Dear Bioconductor Team, In the past week the vignette for our package BrainSABER has been failing to build on the automated builder with a 'subscript out of bounds' error. I am unable to reproduce this error on my local system (Windows x86_64 running devel versions of R and Bioconductor 3.11), therefore I can't get to the bottom of the issue. I also do not have Docker available to test in an independent environment. BrainSABER passed the autobuilder back in March, and I made sure all recent changes were unrelated to the failure. I'm not sure if this is a builder issue or an issue with both the package and my local testing environment. Do you have any insight or suggestions? Best, Evgeni
[Bioc-devel] Unable to reproduce vignette build error
2 messages · USD Biomedical Engineering, Shepherd, Lori
I am able to reproduce this locally.
Make sure you are using R 4.0.0 and have updated versions of all Bioconductor packages
BiocManager::valid()
BiocManager::install()
I did an "R CMD Stangle Installing_and_Using_BrainSABER.Rmd" to produce an R file of code for the vignette and also tried to run the vignette manually with
source("Installing_and_Using_BrainSABER.R", echo=TRUE)
The code that produces the ERROR is:
# Or using the auto-trimmed toySet auto_euc_sim <- getSimScores(data = toySet, similarity_method = "euclidean")
auto_cos_sim <- getSimScores(data = toySet, similarity_method = "cosine")
## ----getAS, results = 'hide'-------------------------------------------------- # Using manually filtered data scores euc_mats <- getSimMatrix( .... [TRUNCATED]
Error in `[<-`(`*tmp*`, a, s, value = sim_score[i]) : subscript out of bounds Or more precisely:
euc_mats <- getSimMatrix(sim_score = euc_sim, relevantGenes = trimmed_AIBSARNA)
Error in `[<-`(`*tmp*`, a, s, value = sim_score[i]) : subscript out of bounds
traceback()
2: getSimMatrix(sim_score = sim_score[, x], relevantGenes = relevantGenes) 1: getSimMatrix(sim_score = euc_sim, relevantGenes = trimmed_AIBSARNA) Hopefully this will help you pinpoint and debug more. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of USD Biomedical Engineering <bicbioeng at gmail.com>
Sent: Monday, April 20, 2020 3:16 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Unable to reproduce vignette build error
Sent: Monday, April 20, 2020 3:16 AM
To: bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: [Bioc-devel] Unable to reproduce vignette build error
Dear Bioconductor Team,
In the past week the vignette for our package BrainSABER has been failing
to build on the automated builder with a 'subscript out of bounds' error. I
am unable to reproduce this error on my local system (Windows x86_64
running devel versions of R and Bioconductor 3.11), therefore I can't get
to the bottom of the issue. I also do not have Docker available to test in
an independent environment.
BrainSABER passed the autobuilder back in March, and I made sure all recent
changes were unrelated to the failure. I'm not sure if this is a builder
issue or an issue with both the package and my local testing environment.
Do you have any insight or suggestions?
Best,
Evgeni
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel at r-project.org mailing list
https://secure-web.cisco.com/18iEdJng0U-iYaV4o4rxB_vQt7Fm7J-z0seqsYRYHft5lspqk7ZYa3BHT-_wYfytAqxe6bV3KBWAZECKoh_f-ePser2gIWjosxT69ioCaqyagEJkOkcMSN-RfdzF1N4V1K7DWzQ8h_1V_jQuHmN0EfBx9AyQEIke1Hre_t9WQsEJU-72-h_B8zDQ1kYEN7ercOBCqI-fQptHwsu5NjhVp0H4S_CrV_uG__FbgpDPWBpEsYK6r4Zc6nAKRZUFOKYEJ5kNwDWpxH_PDRpmB47xpXNO4K4vFFfesCVaTqvUI8wn3dWqSl182clJbosu24IbDrtmyAyYxJtNr-7ZRW_3dZw/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-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.