Re: [R-pkg-devel] Error during automatic check for vignette re-building - The magick package is required to crop

[Pablo Fonseca]

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 figure out a possible reason for this issue. Any comment or suggestion 
will be very welcome.

Kind regards.


Pablo Augusto de Souza Fonseca, Ph.D.
Postdoctoral Fellow at University of Guelph
Centre for Genetic Improvement of Livestock
E pfons...@uoguelph.ca  <mailto:pfons...@uoguelph.ca>
W http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca  
<http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca>

From: Llu�s Revilla 
Sent: Thursday, November 5, 2020 11:38 AM
To: Pablo Fonseca 
Cc: Duncan Murdoch ; r-package-devel@r-project.org 

Subject: Re: [R-pkg-devel] Error during automatic check for vignette 
re-building - The magick package is required to crop

CAUTION: This email originated from outside of the University of Guelph. Do not 
click links or open attachments unless you recognize the sender and know the 
content is safe. If in doubt, forward suspicious emails to ith...@uoguelph.ca


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
(https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html) it
is mentioned to use knitr::opts_chunk$set(crop = NULL) to solve it.
If the package is intended for CRAN I would recommend not using
BiocStyle template, which would also solve this.

Best,

Llu�s

On Thu, 5 Nov 2020 at 17:28, Pablo Fonseca  wrote:
>
> 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 of Livestock
> E pfons...@uoguelph.ca  <mailto:pfons...@uoguelph.ca>
> W http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca  
> <http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca>
> ________
> From: Duncan Murdoch 
> Sent: Thursday, November 5, 2020 11:22 AM
> To: Pablo Fonseca ; r-package-devel@r-project.org 
> 
> Subject: Re: [R-pkg-devel] Error during automatic check for vignette 
> re-building - The magick package is required to crop
>
> CAUTION: This email originated from outside of the University of Guelph. Do 
> not click links or open attachments unless you recognize the sender and know 
> the content is safe. If in doubt, forward suspicious emails to 
> ith...@uoguelph.ca
>
>
> 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 email (my email in 
> > the case), which is correct. I really think that this is not the cause of 
> > the package failure during the automatic checking.
>
> The first one is actually about your version number:  you called it
> version 1.0, but CRAN already has 1.0.  You need to increase the number.
>
>
> >
> > The second warning is a problem during the vignette rebuilding. The warning 
> > is "The magick package is required to crop". In my first submission I 
> > didn't experience this error. In the recent submissions for updates, I 
> > included the magick package as a dependency of the package. However, this 
> > didn't fixed the issue. Additionally, I can't reproduce the errors in my 
> > machines, even when running R CMD check --as-cran. The error seems to be 
> > related with the lines 465-495 from the vignette. I double checked the code 
> > and introduced some small changes (such as reducing the figure dimensions).
>
> I am not sure about this one; I'd need to look at the package to check.
> Is it on Github?
>
> Duncan Murdoch
>
> >
> > Have ever someone faced a similar issue? However, it seems ineffective. Is 
> > there any possibility to be a false negative?
> >
> > I am sending bellow the links for the check logs.
> >
> > package GALLO_1.0.tar.gz does not pass the incoming checks automatically, 
> > please see the following pre-tests:
> > Windows: 
> > <https://win-builder.r-project.org/incoming_pretest/GALLO_1.0_2

Re: [R-pkg-devel] Error during automatic check for vignette re-building - The magick package is required to crop

[Pablo Fonseca]

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 of Livestock
E pfons...@uoguelph.ca  <mailto:pfons...@uoguelph.ca>
W http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca  
<http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca>

From: Duncan Murdoch 
Sent: Thursday, November 5, 2020 11:22 AM
To: Pablo Fonseca ; r-package-devel@r-project.org 

Subject: Re: [R-pkg-devel] Error during automatic check for vignette 
re-building - The magick package is required to crop

CAUTION: This email originated from outside of the University of Guelph. Do not 
click links or open attachments unless you recognize the sender and know the 
content is safe. If in doubt, forward suspicious emails to ith...@uoguelph.ca


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 email (my email in the 
> case), which is correct. I really think that this is not the cause of the 
> package failure during the automatic checking.

The first one is actually about your version number:  you called it
version 1.0, but CRAN already has 1.0.  You need to increase the number.


>
> The second warning is a problem during the vignette rebuilding. The warning 
> is "The magick package is required to crop". In my first submission I didn't 
> experience this error. In the recent submissions for updates, I included the 
> magick package as a dependency of the package. However, this didn't fixed the 
> issue. Additionally, I can't reproduce the errors in my machines, even when 
> running R CMD check --as-cran. The error seems to be related with the lines 
> 465-495 from the vignette. I double checked the code and introduced some 
> small changes (such as reducing the figure dimensions).

I am not sure about this one; I'd need to look at the package to check.
Is it on Github?

Duncan Murdoch

>
> Have ever someone faced a similar issue? However, it seems ineffective. Is 
> there any possibility to be a false negative?
>
> I am sending bellow the links for the check logs.
>
> package GALLO_1.0.tar.gz does not pass the incoming checks automatically, 
> please see the following pre-tests:
> Windows: 
> <https://win-builder.r-project.org/incoming_pretest/GALLO_1.0_20201105_154946/Windows/00check.log>
> Status: 2 WARNINGs
> Debian: 
> <https://win-builder.r-project.org/incoming_pretest/GALLO_1.0_20201105_154946/Debian/00check.log>
> Status: 2 WARNINGs
>
> Last released version's CRAN status: ERROR: 1, WARN: 11
> See: <https://CRAN.R-project.org/web/checks/check_results_GALLO.html>
>
>
> Kind regards.
>
>
> Pablo Augusto de Souza Fonseca, Ph.D.
> Postdoctoral Fellow at University of Guelph
> Centre for Genetic Improvement of Livestock
> E pfons...@uoguelph.ca  <mailto:pfons...@uoguelph.ca>
> W http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca  
> <http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca>
>
>[[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>


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[R-pkg-devel] Error during automatic check for vignette re-building - The magick package is required to crop

[Pablo Fonseca]

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 really think that this is not the cause of the 
package failure during the automatic checking.

The second warning is a problem during the vignette rebuilding. The warning is 
"The magick package is required to crop". In my first submission I didn't 
experience this error. In the recent submissions for updates, I included the 
magick package as a dependency of the package. However, this didn't fixed the 
issue. Additionally, I can't reproduce the errors in my machines, even when 
running R CMD check --as-cran. The error seems to be related with the lines 
465-495 from the vignette. I double checked the code and introduced some small 
changes (such as reducing the figure dimensions).

Have ever someone faced a similar issue? However, it seems ineffective. Is 
there any possibility to be a false negative?

I am sending bellow the links for the check logs.

package GALLO_1.0.tar.gz does not pass the incoming checks automatically, 
please see the following pre-tests:
Windows: 

Status: 2 WARNINGs
Debian: 

Status: 2 WARNINGs

Last released version's CRAN status: ERROR: 1, WARN: 11
See: 


Kind regards.


Pablo Augusto de Souza Fonseca, Ph.D.
Postdoctoral Fellow at University of Guelph
Centre for Genetic Improvement of Livestock
E pfons...@uoguelph.ca  
W http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca  


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