error in RnBeads installation
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Jitendra ▴ 10
@nabiyogesh-11718
Last seen 4 months ago
United Kingdom

Hi all,

I am trying to install RnBeads on HPC server, but keep getting below error;

source('https://rnbeads.org/data/install.R') 
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'RnBeads'
also installing the dependencies ‘gsl’, ‘genefilter’, ‘GSEABase’, ‘lumi’, ‘aws’, ‘IlluminaHumanMethylationEPICanno.ilm10b4.hg19’, ‘IlluminaHumanMethylationEPICmanifest’, ‘geneplotter’, ‘methylumi’, ‘Category’, ‘GOstats’, ‘IlluminaHumanMethylation450kmanifest’, ‘annotate’, ‘isva’, ‘minfi’, ‘sva’, ‘wateRmelon’, ‘glmnet’, ‘GLAD’, ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’, ‘missMethyl’, ‘MethylSeekR’, ‘sesame’
 Installation paths not writeable, unable to update packages
  path: /mnt/scratch2/users/jsanchez/R/4.1.0/lib64/R/library
  packages:
    class, cli, colorspace, crayon, foreign, future, glue, jsonlite, lattice,
    MASS, Matrix, mgcv, nlme, nnet, openssl, rlang, rpart, scattermore,
    spatial, spatstat.core, spatstat.geom, survival, tidyselect, withr, yaml
Error in library(RnBeads) : there is no package called ‘RnBeads’
In addition: There were 26 warnings (use warnings() to see them)

Many thanks, nabiyogesh
Epigenetics RnBeads R • 2.2k views
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Hi nabiyogesh,

Can you try to install RnBeads through Bioconductor, i.e., using

BiocManager::install('RnBeads', dependencies=TRUE)

By default, the RnBeads installation script surpresses the error/warning messages while installing.

Best,

Michael

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thank you so much, it is installed now. but I am getting another error while running RnBeads on server;

Hi,

I was running RnBeads Rscript on Kelvin,but getting an error at the end like;

ReportGgPlot error ('off' method): X11 is not available

could you please help how to resolve this.

......
opening ff /tmp/RtmpyJdOnJ/ff/ffee1d5800e32e.ff
2022-03-14 11:31:55     7.9  STATUS         COMPLETED Writing export report
2022-03-14 11:31:55     7.9  STATUS     COMPLETED Tracks and Tables
2022-03-14 11:31:55     7.9    INFO     Initialized report index and saved to index.html
2022-03-14 11:32:08     6.8  STATUS     STARTED Exploratory Analysis
2022-03-14 11:32:08     6.8    INFO         Number of cores: 1
2022-03-14 11:32:08     6.8  STATUS         Designed color mappings for probe type and CGI status
2022-03-14 11:32:10     6.8 WARNING         ReportGgPlot error ('off' method): X11 is not available
Error in png_dev(..., res = dpi, units = 'in') : X11 is not available
Calls: rnb.run.analysis ... Anonymous - do.it - Anonymous - dev - png_dev
In addition: There were 24 warnings (use warnings() to see them)
Execution halted

I am not sure how to role this.

Many thanks, nabiyogesh

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Hi,

This error is a bit cryptic and is probably related to your R session/installation rather than to RnBeads. Can you do something like this or does this also throw an error?

png('plot.png')
plot(1:4, 1:4)
dev.off()
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Hi,

This also shows error;

> png('plot.png')
Error in png("plot.png") : X11 is not available

Many thanks, nabiyogesh

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Hi, Then you have an issue with your general R installation, please follow instructions on the web, for instance here: https://stackoverflow.com/questions/36819334/x11-is-not-available-in-r

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Thanks, this is also sorted, but now I am getting this below error;

Error in dev.control(displaylist = "enable") :
  dev.control() called without an open graphics device
Calls: rnb.run.analysis ... new -> initialize -> initialize -> .local -> dev.control
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted

RnBeads code;

#Set rnbeads options






rnb.options(analysis.name = "example")

rnb.options(logging = TRUE)

rnb.options(assembly = "hg19")

rnb.options(identifiers.column = "Sample_ID")

rnb.options2xml(pretty=TRUE)

rnb.options(min.group.size = 1)




