Warning: Error in pngfun: invalid 'height' argument in logfiles

ipb-halle / MetFamily

Understanding metabolism is fundamental in biomedical and plant research and the identification and quantification of thousands of metabolites by mass spectrometry in modern metabolomics is a prerequisite for elucidating this area. However, the identification of metabolites is a major bottleneck in traditional approaches hampering advances. Here, we present a novel approach for the untargeted discovery of metabolite families offering a bird's eye view of metabolic regulation in comparative metabolomics. We implemented the presented methodology in the easy-to-use web application MetFamily to enable the analysis of comprehensive metabolomics studies for all researchers worldwide. MetFamily is available under http://msbi.ipb-halle.de/MetFamily/.

GNU General Public License v3.0

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Warning: Error in pngfun: invalid 'height' argument in logfiles #49

Open sneumann opened 4 years ago

sneumann commented 4 years ago

Hi, we're getting in our logs:

Warning: Error in pngfun: invalid 'height' argument
  127: pngfun
  126: startPNG
  125: drawPlot
  111: <reactive:plotObj>
   95: drawReactive
   82: origRenderFunc
   81: output$plotScoresGroupsLegend
    1: runApp

Suggestion in https://github.com/rstudio/shiny/issues/2136#issuecomment-421960130 is to replace uiOutput("distPlot") with plotOutput("distPlot"). We have uiOutput() in two places: https://github.com/ipb-halle/MetFamily/search?q=uiOutput&unscoped_q=uiOutput

culpinnis commented 4 years ago

In server_guiTabPca.R the default height is set to -1 https://github.com/ipb-halle/MetFamily/blob/9f239cfec313ff2ed8c9c1c106bf97809d3799c6/MetFamily/app_files/server_guiTabPca.R#L31 https://github.com/ipb-halle/MetFamily/blob/9f239cfec313ff2ed8c9c1c106bf97809d3799c6/MetFamily/app_files/server_guiTabPca.R#L28 It should be calculated to the real value in server_guiPlots.R:
https://github.com/ipb-halle/MetFamily/blob/9f239cfec313ff2ed8c9c1c106bf97809d3799c6/MetFamily/app_files/server_guiPlots.R#L209 and for Hca

https://github.com/ipb-halle/MetFamily/blob/9f239cfec313ff2ed8c9c1c106bf97809d3799c6/MetFamily/app_files/server_guiPlots.R#L81 when drawDendrogramPlotImpl is called. The error could be caused if the plot should be drawn without calling drawDendrogramPlotImpl or when the height value is overwritten by -1 again. The function in https://github.com/ipb-halle/MetFamily/blob/9f239cfec313ff2ed8c9c1c106bf97809d3799c6/MetFamily/app_files/server_guiTabPca.R#L33 could cause a reset of this value. Further investigation is needed and will be done.

culpinnis commented 3 years ago

There are still plots with invalid height.

container (2).log

Maybe the same fix can be applied to output$plotHeatmap as in https://github.com/ipb-halle/MetFamily/commit/6e0fc5427e39e7bf8e090d21cad9b1636799f04e#diff-0eff2e186b3075ea2ff8f167189909acR972-R974.

sneumann commented 4 months ago

Hi, we found that the "invalid height" happens if the user selects a 90% zoom scale in the Browser window, which makes the heatmap below the dendrogram causing the error message and to disappear. So current workaround is "don't zoom". Yours, Steffen

P.S.: This sounds like same issue as https://stackoverflow.com/questions/59213316/shiny-renderplot-with-dynamic-height#comment104644786_59213670, and maybe there is a solution in the first post in https://github.com/rstudio/shiny/issues/2373#issue-430972059, and the original poster in https://stackoverflow.com/a/69668085 said he was not using the correct height function.