bottom of the BiocCheck::BiocCheck():
---
See the .BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
---
Can you provide more details, e.g., the repository of the package?
Thanks.
Best regards,
Marcel
On 10/4/22 4:44 AM, Giulia Pais wrote:
> Hello,
Hello,
I�m having some issues in interpreting BiocCheck outputs, maybe someone can
tell me how to fix the issues.
I�ve got 2 main issues that cause the check to fail after normal CRAN check has
passed:
1. I get this error message
* Checking if other packages can import this one...
* ER
, sorry.
Thank you
From: Vincent Carey
Date: Thursday, July 7, 2022 at 11:40
To: Giulia Pais
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] BiocParallel and Shiny
Interesting question. Have you looked at
https://shiny.rstudio.com/articles/progress.html ...? There is
also a file called
unfortunately.
Thanks in advance,
Giulia Pais
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e:
I do not see it from the build report here:
http://bioconductor.org/checkResults/devel/bioc-LATEST/ISAnalytics/riesling1-checksrc.html
Can you please provide a reproducible example? It can be very helpful
to locate the issue
On Mon, Oct 25, 2021 at 7:53 PM Giulia Pais wrote
I mean that trying to modify the code of one of the functions that raises
errors and setting the option "exportglobals = TRUE" on SnowParam, somehow it
still fails and says it doesn't find the function "mandatory_is_vars()" which
is a function exported by the package
On 10/25/21, 13:49, "Jiefe
obals, you can
also add the global option "ISAnalytics.verbose" manually at the
beginning of the function in bplapply.
Best,
Jiefei
On Mon, Oct 25, 2021 at 5:42 PM Giulia Pais wrote:
>
> Hello,
> I’m the developer of the package ISAnalytics. Since the las
and fails at several jobs that
did just fine a few versions ago.
We�re using MulticoreParam for Linux and Mac and SnowParam for Windows as
suggested, I�m not really sure how to fix this issue and I�ll appreciate any
help,
Thank you
Giulia Pais
[[alternative HTML version deleted
Tried removing completely all DT calls but we�re still slightly above the
limit. Is there no other way other than removing vignettes or files?
From: Vincent Carey
Date: Thursday, September 23, 2021 at 15:51
To: Giulia Pais
Cc: "Kern, Lori" , Zuguang Gu
, "bioc-devel@r-projec
Hi Lori,
It is mainly data and a couple of plots, no images. Even if there is very
minimal data somehow we can�t obtain vignettes smaller than 1 MB.
From: "Kern, Lori"
Date: Thursday, September 23, 2021 at 14:52
To: Zuguang Gu , Giulia Pais
Cc: "bioc-devel@r-project.org"
much documentation as possible and we already tried to reduce data
included but it�s not sufficient.
Thanks in advance
Giulia Pais
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://github.com/jokergoo/circlize
Note. FWIW write temporary files using tempfile() rather than getwd().
Best regards,
Marcel
On 8/3/21 4:10 AM, Giulia Pais wrote:
> Hope somebody can help with this.
> I�ve implemented a function in the package I�m developing that uses circlize.
> The
this?
Also, I noticed that sometimes Windows builds fail due to some tests that need
to write temporary files on disk, should I skip such tests on Windows?
Thank you
Giulia Pais
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from lines like this
https://github.com/calabrialab/ISAnalytics/blob/69341f6591c6765a4a70253f7ab85e64cca9845d/vignettes/collision_removal.bib#L18
in your github repository?
Martin
On 2/3/21, 11:32 AM, "Bioc-devel on behalf of Giulia Pais"
wrote:
Hello
Hello,
I'm trying to push updates to the release 3.12 branch of the
bioconductor repo but I got an odd error from git:
remote: Error: You cannot push without resolving merge conflicts.
remote:
remote: Please check the files in the commit pushed to the git-server
remote: for merge conflict mark
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at warning should not be ignored as it is most likely
reporting a real problem.
Best,
H.
On 10/21/20 02:58, Giulia Pais wrote:
Hello, bioconductor team,
I'm one of the contributors for the package ISAnalytics. We pushed some
changes we would like to be included in the release for bioconduct
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e Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ----
> *From:* Bioc-devel on behalf of
> Giulia Pais
> *Sent:*
s and there were no
errors or warnings. From what we can see from the report it seems a
BiocParallel problem, could you give us feedback on this please? The
link to the build report:
http://bioconductor.org/checkResults/devel/bioc-LATEST/ISAnalytics/
Thank you in advance,
Giulia
s and there were no
errors or warnings. From what we can see from the report it seems a
BiocParallel problem, could you give us feedback on this please? The
link to the build report:
http://bioconductor.org/checkResults/devel/bioc-LATEST/ISAnalytics/
Thank you in advance,
Giulia
st have to wait for
them to resolved upstream/elsewhere.
/Henrik
On Thu, Jul 30, 2020 at 2:05 AM Giulia Pais wrote:
Thanks for the reply,
Unfortunately what I'm mentioning only happens in Github actions, which
are the standard ones (we used
usethis::use_github_action_check_standard), we hav
pting for removal of this lines.
Could this be a real issue with our package or just a problem with
Github actions?
Thanks in advance,
Giulia Pais
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