enrichmentVolcanoPlot error

[benoitballester]

I have an error when plotting a volcano plot. It says "promise already under evaluation: recursive default argument reference or earlier problems?"

Not sure where it comes from

> enrichmentVolcanoPlot(na.omit(enrichment.df), sigDisplayQuantile = 0.1)
Error in enrichmentVolcanoPlot(na.omit(enrichment.df), sigDisplayQuantile = 0.1) : 
  promise already under evaluation: recursive default argument reference or earlier problems?

[benoitballester]

To reproduce the bug:

# Plots for figure 1 

# Install packages 
install.packages("devtools") 
install.packages("wesanderson")
install.packages("ggsci")
library(devtools)
install_github("remap-cisreg/ReMapEnrich")

# Load librries
library(ReMapEnrich)
library(RColorBrewer)
library(wesanderson)
library(ggsci)
demo.dir <- "~/Google Drive/ReMapEnrich_paper/figure/" 
data.dir <- "~/roken_demo"

# https://github.com/karthik/wesanderson
col_wes=wes_palette(n=3, name="Zissou1")

# https://cran.r-project.org/web/packages/ggsci/vignettes/ggsci.html#npg
mypal = pal_npg("nrc")(9)


# Get Enhancers from H3K27ac from MCF-7 cells
# Here we are using the  bed narrowPeak from 
# https://www.encodeproject.org/experiments/ENCSR752UOD/ 

ENCFF784QFH <- bedToGranges(downloadEncodePeaks("ENCFF784QFH", data.dir))

# Download ReMap
remapCatalog2018hg38 <- downloadRemapCatalog(data.dir)
# Load the ReMap catalogue and convert it to Genomic Ranges
remapCatalogGR <- bedToGranges(remapCatalog2018hg38)

# Download a universe ? 
# https://www.encodeproject.org/experiments/ENCSR000EPJ/ 
universe <- bedToGranges(downloadEncodePeaks("ENCFF718QVA", data.dir))


# Compute enrichment
enrichment.df <- enrichment(ENCFF784QFH, remapCatalogGR, universe=universe, fractionQuery = 0.35)

#enrichmentBarPlot(enrichment.df, top = 9, col=col_wes)
enrichmentBarPlot(enrichment.df)

# Erreur ici !! 
# Error in enrichmentVolcanoPlot(na.omit(enrichment.df)) : 
#    promise already under evaluation: recursive default argument reference or earlier problems?
enrichmentVolcanoPlot(na.omit(enrichment.df))

# Pas d'erreur porr ce plot
enrichmentDotPlot(enrichment.df, col=col_wes)

[Laurent-Tichit]

Tried to reproduce now. Everything seems fine (on Ubuntu 18.04.2). Please find enclosed
console_output.log
the output log

[yeroslaviz]

I have the same error on my iMac running the basic example from your github repository.

running

# Display a volcano plot (na.omit() is mandatory as there is NAs in the enrichment data frame).
enrichmentVolcanoPlot(na.omit(enrichment.df), sigDisplayQuantile = 0.9, aRisk = 0.00001)

gives this error

Error in enrichmentVolcanoPlot(na.omit(enrichment.df), sigDisplayQuantile = 0.9,  : 
  promise already under evaluation: recursive default argument reference or earlier problems?

[benoitballester]

Hi @yeroslaviz ,
This may be a mac specific related issue.
Have you tried on a Linux/Ubuntu instance ?
Try without the na.omit this may be the issue

[yeroslaviz]

Hi, just removing the na.omit does not work. I have tried it already.

it produces the error

Error in quantile.default(x = y, probs = sigDisplayQuantile) : missing values and NaN's not allowed if 'na.rm' is FALSE

I haven't tried it on a different OS yet. I will and report back asap.

[sarahhp]

I'm also getting this issue on Windows Rstudio. I'm moving through the basic tutorial and I get the same error message, and removing na.omit doesn't work.

[benoitballester]

Dear Sarah,
Sorry about this.
Let me double check this again.

Could you please copy/paste here exactly the code you execute ?

[JohnMoore-Weiss]

Try making sure to set "pch=" (I like 16 to start with). I think that they way the function was written, pch=pch is a circular definition in R. (It wouldn't be in most languages I know that allow default values, so I can see where it might catch someone by surprise.)