Re: [Bioc-devel] "there is no package called 'BSgenome.Athaliana.TAIR.TAIR9'"

[Martin Morgan]

This warning

* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘BSgenome.Athaliana.TAIR.TAIR9’

means that you have used BSgenome.Athaliana.TAIR.TAIR9 in your code, but you 
have not declared it in your DESCRIPTION file, either as Imports: or Suggests:. 
Since it isn't in your DESCRIPTION file, the build system does not know that it 
should be installed for checking your package.

~/b/git/trena master$ grep Athal DESCRIPTION
~/b/git/trena master$

This is a little surprising, implying that no other package in the build system 
has this package in the DESCRIPTION file, but...

It looks like this needs to be added to the Imports: field, or perhaps Suggests:

Martin

On 10/12/20, 12:36 PM, "Bioc-devel on behalf of Paul Shannon" 
 
wrote:

My package trena fails on all platforms with this error:

   there is no package called ‘BSgenome.Athaliana.TAIR.TAIR9’

Is Arabidopsis no longer supported by bioc?  I remember some discussion 
related to this over the summer.

 - Paul
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Re: [Bioc-devel] Sorry confused about version numbers etc...

[Martin Morgan]

The version scheme is outlined at 
https://bioconductor.org/developers/how-to/version-numbering/

Within a 'release', the version x.y.z is always bumped in the z field. You are 
at 1.8.0 in release, so the version bump is to 1.8.1, 1.8.2, ...

Meanwhile, in devel you were at 1.9.0, so the version bumps are 1.9.1, 1.9.2, 
...

The solution to your current dilemma is to bump the version of the RELEASE_3_11 
branch to 1.8.1. But beware that this will be your last shot at committing to 
the RELEASE_3_11 branch, because commits to the 3_11 branch will stop tomorrow 
-- I'd only bump the release version if this were an important bug fix, and you 
were sure you'd got it right.

'devel' will become 'release' on October 27 (see 
https://bioconductor.org/developers/release-schedule/) when the BIOCONUCTOR 
team will create a new 'RELEASE_3_12' branch from your current 'devel' branch. 
The 3_12 release will have version 1.10.0. the 'devel' branch will also be 
incremented, to 1.11.0. Subsequently, your version bumps are 1.10.1, 1.10.2, 
... in RELEASE_3_12, and 1.11.1, 1.11.2, ... in devel.

Martin

On 10/12/20, 2:22 PM, "Bioc-devel on behalf of Paul Brennan" 
 
wrote:

Hi,
Sorry to be a pain but I'm getting in quite a muddle - probably due to
inexperience as a developer.
So basically, I have made a small but important change to my package
drawProteins. The addition of 10 lines to the function extract_feat_acc()
in file called extract_from_api.R
I have made these changes to my master on Github (V 1.9.0) and pushed
upstream to Bioconductor, I think...
I have tried to make these changes to RELEASE_3_11 as I thought that
was what was required. However, it doesn't seem to allow me to change
the Version numbers. However, as I say I have got confused...
I hope I am making sense.
Any advice or help would be great. I've spent the last number of hours
trying to work all this out with very little success :-(
Thanks in advance,
Paul

Paul Brennan

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[Bioc-devel] Sorry confused about version numbers etc...

[Paul Brennan]

Hi,
Sorry to be a pain but I'm getting in quite a muddle - probably due to
inexperience as a developer.
So basically, I have made a small but important change to my package
drawProteins. The addition of 10 lines to the function extract_feat_acc()
in file called extract_from_api.R
I have made these changes to my master on Github (V 1.9.0) and pushed
upstream to Bioconductor, I think...
I have tried to make these changes to RELEASE_3_11 as I thought that
was what was required. However, it doesn't seem to allow me to change
the Version numbers. However, as I say I have got confused...
I hope I am making sense.
Any advice or help would be great. I've spent the last number of hours
trying to work all this out with very little success :-(
Thanks in advance,
Paul

Paul Brennan

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[Bioc-devel] "there is no package called 'BSgenome.Athaliana.TAIR.TAIR9'"

[Paul Shannon]

My package trena fails on all platforms with this error:

   there is no package called ‘BSgenome.Athaliana.TAIR.TAIR9’

Is Arabidopsis no longer supported by bioc?  I remember some discussion related 
to this over the summer.

 - Paul
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Re: [Bioc-devel] Lost access to my package "AffiXcan", and gained W permissions to empty repo "AffiXan"

[Nitesh Turaga]

Hi Alessandro,

This package seems to have been added with the wrong name in our 
BiocCredentials system. It is fixed now. 

