Good day, There is an error for ClassifyR on malbec1 and merida1 caused by a documentation example. However, it doesn't occur on tokay1. Can I get more information about which example is emitting the error on malbec1 server? -------------------------------------- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia
[Bioc-devel] ClassifyR Check Error on Linux and MacOS Systems
4 messages · Dario Strbenac, Shepherd, Lori
5 days later
I tried to build/check your package locally and actually get a different ERROR in the build process ... You might try using devtools::run_examples() - it runs only the examples in the package When I use devtools::run_examples()
### Name: edgesToHubNetworks ### Title: Convert a Two-column Matrix or Data Frame into a Hub Node List ### Aliases: edgesToHubNetworks ### ** Examples interactor <- sapply(1:10000, function(index)
+ paste(c(sample(LETTERS, 3), sample(1:9, 1)), collapse = ''))
otherInteractor <- sapply(1:10000, function(index)
+ paste(c(sample(LETTERS, 3), sample(1:9, 1)), collapse = ''))
edges <- data.frame(interactor, otherInteractor, stringsAsFactors = FALSE)
edgesToHubNetworks(edges, minCardinality = 4)
Error in object at sets[[1]] : subscript out of bounds In addition: Warning messages: 1: roxygen2 requires Encoding: UTF-8 2: Removed 2 rows containing missing values (geom_bar). Loading ClassifyR I ran this using Bioc 3.9 R 3.6
sessionInfo()
R Under development (unstable) (2018-12-10 r75821) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS 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 Dario Strbenac <dstr7320 at uni.sydney.edu.au>
Sent: Thursday, December 6, 2018 8:00:05 PM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] ClassifyR Check Error on Linux and MacOS Systems
Sent: Thursday, December 6, 2018 8:00:05 PM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] ClassifyR Check Error on Linux and MacOS Systems
Good day, There is an error for ClassifyR on malbec1 and merida1 caused by a documentation example. However, it doesn't occur on tokay1. Can I get more information about which example is emitting the error on malbec1 server? -------------------------------------- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia _______________________________________________ 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.
4 days later
Good day, Thanks for running it. I found the error you had happens because of an example which used random sampling and rarely returned a zero-length result. I have made the example deterministic so that it always succeeds. The error you saw is not related to the problem seen on the build servers, though. I found a browser() inside an R function which I forgot to remove before committing. After removal and committal, the error on malbec1 and merida1 is gone. It is surprising that it did not trigger an error when checking the package before committing it and that the error message observed on the build servers was not clear about what the problem was. -------------------------------------- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia
Thank you. I thought we had a BiocCheck for browser that would print a clearer message. I will look into this but thank you for correcting your package. Cheers, 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 Dario Strbenac <dstr7320 at uni.sydney.edu.au>
Sent: Monday, December 17, 2018 3:00:02 AM
To: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] ClassifyR Check Error on Linux and MacOS Systems
Sent: Monday, December 17, 2018 3:00:02 AM
To: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] ClassifyR Check Error on Linux and MacOS Systems
Good day, Thanks for running it. I found the error you had happens because of an example which used random sampling and rarely returned a zero-length result. I have made the example deterministic so that it always succeeds. The error you saw is not related to the problem seen on the build servers, though. I found a browser() inside an R function which I forgot to remove before committing. After removal and committal, the error on malbec1 and merida1 is gone. It is surprising that it did not trigger an error when checking the package before committing it and that the error message observed on the build servers was not clear about what the problem was. -------------------------------------- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia _______________________________________________ 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.