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-boun...@r-project.org><mailto:bioc-devel-boun...@r-project.org> on
behalf of Skidmore, Zach <zskid...@wustl.edu><mailto:zskid...@wustl.edu>
Sent: Tuesday, February 26, 2019 11:10 AM
To: bioc-devel@r-project.org<mailto:bioc-devel@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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