[Bioc-devel] Unable to reproduce vignette build error

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Mon Apr 20 14:59:52 CEST 2020

I am able to reproduce this locally.
Make sure you are using R 4.0.0 and have updated versions of all Bioconductor packages

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 using r-project.org> on behalf of USD Biomedical Engineering <bicbioeng using gmail.com>
Sent: Monday, April 20, 2020 3:16 AM
To: bioc-devel using r-project.org <bioc-devel using 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?


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