Please check it on your end.

Best,

Nitesh 



> On Oct 11, 2020, at 9:08 AM, Alessandro Lussana via Bioc-devel 
>  wrote:
> 
> Hi,
> 
> Unexpectedly I found to have lost write permissions to the package (AffiXcan) 
> I'm maintaining (I still have R permissions).
> I checked in my BiocCredentials and, very strangely, I found that I have R 
> and W access to a package named "AffiXan", instead of "AffiXcan".
> I have no idea how this happened, and I did not found incoherence in the 
> package documentation concerning typos (grep -r AffiXan returns nothing).
> Also, git clone g...@git.bioconductor.org:packages/AffiXan results in
> 
> Cloning into 'AffiXan'...
> warning: You appear to have cloned an empty repository.
> 
> I could use some help to regain W permissions to "AffiXcan", and to 
> understand where this "AffiXan" empty repo came from.
> Thanks!
> 
> Best regards,
> 
> ——
> Alessandro
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] How to handle namespace/import of Rcurl

[Martin Morgan]

The message is trying to say that RCurl has not been declared in the 
DESCRIPTION file; add Imports: RCurl to the DESCRIPTION.

I know that you indicate that you have done this already, but it is not present 
in the current DESCRIIPTION file, and it is the reason for the current warning 
message.

Other WARNINGS are also due to incorrect issues related to imports. For 
instance, 

  analyzeIUPred2A: no visible global function definition for 'queryHits'

is because the NAMESPACE does not have

  importFrom(S4Vectors, queryHits)

or simply

  import(S4Vectors)

Warnings such as

  expressionAnalysisPlot: no visible binding for global variable 'CI_up'

occur because of use of 'non-standard' evaluation in ggplot / dplyr. The 
current recommended solution seems to be to use `.data$CI_up` from rlang; 
update the code to use this syntax, and be sure to Import: rlang / 
importFrom(rlang, .data)

It would be good to address these.

For what it's worth, long lines in the DESCRIPTION file can be split, provided 
they are indented. So for instance

Imports: methods, BSgenome, plyr, reshape2, gridExtra, Biostrings (>= 2.50.0), 
IRanges,
GenomicRanges, DRIMSeq, RColorBrewer, rtracklayer, VennDiagram, DBI, 
grDevices, graphics,
stats, utils, GenomeInfoDb, grid, tximport (>= 1.7.1), tximeta (>= 1.7.12), 
edgeR,
futile.logger, stringr, dplyr, magrittr, readr, tibble, XVector, 
BiocGenerics

Martin

On 10/12/20, 3:51 AM, "Bioc-devel on behalf of Kristoffer Vitting-Seerup" 
 
wrote:

Hi Devel

I've recently added a function which relies on Rcurl but I'm having trouble
figuring out how to handle it in the namespace/import since it behaves
differently from other packages I rely on.

As seen here

I
currently I get a warning stating:
"*'::' or ':::' import not declared from: 'RCurl'*"

Due to inclusion of this code on one of my functions:

*RCurl::url.exists(isoformExonAnnoation)*

I've over the last couple of weeks tried several different things to avoid
warnings:
- Added it to namespace (*importFrom("RCurl", "*url.exists*" *)
- Imported the entire package in the namespace
- Added it to the Imports in the DESCRIPTION

For all of these I keep getting errors or warnings saying this is not
necessary for RCurl. Can somebody help me out with what the proper way to
avoid the warning above without causing any other errors/warning?

Cheers
Kristoffer

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[Bioc-devel] How to handle namespace/import of Rcurl

[Kristoffer Vitting-Seerup]

Hi Devel

I've recently added a function which relies on Rcurl but I'm having trouble
figuring out how to handle it in the namespace/import since it behaves
differently from other packages I rely on.

As seen here
I
currently I get a warning stating:
"*'::' or ':::' import not declared from: 'RCurl'*"

Due to inclusion of this code on one of my functions:

*RCurl::url.exists(isoformExonAnnoation)*

I've over the last couple of weeks tried several different things to avoid
warnings:
- Added it to namespace (*importFrom("RCurl", "*url.exists*" *)
- Imported the entire package in the namespace
- Added it to the Imports in the DESCRIPTION

For all of these I keep getting errors or warnings saying this is not
necessary for RCurl. Can somebody help me out with what the proper way to
avoid the warning above without causing any other errors/warning?

Cheers
Kristoffer

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