Dear Pablo,
Sometimes when building a vignette the lines reported are a bit off (I
usually check the code above and below those lines).
I could reproduce the error on R 4.0.1, the error is triggered on
lines 515-519 on the following code:
relationship_plot(qtl_file=out.qtls.filtered, x="Abbrev",
Dear Llu�s Revilla,
Thank you very much for the comments and suggestions. I changed the vignette
format from the BiocStyle to a regular html. However, I am still getting an
error. Now, the error is "Input vector too short" and it is related with the
same code chunk lines 465-506.
I can't
...it would be useful to know whether 'timeout' settings, e.g., options(timeout
= 180) improves things. I've introduced pull request on BiocManager to do this,
at
https://github.com/Bioconductor/BiocManager/pull/81
Martin
On 11/5/20, 11:04 AM, "Martin Morgan" wrote:
I noticed in
Hi Pablo,
"The magick package is required to crop" is related to using
BiocStyle for your vignette. Not sure what causes it, but I reported
this error some time ago:
https://github.com/Bioconductor/BiocStyle/issues/77.
On related issues and on bioc-devel mailing list
Dear Duncan Murdoch,
Thank you for the quickly reply. Yes, the package is on Github. Any comment or
suggestion will be very welcome.
https://github.com/pablobio/GALLO
Kind regards.
Pablo Augusto de Souza Fonseca, Ph.D.
Postdoctoral Fellow at University of Guelph
Centre for Genetic Improvement
On 05/11/2020 10:55 a.m., Pablo Fonseca wrote:
Dear all,
Currently I am trying to update my package (GALLO) with some small edits in the
code. However, the package is not passing in the automatic check. I am getting
only two warnings:
The first one is a warning related with the maintainer
Dear all,
Currently I am trying to update my package (GALLO) with some small edits in the
code. However, the package is not passing in the automatic check. I am getting
only two warnings:
The first one is a warning related with the maintainer email (my email in the
case), which is correct. I
I noticed in Johannes' message
> In addition: Warning messages:
...
> 2: In download.file(url, destfile, method, mode = "wb", ...) :
> URL
'https://bioconductor.org/packages/3.13/data/experiment/src/contrib/msdata_0.31.0.tar.gz':
Timeout of 60 seconds was reached
I looked at
Thanks Mike!
that did the trick
cheers, jo
Johannes Rainer, PhD
Eurac Research
Institute for Biomedicine
Via Galvani 31, I-39100 Bolzano, Italy
M +39 327 4075490
T +39 0471 055 491
email: johannes.rai...@eurac.edu
github: jorainer
twitter: jo_rainer
Legal Seat
Viale Druso 1, I-39100 Bolzano,
> Duncan Murdoch writes:
> The source to the noquote() function looks like this:
> noquote <- function(obj, right = FALSE) {
> ## constructor for a useful "minor" class
> if(!inherits(obj,"noquote"))
> class(obj) <- c(attr(obj, "class"),
> if(right)
The source to the noquote() function looks like this:
noquote <- function(obj, right = FALSE) {
## constructor for a useful "minor" class
if(!inherits(obj,"noquote"))
class(obj) <- c(attr(obj, "class"),
if(right) c(right = "noquote") else "noquote")
Your report underlines the importance of the checks implemented by CRAN.
In fact, checkbashisms has become an optional part of R CMD check in R
4.0.0, whose NEWS say
> R CMD check now optionally checks configure and cleanup scripts for
> non-Bourne-shell code ('bashisms').
The R Internals
Hi Jo,
There was some discussion of a similar issue on the support forum at
https://support.bioconductor.org/p/p132470/
The suggestion there was to try changing R's download.file.method option
e.g. options(download.file.method = "curl")
Best,
Mike
On Thu, 5 Nov 2020 at 13:21, Rainer Johannes
Hi Johannes,
I’ll take a look at this and get back to you.
Best,
Nitesh
> On Nov 5, 2020, at 7:21 AM, Rainer Johannes wrote:
>
> Dear all,
>
> I'm unable to install the "msdata" package for the current BioC 3.13 release.
> I keep getting the following error:
>
>>
Dear all,
I'm unable to install the "msdata" package for the current BioC 3.13 release. I
keep getting the following error:
> BiocManager::install("msdata")
Bioconductor version 3.13 (BiocManager 1.30.10), R Under development (unstable)
(2020-10-24 r79367)
Installing package(s) 'msdata'
Dear R-devel,
Recently I ran into trouble installing two separate packages, nloptr and ncdf4,
both due to the same issue: they have scripts that have the shebang `#!
/bin/sh', but have bashisms in them, i.e. non-POSIX-compliant bash scripts.
I use dash [1] as my shell environment, since it's
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