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
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
When running BiocCheck::BiockCheck() on my package, it gets through almost
everything and then produces an error:
...
* Checking for bioc-devel mailing list subscription...
* NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin
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
>> do this.
>>
>> H.
>>
>>>
>>>
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:* We
gt; *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
.
>
> 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-d
?
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
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
9 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 github repo, please give
the details.
If it is already in Bioconductor please give the name of the package and
ensure we can
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
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
Hi I am running BiocCheck on my new package and I get the following error
message
* Checking for deprecated package usage... Warning in readLines(file,
skipNul = TRUE) : InternetOpenUrl failed: 'The server name or address could not
be resolved' Error in readLines(file, skipNul = TRUE) :
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
>
>
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,
I used "R CMD check PathwaySplice_1.3.0.tar.gz", and get it passed
without errors and warnings.
However I get the following error when I use "R CMD BiocCheck
PathwaySplice_1.3.0.tar.gz"
R CMD BiocCheck PathwaySplice_1.3.0.tar.gz
This is BiocCheck version 1.15.8. BiocCheck is a work in progress.
Greetings,
Apologies if this is a double post, I was over zealous in my initial
submission that I didn't wait for my membership to be confirmed.
I have 'finished' creating a package I would like to submit to
bioconductor. As per the instructions on the bioconductor website I am
trying to get
- Original Message -
From: Charles Determan Jr deter...@umn.edu
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
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