Question: Errors in build report previously working
0
3.1 years ago by
United Kingdom
Miguel Juliá0 wrote:

Hi all,

My package was compiled without any problems until this happened yesterday: http://bioconductor.org/checkResults/release/bioc-LATEST/sincell/

Summarising, there are 2 types of error:

1. In Linux and Mac:
...
No methods found in "BiocGenerics" for requests: as.vector, unlist
Quitting from lines 170-185 (sincell-vignette.Rnw)
Error: processing vignette 'sincell-vignette.Rnw' failed with diagnostics:
1: Extra content at the end of the document
2. In Windows:
...
Error: processing vignette 'sincell-vignette.Rnw' failed with diagnostics:
package 'Biobase' required by 'monocle' could not be found

Does anyone know why is this happening now but not before? I already checked the vignette for the Linux/Mac error and there is nothing after the end of document...

Thanks!

build report • 514 views
modified 3.1 years ago by Martin Morgan ♦♦ 23k • written 3.1 years ago by Miguel Juliá0
Answer: Errors in build report previously working
2
3.1 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Questions about package development (including the build system) should be asked on the bioc-devel mailing list. You'll see there that there are ongoing problems with our Windows builds, where we sometimes have 'catastrophic' failures where a package with many dependencies fails to install, and hence many packages fail. This is what happened during the last build, and affected your package.

I'm not sure about the linux builds; there is this question Error: 1: Extra content at the end of the document in using biomaRt which suggests a biomaRt problem, and indeed biomaRt was perhaps not available this weekend https://www.biostars.org/p/208733.