###### modules

rnb.options(import = TRUE)

rnb.options(preprocessing = TRUE)

rnb.options(qc = TRUE)

rnb.options(inference = FALSE)

rnb.options(exploratory = TRUE)

rnb.options(differential = TRUE)




##############some selected options (see more at help("rnb.options"))




#rnb.options(import.default.data.type = "infinium.idat.dir") # NGS: "bs.bed.dir"

#rnb.options(import.table.separator = ",") # for TABdel: "\t"

#rnb.options(import.gender.prediction = FALSE) # only for array datasets




#normalization

rnb.options(normalization = NULL)

rnb.options(normalization.method = "wm.dasen")

rnb.options(normalization.background.method = "none")

rnb.options(normalization.plot.shifts = TRUE)




#qc

rnb.options(qc.boxplots = TRUE)

rnb.options(qc.barplots = TRUE)

rnb.options(qc.negative.boxplot = TRUE)

rnb.options(qc.snp.distances = TRUE)

rnb.options(qc.snp.boxplot = TRUE)

rnb.options(qc.snp.barplot = TRUE)

rnb.options(qc.sample.batch.size = 50)

rnb.options(qc.coverage.plots = FALSE)

rnb.options(qc.coverage.threshold.plot = 1:10)

rnb.options(qc.coverage.histograms = FALSE)

rnb.options(qc.coverage.violins = FALSE)




#filtering

rnb.options(filtering.whitelist = NULL)

rnb.options(filtering.blacklist = NULL)

rnb.options(filtering.snp = "3")

rnb.options(filtering.cross.reactive = FALSE)

rnb.options(filtering.greedycut = TRUE)

rnb.options(filtering.greedycut.pvalue.threshold = 0.05)

rnb.options(filtering.greedycut.rc.ties = "row")

rnb.options(filtering.sex.chromosomes.removal = TRUE)

rnb.options(filtering.missing.value.quantile = 0.8)

rnb.options(filtering.coverage.threshold = 5)

rnb.options(filtering.low.coverage.masking = FALSE)

rnb.options(filtering.high.coverage.outliers = FALSE)

rnb.options(filtering.deviation.threshold = 0)




#regions

rnb.load.annotation.from.db("ensembleRegBuildBPall")

rnb.load.annotation.from.db("ensembleRegBuildBPproximal")

rnb.load.annotation.from.db("ensembleRegBuildBPdistal")

rnb.options(region.types=c("promoters","genes","cpgislands","tiling","ensembleRegBuildBPall","ensembleRegBuildBPproximal","ensembleRegBuildBPdistal")) 




#differential analysis

rnb.options(differential.site.test.method = "ttest") #limma"

rnb.options(differential.comparison.columns = c("Sample_Group", "Treatment")) #Set column used for differential comparision




rnb.options(covariate.adjustment.columns = NULL)

rnb.options(differential.adjustment.sva = TRUE)

rnb.options(differential.adjustment.celltype = FALSE)

rnb.options(differential.enrichment.go = TRUE)

rnb.options(differential.enrichment.lola = FALSE)

rnb.options(differential.variability = FALSE)

rnb.options(differential.report.sites = TRUE)




rnb.options(export.to.bed = TRUE)

rnb.options(export.to.trackhub = c("bigBed","bigWig"))

rnb.options(export.to.csv = TRUE) #default = FALSE #creates big tables

rnb.options(export.to.ewasher = FALSE)

rnb.options(export.types = "sites")




rnb.options(disk.dump.big.matrices = TRUE)

rnb.options(enforce.memory.management = TRUE)

rnb.options(enforce.destroy.disk.dumps = TRUE)




##############################################################################




##### Run Analysis





rnb.run.analysis(dir.reports=report.dir,

                   sample.sheet=sample.annotation,

                   data.dir=idat.dir,

                   data.type="infinium.idat.dir")

Many thanks, nabiyogesh

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Hi,

If I check r capabilities then it shows png, Cairo, x11 as False. I am not sure how I can make them True on HPC.

Many thanks, nabiyogesh

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Thanks, it is sorted, there was some settings in R environment.

Many thanks,

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