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 <sneum...@ipb-halle.de<mailto:sneum...@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 < sneum...@ipb-halle.de<mailto:sneum...@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. 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