[Bioc-devel] plotMotifLogo function of motifStack package generates an empty plot

Shin, Sunyoung Sunyoung@Sh|n @end|ng |rom utd@||@@@edu
Wed Feb 19 08:44:06 CET 2020 

Hello,

I got it. Thank you. I pushed changes made to atSNP Bioconductor.

I am fixing the graphic error in creating vignettes with plotMotifMatch function. This graphic function uses plotMotifLogo function from motifStack package. The issue seemed to be linked to that plotMotifLogo produces an empty plot by itself. I added graphics.off() after using plotMotifLogo based on the suggestion of Jianhong, the motifStack developer. This could fix the problem on windows machine, but did not work on linux machine. What else should I modify to fix the error on linux machine?

FYI, I added BUILD reports of atSNP Bioconductor:
http://bioconductor.org/checkResults/3.10/bioc-LATEST/atSNP/malbec1-buildsrc.html and http://bioconductor.org/checkResults/devel/bioc-LATEST/atSNP/malbec2-checksrc.html


Best,
Sunyoung

On Feb 17, 2020, at 1:59 AM, Neumann, Steffen <sneumann using ipb-halle.de<mailto:sneumann using ipb-halle.de>> wrote:

Hi,

the source package on 3.11/bioc/html/atSNP.html
will only be updated with a new one if all checks succeed.
This prevents that you download a broken package.

Nowadays one would call that a continuous integration pipeline,
but the BioC team already does that since, um, more than a decade ;-)

Yours,
Steffen


On Mon, 2020-02-17 at 07:44 +0000, Shin, Sunyoung wrote:
Hello Steffen,

Thank you for the response. You are right, and I also recognized it.
However, I don’t see the updates from the source package I downloaded
from the package webpage at
https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2Fpackages%2F3.11%2Fbioc%2Fhtml%2FatSNP.html&data=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C07c7b31c220b40962c4b08d7b37f4ad4%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C0%7C637175231610633533&sdata=fCnYXHnxM%2BJTDxYeXTGdpw5H6o4DObbwEGhVC81KVfY%3D&reserved=0. I updated
both DESCRIPTION and graphic.R, but neither were updated.


Best,
Sunyoung

On Feb 17, 2020, at 1:38 AM, Neumann, Steffen <
sneumann using ipb-halle.de<mailto:sneumann using ipb-halle.de>> wrote:

Hi,

please have a look at the build report first:

https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbioconductor.org%2FcheckResults%2Fdevel%2Fbioc-LATEST%2FatSNP%2F&data=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C07c7b31c220b40962c4b08d7b37f4ad4%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C0%7C637175231610633533&sdata=ni0I8fqdIf2j8grnIAAR8eS5HdBxs7g2IZRGwntSnhc%3D&reserved=0

where your commit 2020-02-12 has been picked up.
The check has an ERROR, most likely in the examples
to plotMotifMatch().

Also, I guess the version 1.3.0 was the version number
bumped after the last BioC release, so consider
to bump atSNP to 1.3.1 with you next commit.

Hope that helped,

Yours,
Steffen


On Mon, 2020-02-17 at 05:10 +0000, Shin, Sunyoung wrote:
Dear all,

I used "git push upstream master” to commit changes for atSNP
package
to Bioconductor 4 days ago. But, Bioconductor does not take the
updated version, but sticks with the old version of the package,
which I committed in October. Does someone have an idea about how
to
fix it? Thanks.


Best,
Sunyoung
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---
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann
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Current bits of interest:

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---
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.IPB-Halle.DE&data=02%7C01%7CSunyoung.Shin%40utdallas.edu%7C07c7b31c220b40962c4b08d7b37f4ad4%7C8d281d1d9c4d4bf7b16e032d15de9f6c%7C0%7C0%7C637175231610643528&sdata=QpTG%2FOBswxkt74usqqByjKhVJie9ZMW111qfjwUV%2FbM%3D&reserved=0
Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
06120 Halle                       +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409


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