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 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
[Bioc-devel] GenVisR Package Failing
4 messages · Skidmore, Zach, Shepherd, Lori
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 at r-project.org> on behalf of Skidmore, Zach <zskidmor at wustl.edu>
Sent: Tuesday, February 26, 2019 11:10 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] GenVisR Package Failing
Sent: Tuesday, February 26, 2019 11:10 AM
To: bioc-devel at 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 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
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 at r-project.org><mailto:bioc-devel-bounces at r-project.org> on behalf of Skidmore, Zach <zskidmor at wustl.edu><mailto:zskidmor at wustl.edu>
Sent: Tuesday, February 26, 2019 11:10 AM
To: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>
Subject: [Bioc-devel] GenVisR Package Failing
Sent: Tuesday, February 26, 2019 11:10 AM
To: bioc-devel at r-project.org<mailto:bioc-devel at 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 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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 at wustl.edu>
Sent: Tuesday, February 26, 2019 6:10:59 PM
To: Shepherd, Lori; bioc-devel at r-project.org
Subject: Re: GenVisR Package Failing
Sent: Tuesday, February 26, 2019 6:10:59 PM
To: Shepherd, Lori; bioc-devel at 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 at r-project.org><mailto:bioc-devel-bounces at r-project.org> on behalf of Skidmore, Zach <zskidmor at wustl.edu><mailto:zskidmor at wustl.edu>
Sent: Tuesday, February 26, 2019 11:10 AM
To: bioc-devel at r-project.org<mailto:bioc-devel at 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
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.