Hi Marek,
Thanks for pointing this out in release.
I have applied the patch to BiocCheck version 1.38.1.
FWIW, this issue was first opened here
https://github.com/Bioconductor/BiocCheck/issues/135
Best regards,
Marcel
On 1/25/24 9:24 AM, Marek Gierlinski (Staff) wrote:
> Yes, it must be this.
Yes, it must be this. I�ve installed the devel version and the error is gone.
Marek
From: Kern, Lori
Date: Thursday, 25 January 2024 at 14:13
To: James W. MacDonald , Marek Gierlinski (Staff)
, bioc-devel@r-project.org
Subject: Re: BiocCheck error
I believe this bug with BiocCheck is fixed in
ject.org
Subject: Re: [Bioc-devel] BiocCheck error
Are you subscribed to the bioc-devel mailing list?
-Original Message-
From: Bioc-devel On Behalf Of Marek
Gierlinski (Staff)
Sent: Thursday, January 25, 2024 5:51 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] BiocCheck error
When
Yes, I am. And BiocCheck used to work for me before, suddenly it is crashing
with error.
Marek
From: James W. MacDonald
Date: Thursday, 25 January 2024 at 14:07
To: Marek Gierlinski (Staff) ,
bioc-devel@r-project.org
Subject: RE: BiocCheck error
Are you subscribed to the bioc-devel mailing l
Are you subscribed to the bioc-devel mailing list?
-Original Message-
From: Bioc-devel On Behalf Of Marek
Gierlinski (Staff)
Sent: Thursday, January 25, 2024 5:51 AM
To: bioc-devel@r-project.org
Subject: [Bioc-devel] BiocCheck error
When running BiocCheck::BiockCheck() on my package, it
HI Mike,
Thanks so much for taking the time to go through everything so carefully.
It's very much appreciated.
I originally found the issue with BiocCheck by instantiating the bioc-devel
container locally. That one's sorted now so the devel version of ngsReports
builds on r-devel using linux. A f
Hi Stevie,
To follow up on this, BiocCheck is missing from devel because some changes
in R-devel tripped up a few unit tests, and the package hasn't been built
successfully. It looks like Marcel has fixed those issues (
https://code.bioconductor.org/browse/BiocCheck/commits/master) and it
should
Hi Stevie,
It might be helpful to link to the workflow runs so people can see exactly
what you're doing and what's happening. Hopefully I'm looking in the right
place at https://github.com/steveped/ngsReports/actions/runs
I'm not sure about the error message regarding BiocCheck. However there
a
> I believe in the past we tried suggesting removing a R dependency
>> > altogether but that R CMD check complained not having an R dependency?
>> > Maybe someone remembers more about this.
>> >
>> >
>> >
>> >
>> > Lori Shepherd
>
;
> >
> > Lori Shepherd
> >
> > Bioconductor Core Team
> >
> > Roswell Park Comprehensive Cancer Center
> >
> > Department of Biostatistics & Bioinformatics
> >
> > Elm & Carlton Streets
> >
> > Buffalo, New York 14263
> >
> >
ive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ________
> From: Kasper Daniel Hansen
> Sent: Thursday, April 8, 2021 1:33 PM
> To: Kern, Lori
> Cc: bioc-devel
> S
ics
Elm & Carlton Streets
Buffalo, New York 14263
From: Kasper Daniel Hansen
Sent: Thursday, April 8, 2021 1:33 PM
To: Kern, Lori
Cc: bioc-devel
Subject: Re: [Bioc-devel] BiocCheck and version requirement
But why is it even a warning? The submission polic
But why is it even a warning? The submission policy is that warnings are
discouraged. This means that developers will adapt to this warning.
The check is also against the policies on the website which state you don't
need a formal dependency.
Best,
Kasper
On Thu, Apr 8, 2021 at 3:53 PM Kern, Lor
This requirement has been around for awhile. New package submissions are
checked against the devel version of Bioconductor. At the moment this is R
devel (R 4.1) and Bioconductor packages in devel for 3.13. Given that
Bioconductor releases are closely tied to a R release, and changes in R can
Thanks, Martin, that is actually my bug report. I'm considering doing a
pull-request with a fix. However, I don't have a clear idea yet on how to
deal with the YAML portion of a .rmd file.
Regards
Carlos A. Catania (AKA Harpo)
El dom., 26 jul. 2020 a las 10:14, Martin Morgan ()
escribió:
> See a
Hello, Mike,
Thanks for your answer and info about the review process.
As recommended by Lori we filled a bug report about the issue.
Thanks again and best regards
Carlos A. Catania (AKA Harpo)
El sáb., 25 jul. 2020 a las 17:56, Mike Smith ()
escribió:
> Hi Carlos,
>
> I don't think you need t
See also this issue https://github.com/Bioconductor/BiocCheck/issues/100 .
