vdjtools
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mikessh
R execution halted due to package loading error
Hey,
when I run VDJtools commands that plot graphs with R they fail at loading packages. This is the error message:
[RUtil] Executing Rscript intersect_pair_scatter.r VDJTOOLS_SF119_S17_MIXCR_IMGT MERGED_CUT_SR6 Overlap_.xy.txt Overlap_.xx.txt Overlap_.yy.txt Overlap_.strict.paired.scatter.pdf
[ERROR] Loading required package: ggplot2
Loading required package: grid
Loading required package: gridExtra
Loading required package: reshape
Warning: Ignoring unknown aesthetics: weight
Warning: Ignoring unknown aesthetics: weight
Warning: Ignoring unknown aesthetics: weight
Warning: Ignoring unknown aesthetics: weight
Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) :
0 (non-NA) cases
Calls: grid.arrange ... scales_add_defaults -> lapply -> FUN -> lm_eqn -> lm -> lm.fit
Execution halted
[RUtil] Executing Rscript intersect_pair_area.r VDJTOOLS_SF119_S17_MIXCR_IMGT MERGED_CUT_SR6 Overlap_.paired.strict.table.collapsed.txt Overlap_.paired.strict.table.collapsed.pdf
[ERROR] Loading required package: ggplot2
Loading required package: RColorBrewer
Error: Aesthetics must be either length 1 or the same as the data (1): x, y, label, size, alpha
Execution halted
I ran Rinstall and it passed without errors. When I load the libraries by starting R manually in the terminal I can load them also without error. I figured still maybe some dependencies of ggplot2 are not installed so I installed those too (install.packages("ggplot2", dependencies = TRUE, repos = "http://cran.us.r-project.org")). That didnt help either. When I run Rinstall all packages are put in a folder located where the vdjtools.jar is. So I thought maybe the .libPaths() is not correct and I put it in my .Rprofile, so whenever R starts that folder is included in the .libPaths().
From the error message I cant tell if the package loading error is just for ggplot2 or for all packages that it needs to require. And I believe all subsequent errors that lead to the halting of the Rscripts is due to the fact that the packages are not loaded properly.
Has this error occured before, I couldnt find it searching the issues.
I tried older versions of VDJ and also changed the java versions from jre-11 to jre-8. same result. However what I found was that other samples didnt have this outcome. The other samples, that work, were samples aligned via IMGT. The one sample that keeps bringin up this issue was aligned using MIXCR with a IMGT library.
It cant be wrong parsing for VDJ format, as other VDJ commands work with the sample, for example VJUSAGE produces a correct graph. So only overlap analysis in which that specific sample is used result in the error.
We have the same error over here. Similar setup, MIXCR with a IMGT library. VDJtools working with example datasets then failing on this ggplot2 error with our data...
What samples are you using? What I noticed now is that we, by accident, tried to check for overlap data between mice and human samples. So whenever a human sample was compared to mouse sample we got that error. Thats the sample I mentioned in my previous post that kept bringing up the error. However, I still have to see what happens when we compare 2 human samples and wether or not the error consists.
What VDJ function do you do in which you receive that error? Is it also just overlap analysis or any VDJ plot?
just: VDJTOOLS OverlapPair -p CD8.txt CD4.txt Overlap
mouse samples...
VJUSAGE on the same files works fine no errors...