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https://rnbeads.org/
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Error in UseMethod("rleunpack") #4

Closed loganylchen closed 5 years ago

loganylchen commented 5 years ago

Hi there～

When I run the Rnbeads, there is a problem:

2018-12-20 14:00:07    12.9  STATUS STARTED Computing differential methylation tables
2018-12-20 14:00:07    12.9  STATUS     STARTED Comparing: Normal vs. Tumor (based on Condition)
2018-12-20 14:00:07    12.9  STATUS         STARTED Computing Differential Methylation Table
2018-12-20 14:00:40    19.5    INFO             Conducting differential analysis using limma
2018-12-20 14:14:50    23.6    INFO             4488224 p-values are NA. They are treated as 1 in FDR adjustment
2018-12-20 14:15:51    19.9  STATUS         COMPLETED Computing Differential Methylation Table
2018-12-20 14:16:15    25.6  STATUS         STARTED Computing Differential Methylation Tables (Region Level)
2018-12-20 14:25:04    16.2    INFO             169979 p-values are NA. They are treated as 1 in FDR adjustment
2018-12-20 14:25:04    16.2  STATUS             Computed table for tiling
2018-12-20 14:31:04    28.7    INFO             6982 p-values are NA. They are treated as 1 in FDR adjustment
2018-12-20 14:31:04    28.7  STATUS             Computed table for genes
2018-12-20 14:32:27    28.7    INFO             12460 p-values are NA. They are treated as 1 in FDR adjustment
2018-12-20 14:32:27    28.7  STATUS             Computed table for promoters
2018-12-20 14:33:49    28.7    INFO             784 p-values are NA. They are treated as 1 in FDR adjustment
2018-12-20 14:33:49    28.7  STATUS             Computed table for cpgislands
2018-12-20 14:33:49    28.7  STATUS         COMPLETED Computing Differential Methylation Tables (Region Level)
2018-12-20 14:33:50    28.7  STATUS     COMPLETED Comparing: Normal vs. Tumor (based on Condition)
2018-12-20 14:33:50    28.7  STATUS COMPLETED Computing differential methylation tables

Warning messages:
1: Partial NA coefficients for 4488224 probe(s)
2: Zero sample variances detected, have been offset away from zero
Error in UseMethod("rleunpack") :
  no applicable method for 'rleunpack' applied to an object of class "list"
Calls: get.table ... as.integer -> as.integer.hi -> unsort.hi -> rleunpack
Execution halted

Can You help me?

schmic05 commented 5 years ago

Hi @btrspg, This error is odd. It seems like the RnBeads routine for differential methylation finished successfully. Could you please check if there are any results? Furthermore, the function "rleunpack" is never used within RnBeads.

In order to help you an to solve the potential problem, we would need some more information on your R session, RnBeads version, the dataset you used and on the option setting/Rscript that you use to start RnBeads.

loganylchen commented 5 years ago

@schmic05

Thanks for your quick reply. First of all, when the error occur, there were no any results.

I have run the Rnbeads successful in another R environment. But I think it is really odd.

Raise ERROR one

I used conda to install an new conda env for rnbeads(both on Linux and Macos)