On 7/25/20, 4:57 PM, "Bioc-devel on behalf of Mike Smith"
wrote:
Hi Carlos,
I don't think you need to worry about this.
The 4 space indentation is a style recommendation (not a requirement), and
if the
Hi Carlos,
I don't think you need to worry about this.
The 4 space indentation is a style recommendation (not a requirement), and
if the only place that your code isn't meeting that recommendation is the
YAML header then I can't imagine that any reviewer will worry too much
about this. The revie
>>> situation?
>>
>> But then isn't it going to be somewhat painful to keep the 2 repos in
>> sync? Sounds like using some kind of alias or redirect mechanism would
>> be better but you would need to ask the Git or GitHub experts on how to
>>
>sync? Sounds like using some kind of alias or redirect mechanism would
>be better but you would need to ask the Git or GitHub experts on how to
>do this.
>
>H.
>
>>
>> Zhezhen
>> ------------
>&
---
> *From:* Pages, Herve
> *Sent:* Wednesday, August 21, 2019 7:47 PM
> *To:* Zhezhen Wang ; Martin Morgan
> ; Vincent Carey
> *Cc:* bioc-devel@r-project.org
> *Subject:* Re: [Bioc-devel] BiocCheck error
> Note that t
s.
H.
>
> Zhezhen
>
> *From:* Pages, Herve
> *Sent:* Wednesday, August 21, 2019 7:47 PM
> *To:* Zhezhen Wang ; Martin Morgan
> ; Vincent Carey
> *Cc:* bioc-devel@r-project.org
> *Subject:* Re: [Bioc-dev
?
Zhezhen
From: Pages, Herve
Sent: Wednesday, August 21, 2019 7:47 PM
To: Zhezhen Wang ; Martin Morgan
; Vincent Carey
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] BiocCheck error
Note that the name of the package (BioTIP) differs from the name of the
From: Martin Morgan
> Sent: Tuesday, August 20, 2019 11:15 AM
> To: Zhezhen Wang ; Vincent Carey
>
> Cc: bioc-devel@r-project.org
> Subject: Re: [Bioc-devel] BiocCheck error
>
> I think this is from BiocCheck, needing access to CRAN / Bioconductor to look
> at pac
I see, thank you Martin!
Zhezhen
From: Martin Morgan
Sent: Tuesday, August 20, 2019 11:15 AM
To: Zhezhen Wang ; Vincent Carey
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] BiocCheck error
I think this is from BiocCheck, needing access to CRAN
AM
To: Zhezhen Wang
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] BiocCheck error
If your package that generates the error is in a github repo, please give
the details.
If it is already in Bioconductor please give the name of the package and
ensure we can
get
The github repo is https://github.com/xyang2uchicago/NPS
From: Vincent Carey
Sent: Tuesday, August 20, 2019 10:52 AM
To: Zhezhen Wang
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] BiocCheck error
If your package that generates the error is in a
If your package that generates the error is in a github repo, please give
the details.
If it is already in Bioconductor please give the name of the package and
ensure we can
get access to the code that is generating the error. In general it is very
hard to help unless
we can reproduce the error yo
Martin,
Thank you. yes, you are right.
Now it works, I also changed outputs to tempfile() or tempdir().
Aimin
On Tue, Apr 10, 2018 at 6:07 PM, Martin Morgan <
martin.mor...@roswellpark.org> wrote:
> Hi Aimin -- the problem is that your vignette has two VignetteEngine
> commands in it
>
> Pathw
Hi Aimin -- the problem is that your vignette has two VignetteEngine
commands in it
PathwaySplice/vignettes master$ grep VignetteEngine *
tutorial.Rmd: %\VignetteEngine{knitr::rmarkdown}
tutorial.Rmd: %\VignetteEngine{knitr::knitr}
Also, please avoid writing to files in the user system, repla
Good day,
You could make use of the package named BSgenome.Celegans.UCSC.ce11. It
contains the DNA sequences of all of the chromosomes of the roundworm and
doesn't add any size to your package.
--
Dario Strbenac
University of Sydney
Camperdown NSW 2050
Austra
On 03/10/2018 09:03 AM, Pariksheet Nanda wrote:
Hi Claris,
On Sat, Mar 10, 2018 at 2:49 AM, Claris Baby via Bioc-devel <
bioc-devel@r-project.org> wrote:
[1] "The following files are over 5MB in size:
'dataset/Caenorhabditis_elegans.WBcel235.dna.chromosome.I.fa'."
This as well as other d
> disk efficient compression algorithm
Whoops, meant to say compression format.
