f/cyanoFilter'
  ---
ERROR: package installation failed


### Error related to git tracked files #

This is BiocCheckGitClone version 1.27.2. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
.Renviron
cyanoFilter.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

[[alternative HTML version deleted]]

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[Bioc-devel] Moving minfi classes definition to a lighter package

2021-03-01 Thread Carlos Ruiz 
Dear Bioc developers,

I have been developing different packages to analyze DNA methylation. In
all of them, I have used minfi's class GenomicRatioSet to manage DNA
methylation data, in order to take profit of the features of
RangedSummarizedExperiment.

Although I am very happy with the potential of the class, importing its
definition from minfi, makes me add the package to imports. As minfi has a
high number of dependencies (129 in the current release), my packages end
up having hundreds of dependencies too. This is particularly problematic as
I do not use any of the other functions of minfi.

I am wondering whether it could be possible to move minfi's class (or at
least GenomicRatioSet) to a lighter package, so people developing packages
on DNA methylation could rely on this class without having to import the
whole minfi package and its dependencies.

Thank you very much,
-- 

Carlos Ruiz

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[Bioc-devel] Error on BiocCheckGitClone and Windows build

2021-03-01 Thread Oluwafemi OLUSOJI 
Dear All,

I recently submitted a package to Bioconductor and got this error message
as part of the reply email. I am not sure what to do about it.

The two files are git tracked,  but they are also named in .Rbuildignore so
I felt they should have been avoided. This is my first experience with
Bioconductor so any help would be appreciated.

Furthermore, there are errors related to dependencies on the windows build.
Should I worry about these?

Regards,
Olusoji Oluwafemi Daniel

## Error Related to Windows test build 

===

 R CMD BUILD

===

* checking for file 'cyanoFilter/DESCRIPTION' ... OK
* preparing 'cyanoFilter':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
  ---
ERROR: dependencies 'flowCore', 'flowDensity' are not available for
package 'cyanoFilter'
* removing 
'C:/Users/pkgbuild/AppData/Local/Temp/Rtmp0gaTHW/Rinst8fd05a8549f/cyanoFilter'
  ---
ERROR: package installation failed


### Error related to git tracked files #

This is BiocCheckGitClone version 1.27.2. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
.Renviron
cyanoFilter.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...

[[alternative HTML version deleted]]

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