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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