Pariksheet
[[alternative HTML version deleted]]
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Hi Claris,
On Sat, Mar 10, 2018 at 2:49 AM, Claris Baby via Bioc-devel <
bioc-devel@r-project.org> wrote:
>
> [1] "The following files are over 5MB in size:
> 'dataset/Caenorhabditis_elegans.WBcel235.dna.chromosome.I.fa'."
> This as well as other data like .gff files, that are being used
> for
sday, May 31, 2017 20:51
> *To: *Arman Sh
> *Cc: *Michael Lawrence ;
> bioc-devel@r-project.org
> *Subject: *Re: [Bioc-devel] BiocCheck requires example for a function
> withnoargument.
>
>
>
> And nothing shows up in the list?
>
>
>
> On Wed, May 31, 2017 at 8
On 05/31/2017 11:29 AM, Arman Sh wrote:
Hi every one,
BiocCheck is really annoying. My package contains three functions. Two of them
are flexible with multiple argument. The third one is requires internet to
check available data types and returns the result as an excel file. It’s a
simple fun
> examples. The following pages do not:"
>
>
>
> Best regards, arman
>
>
>
> *From: *Michael Lawrence
> *Sent: *Wednesday, May 31, 2017 20:12
> *To: *Arman Sh
> *Cc: *bioc-devel@r-project.org
> *Subject: *Re: [Bioc-devel] BiocCheck requires example
You could embed the example in \dontrun{}. Does BiocCheck detect cases
where the entire example is not run?
Btw, I'm pretty suspicious about this R function that takes no arguments
and downloads an Excel file. Seems like the file could be bundled with the
package, or internally lazily downloaded a
- Original Message -
> From: "David Kuo"
> To: "bioc-devel"
> Sent: Friday, April 1, 2016 1:13:47 PM
> Subject: [Bioc-devel] BiocCheck Local and Single Package Builder Discrepancy
> Hi,
>
> I'm observing different results from executing BiocCheck, version 1.7.9
> locally
> and the bu
You found a bug in BiocCheck!
Now fixed in version 1.7.2 in devel.
Please update from git (https://github.com/Bioconductor/BiocCheck), svn
(https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiocCheck) or wait
till tomorrow afternoon and install it with biocLite().
Thanks,
Dan
-
- Original Message -
> From: "Samuel E Zimmerman"
> To: bioc-devel@r-project.org
> Sent: Wednesday, September 30, 2015 2:02:06 PM
> Subject: [Bioc-devel] BiocCheck failing
>
> Hi everyone,
>
> I just submitted a package to Bioconductor. All the tests passed
> except for the BiocCheck s
- Original Message -
> From: "Thomas Lin Pedersen"
> To: "Dan Tenenbaum"
> Cc: bioc-devel@r-project.org
> Sent: Thursday, September 3, 2015 10:50:19 AM
> Subject: Re: [Bioc-devel] BiocCheck required import
>
> It might be related to the
riginal Message -
>> From: "Thomas Dybdal Pedersen"
>> To: "Dan Tenenbaum"
>> Cc: bioc-devel@r-project.org
>> Sent: Thursday, September 3, 2015 8:25:36 AM
>> Subject: Re: [Bioc-devel] BiocCheck required import
>>
>> Sure, sorry. It
- Original Message -
> From: "Thomas Dybdal Pedersen"
> To: "Dan Tenenbaum"
> Cc: bioc-devel@r-project.org
> Sent: Thursday, September 3, 2015 8:25:36 AM
> Subject: Re: [Bioc-devel] BiocCheck required import
>
> Sure, sorry. Its avail
t.org
>> Sent: Thursday, September 3, 2015 7:55:42 AM
>> Subject: Re: [Bioc-devel] BiocCheck required import
>>
>> What's the name of the package?
>
> I mean, is the source available somewhere?
> Dan
>
>
>> Dan
>>
>>
>> - Origina
- Original Message -
> From: "Dan Tenenbaum"
> To: "Thomas Lin Pedersen"
> Cc: bioc-devel@r-project.org
> Sent: Thursday, September 3, 2015 7:55:42 AM
> Subject: Re: [Bioc-devel] BiocCheck required import
>
> What's the name of the packa
What's the name of the package?
Dan
- Original Message -
> From: "Thomas Lin Pedersen"
> To: bioc-devel@r-project.org
> Sent: Thursday, September 3, 2015 1:03:42 AM
> Subject: [Bioc-devel] BiocCheck required import
>
> I’m polishing up a package for release and gets this “REQUIRED”
> me
Hi
Please disregard this thread, I've realised it's an error with our code
Thanks
Glyn
From: Glyn Bradley
Sent: 16 January 2015 15:32
To: 'bioc-devel@r-project.org'
Subject: BiocCheck examples error when using imported package functions
Hi,
Our package uses igraph.
