[Bioc-devel] GenVisR Package Failing

[Shepherd, Lori]

https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Checking-and-building-packages


I think it needed to be in a `.R` directory too -   `~/.R/check.Renviron`



Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Skidmore, Zach <zskidmor using wustl.edu>
Sent: Tuesday, February 26, 2019 6:10:59 PM
To: Shepherd, Lori; bioc-devel using r-project.org
Subject: Re: GenVisR Package Failing


Got it, thanks for the tip! I've pushed a fix that should resolve this but I have another question.


The only way I could get check.Renviron to load was to either


1. explicitly load the file in R with readRenviron("~/check.Renviron")

2. manually set the R ENV variable with Sys.setenv("R_CHECK_ENVIRON"="~/check.Renviron")


>From the docs on bioc I should have been able to just add export R_CHECK_ENVIRON=~/check.Renviron to my .bashrc and R should have recognized the variable was set however this did not work. I also tried putting the file in /Library/Frameworks/R.framework/Resources/etc/ based on what I read here however that did not work either. Any thoughts, I want to avoid having to manually set these variables every time I work on the package?


maybe the easiest thing is to just set these flags in the rstudio config for this project, I see you can do this with --install=value but couldn't find any examples for setting this for a list of parameters and what I tried must have been the wrong syntax


Zach

On 2/26/19 10:28 AM, Shepherd, Lori wrote:

The ERROR your package is experiencing has to do with conditional length greater than 1.  We did send you an email indicating this entitled "Bioconductor Package ERROR"  that had the following information:



In a continued effort to better code, there have been efforts to identify problematic existing code in packages. The current issue at hand is identifying a conditional with a length greater than 1. This could either be an over site of not using any() or all() or could potential indicate problematic code with unexpected multiple output.

dummy example:

```
> check = c(1:5)
> if (check > 3){
+    FALSE
+ }



It is controlled with the following that are implemented on the build system


_R_CHECK_LENGTH_1_CONDITION_ =package:_R_CHECK_PACKAGE_NAME_
_R_CHECK_LENGTH_1_LOGIC2_=package:_R_CHECK_PACKAGE_NAME_

And there is some documentation here which should help get the environment similar to reproduce the error:

http://bioconductor.org/developers/package-guidelines/#checkingenv




There is a more detailed Test output section at the bottom of the build report page that shows the code that was being run.

http://bioconductor.org/checkResults/3.9/bioc-LATEST/GenVisR/malbec2-checksrc.html








Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org><mailto:bioc-devel-bounces using r-project.org> on behalf of Skidmore, Zach <zskidmor using wustl.edu><mailto:zskidmor using wustl.edu>
Sent: Tuesday, February 26, 2019 11:10 AM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>
Subject: [Bioc-devel] GenVisR Package Failing

Hi All,


I maintain the GenVisR package which is currently failing on the devel
branch. I can see it has something to do with the test cases however the
error message is not clear, I don't get a line number for which test
case has failed or any other indication to that effect. Normally this
wouldn't be a problem but I only see failures in the bioc environments
(locally everything is fine). I had thought it might be related to my
visual test cases with the vdiffr package however I skipped all those in
version 1.15.1.


Is there any way I can find the sessionInfo() for the bioc-devel
environment to make sure everything matches my local environment?


Thanks!

Zach


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