Hi all,
I've updated the cache calls in netDx per Martin's suggestion above:
> bfc <- BiocFileCache()
> path <- bfcrpath(bfc, url)
The package now builds on netbbiolo but times out on malbec1 and tokay1,
and has an error on merida1.
I've never had a package timeout before. Is this because of the
To follow up on this:
Please check the package code for adding/accessing resources in the netDx
package. If the BiocFileCache options were used correctly there should not
have been multiple entries added to the builders cache as Martin demonstrated
below.
Once the package has been updated to
bfcquery() just searches the cache, so if you've created two resources that
match the name then you end up with two rids
> xx = bfcnew(bfc, "foo")
> bfcquery(bfc, "foo", "rname")
# A tibble: 1 x 10
rid rname create_time access_time rpath rtype fpath last_modified_t… etag
I'm not a BiocFileCache expert, sorry. You will probably get better help
by opening a BiocFileCache issue on GitHub.
Cheers,
H.
On 9/11/20 12:00, Shraddha Pai wrote:
> Hi Herve,
> Sorry - hit shortcut to "send" by mistake.
>
> This is the code snippet that got cut off:
> if (length(rid)>1) {
Hi Shraddha,
Seems to be a BiocFileCache issue.
On my laptop the following code (taken from your
Predict_CaseControl_from_CNV.Rnw vignette):
require(BiocFileCache)
geneURL <- paste("http://download.baderlab.org/netDx/;,
"supporting_data/refGene.hg18.bed",sep="")
cache <-
At the top of each build report page, e.g.,
http://bioconductor.org/checkResults/3.12/bioc-LATEST/netDx/malbec1-buildsrc.html
there's a link with title 'following settings' describing
build-system-specific settings. Does this help to reproduce the problem?
Martin
On 9/11/20, 11:52 AM,
Hello BioC-devel team,
Any idea why netDx 1.1.4 fails on the bioc devel build system?
This is the error:
--- re-building 'Predict_CaseControl_from_CNV.Rmd' using knitr
Quitting from lines 173-195 (Predict_CaseControl_from_CNV.Rmd)
Error: processing vignette 'Predict_CaseControl_from_CNV.Rmd'