We have
imports: igraph i
- Original Message -
> From: "Karim Mezhoud"
> To: "Dan Tenenbaum"
> Cc: bioc-devel@r-project.org
> Sent: Friday, January 2, 2015 12:15:31 PM
> Subject: Re: [Bioc-devel] BiocCheck result
>
>
>
>
> Dear Dr Dan,
> Thanks,
>
&
Dear Dr Dan,
Thanks,
With GUI package the vignette does not have chunks only for installation
paragraph.
Thanks
Karim
Ô__
c/ /'_;kmezhoud
(*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ
http://bioinformatics.tn/
On Fri, Jan 2, 2015 at 6:55 PM, Dan Tenenbaum
wrote:
>
>
> - Original Message -
> > From:
- Original Message -
> From: "Karim Mezhoud"
> To: bioc-devel@r-project.org
> Sent: Friday, January 2, 2015 4:22:44 AM
> Subject: [Bioc-devel] BiocCheck result
>
> Dear all,
>
> I have these comments and did not found solution for silencing them.
>
> 1 - What about Vignette?
The mess
- Original Message -
> From: "Charles Determan Jr"
> To: bioc-devel@r-project.org
> Sent: Wednesday, December 31, 2014 11:41:09 AM
> Subject: [Bioc-devel] BiocCheck Error 'duplicate label install'?
>
> Greetings,
>
> Apologies if this is a double post, I was over zealous in my initial
Thanks Dan, this solved the problem !
/ Leo
On Mon, Sep 15, 2014 at 6:42 PM, Dan Tenenbaum wrote:
> Hi Leo,
>
> - Original Message -
> > From: "Leo Lahti"
> > To: bioc-devel@r-project.org
> > Sent: Monday, September 15, 2014 10:19:55 AM
> > Subject: [Bioc-devel] BiocCheck crash with pa
Hi Leo,
- Original Message -
> From: "Leo Lahti"
> To: bioc-devel@r-project.org
> Sent: Monday, September 15, 2014 10:19:55 AM
> Subject: [Bioc-devel] BiocCheck crash with package vignette?
>
> Dear Bioc developers,
>
> The BioC guidelines request that package authors run BiocCheck
> su
- Original Message -
> From: "Dan Tenenbaum"
> To: "Kasper Daniel Hansen"
> Cc: bioc-devel@r-project.org
> Sent: Friday, June 13, 2014 4:24:27 PM
> Subject: Re: [Bioc-devel] BiocCheck
>
>
>
> - Original Message -
> &g
- Original Message -
> From: "Kasper Daniel Hansen"
> To: bioc-devel@r-project.org
> Sent: Wednesday, May 28, 2014 7:20:00 AM
> Subject: [Bioc-devel] BiocCheck
>
> 1) The hash bang in the BiocCheck script currently requires
> intervention at
> install time.
>
> It would be much more co
On Thu, May 29, 2014 at 2:47 PM, Dan Tenenbaum wrote:
> #!/bin/sh
>
> R_SCRIPT="suppressPackageStartupMessages(library(methods))"
> R_SCRIPT="$R_SCRIPT; suppressPackageStartupMessages(library(methods))"
> R_SCRIPT="$R_SCRIPT; suppressPackageStartupMessages(library(BiocCheck))"
> R_SCRIPT="$R_SCRI
- Original Message -
> From: "Kasper Daniel Hansen"
> To: "Dan Tenenbaum"
> Cc: bioc-devel@r-project.org
> Sent: Thursday, May 29, 2014 10:51:56 AM
> Subject: Re: [Bioc-devel] BiocCheck
>
>
> This is the content of the Sweave script in
This is the content of the Sweave script in lib/R/bin
# ${R_HOME}/bin/Sweave -*- sh -*-
R_EXE="${R_HOME}/bin/R"
R_SWEAVE_OPTIONS=${R_SWEAVE_OPTIONS:='--no-restore --slave'}
args=
while test -n "${1}"; do
## quote each argument here, unquote in R code.
args="${args}nextArg${1}"
shift
done
Hi Kasper,
- Original Message -
> From: "Kasper Daniel Hansen"
> To: bioc-devel@r-project.org
> Sent: Wednesday, May 28, 2014 7:20:00 AM
> Subject: [Bioc-devel] BiocCheck
>
> 1) The hash bang in the BiocCheck script currently requires
> intervention at
> install time.
>
Only if you don
- Original Message -
> From: "Julian Gehring"
> To: bioc-devel@r-project.org
> Sent: Tuesday, April 1, 2014 10:04:08 AM
> Subject: [Bioc-devel] BiocCheck: Allowed formats for vignette source
>
> Hi,
>
> BiocCheck:::getVigSources check for vignette source files in the
> 'vignettes' dire
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