[Bioc-devel] uncoverappLib problems reported in the Multiple platform build/check report for BioC 3.16

[Kern, Lori]

I am able to reproduce this locally


* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'uncoverappLib-Ex.R' failed
The error most likely occurred in:

> ### Name: buildInput
> ### Title: Build input file
> ### Aliases: buildInput
>
> ### ** Examples
>
> gene.list<- system.file("extdata", "mygene.txt", package = "uncoverappLib")
>
> bam_example <- system.file("extdata", "example_POLG.bam",
+ package = "uncoverappLib")
> cat(bam_example, file = "bam.list", sep = "\n")
> temp_dir=tempdir()
> buildInput(geneList= gene.list, genome= "hg19", type_bam= "chr",
+ bamList= "bam.list",type_input="genes", outDir= temp_dir)
Reading gene name started at:
2022-11-10 12:53:21.140608
Read 1 item
'select()' returned 1:many mapping between keys and columns
Error in buildInput(geneList = gene.list, genome = "hg19", type_bam = "chr",  :
  ERROR: unrecognized GENE NAME. Please remove genes
       stored in preprocessing_log1.txt
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ...



What version of R and Bioc are you using to test?
You should be using R 4.2.2 and Bioc 3.16

Have you run a BiocManager::install()  and BiocManager::valid() to ensure you are using the latest versions of all packages?



Lori Shepherd - Kern

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 Emanuela Iovino <emanuela.iovino using unibo.it>
Sent: Tuesday, November 8, 2022 8:42 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] R: uncoverappLib problems reported in the Multiple platform build/check report for BioC 3.16


Hi,
I keep getting to receive an error in my package during check process, I tried to reproduce the error in my environment, but I cannot understand what it is going wrong, because
devtools::check() and BiocCheck do not return any error, I guess that something's wrong in a file stored as example (mygene.txt) and despite I have modified it I receive the same error.  Could you please help me to handle this?
Thanks


________________________________
Da: BBS-noreply using bioconductor.org <BBS-noreply using bioconductor.org>
Inviato: luned� novembre 2022 18:00
A: Emanuela Iovino <emanuela.iovino using unibo.it>
Oggetto: uncoverappLib problems reported in the Multiple platform build/check report for BioC 3.16

[This is an automatically generated email. Please don't reply.]

Hi uncoverappLib maintainer,

According to the Multiple platform build/check report for BioC 3.16,
the uncoverappLib package has the following problem(s):

  o ERROR for 'R CMD check' on nebbiolo2. See the details here:
      https://secure-web.cisco.com/1ye23e6VILCo8EGm_FZohksBP40u7sJ3WQpoPakwn0933iJny1qcPU7XRyU6P0dZnVrboE-a-vAnunNzohAlhsTPQ4nLnNVREHlrN2OrleZFQtDXV8x89Xc75R-sbHaEtaDT05samq7NVk8rwhF3zxdSA0gh2JkktsHmP2TllJPXGUmBD70gR-FPvSP46-Im5qOExaUKiesueZ2fFJbnnPaGVtAn9yl4nu7_WlJ7eGYQFZRW8219icQjwb5QLkQLvimXYCBrKrSuLonVGPHzXujRWJwhnSVDEAmEthQPbpssmWrriWihf2Gd10CMTIDRV/https%3A%2F%2Fmaster.bioconductor.org%2FcheckResults%2F3.16%2Fbioc-LATEST%2FuncoverappLib%2Fnebbiolo2-checksrc.html

Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org

Notes:

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