conda create -p ~/conda/rnbeads
conda install -y -c bioconda bioconductor-rnbeads
annotate                     AnnotationDbi
                         "1.58.0"                          "1.42.1"
                       assertthat                              base
                          "0.2.0"                           "3.5.1"
                           base64                          beanplot
                            "2.0"                             "1.2"
                               BH                            bibtex
                       "1.66.0-1"                           "0.4.2"
                            bindr                          bindrcpp
                          "0.1.1"                           "0.2.2"
                          Biobase                      BiocGenerics
                         "2.40.0"                          "0.26.0"
                      BiocManager                      BiocParallel
                         "1.30.4"                          "1.14.2"
                          biomaRt                        Biostrings
                         "2.36.1"                          "2.48.0"
                              bit                             bit64
                         "1.1-14"                           "0.9-7"
                           bitops                              blob
                          "1.0-6"                           "1.1.1"
                       bumphunter                           caTools
                         "1.22.0"                        "1.17.1.1"
                              cli                           cluster
                          "1.0.0"                         "2.0.7-1"
                        codetools                        colorspace
                         "0.2-15"                           "1.3-2"
                         compiler                            crayon
                          "3.5.1"                           "1.3.4"
                             curl                        data.table
                            "3.2"                          "1.11.6"
                         datasets                               DBI
                          "3.5.1"                           "1.0.0"
                     DelayedArray                DelayedMatrixStats
                          "0.6.6"                           "1.2.0"
                        dichromat                            digest
                          "2.0-0"                          "0.6.15"
                            doRNG                         dotCall64
                          "1.7.1"                           "1.0-0"
                            dplyr                             fansi
                          "0.7.6"                           "0.2.3"
     FDb.InfiniumMethylation.hg19                                ff
                          "2.2.0"                          "2.2-13"
                           fields                           foreach
                            "9.6"                           "1.4.4"
                          formatR                     futile.logger
                            "1.5"                           "1.4.3"
                   futile.options                             gdata
                          "1.0.1"                          "2.18.0"
                       genefilter                      GenomeInfoDb
                         "1.62.0"                          "1.16.0"
                 GenomeInfoDbData                 GenomicAlignments
                          "1.1.0"                          "1.16.0"
                  GenomicFeatures                     GenomicRanges
                         "1.32.3"                          "1.32.7"
                         GEOquery                           ggplot2
                         "2.48.0"                           "3.0.0"
                             glue                            gplots
                          "1.3.0"                           "3.0.1"
                         graphics                         grDevices
                          "3.5.1"                           "3.5.1"
                             grid                         gridExtra
                          "3.5.1"                             "2.3"
                           gtable                            gtools
                          "0.2.0"                           "3.8.1"
                        HDF5Array                               hms
                          "1.8.1"                           "0.4.2"
                             httr                        illuminaio
                          "1.3.1"                          "0.22.0"
                          IRanges                         iterators
                        "2.14.12"                          "1.0.10"
                         jsonlite                        KernSmooth
                            "1.5"                         "2.23-15"
                         labeling                          lambda.r
                            "0.3"                           "1.2.3"
                          lattice                          lazyeval
                        "0.20-35"                           "0.2.1"
                            limma                            locfit
                         "3.36.5"                         "1.5-9.1"
                         magrittr                              maps
                            "1.5"                           "3.3.0"
                             MASS                            Matrix
                         "7.3-50"                          "1.2-14"
                      matrixStats                            mclust
                         "0.54.0"                           "5.4.1"
                          memoise                           methods
                          "1.1.0"                           "3.5.1"
                        methylumi                              mgcv
                         "2.26.0"                          "1.8-24"
                             mime                             minfi
                            "0.5"                          "1.26.2"
                         multtest                           munsell
                         "2.36.0"                           "0.5.0"
                             nlme                           nor1mix
                        "3.1-137"                           "1.2-3"
                          openssl                      org.Hs.eg.db
                          "1.0.2"                           "3.6.0"
                         parallel                            pillar
                          "3.5.1"                           "1.3.0"
                        pkgconfig                          pkgmaker
                          "2.0.1"                            "0.27"
                            plogr                              plyr
                          "0.2.0"                           "1.8.4"
                   preprocessCore                       prettyunits
                         "1.42.0"                           "1.0.2"
                         progress                             purrr
                          "1.2.0"                           "0.2.5"
                         quadprog                                R6
                          "1.5-5"                           "2.2.2"
                     RColorBrewer                              Rcpp
                          "1.1-2"                         "0.12.18"
                            RCurl                             readr
                      "1.95-4.11"                           "1.1.1"
                         registry                           reshape
                            "0.5"                           "0.8.7"
                         reshape2                             rhdf5
                          "1.4.3"                          "2.24.0"
                         Rhdf5lib                             rlang
                          "1.2.1"                           "0.2.1"
                          RnBeads                      RnBeads.hg19
                         "1.12.1"                          "1.12.0"
                     RnBeads.mm10                       RnBeads.mm9
                         "1.12.0"                          "1.12.0"
                         rngtools                         Rsamtools
                          "1.3.1"                          "1.32.3"
                          RSQLite                       rtracklayer
                          "2.1.1"                          "1.40.6"
                        S4Vectors                            scales
                         "0.18.3"                           "0.5.0"
                         siggenes                              snow
                         "1.54.0"                           "0.4-3"
                             spam                           splines
                          "2.2-0"                           "3.5.1"
                            stats                            stats4
                          "3.5.1"                           "3.5.1"
                          stringi                           stringr
                          "1.2.4"                           "1.3.1"
             SummarizedExperiment                          survival
                         "1.10.1"                          "2.42-6"
                            tcltk                            tibble
                          "3.5.1"                           "1.4.2"
                            tidyr                        tidyselect
                          "0.8.1"                           "0.2.4"
                            tools TxDb.Hsapiens.UCSC.hg19.knownGene
                          "3.5.1"                           "3.2.2"
                             utf8                             utils
                          "1.1.4"                           "3.5.1"
                      viridisLite                             withr
                          "0.3.0"                           "2.1.2"
                              XML                              xml2
                      "3.98-1.12"                           "1.2.0"
                           xtable                           XVector
                          "1.8-2"                          "0.20.0"
                         zlibbioc
                         "1.26.0"

NO Raise ERROR one

In Linux, and use the local R to use bioconductor to install the Rnbeads.

It can run without any error.

annotate                     AnnotationDbi
                         "1.60.0"                          "1.44.0"
                       assertthat                            base64
                          "0.2.0"                             "2.0"
                         beanplot                                BH
                            "1.2"                        "1.66.0-1"
                           bibtex                             bindr
                          "0.4.2"                           "0.1.1"
                         bindrcpp                           Biobase
                          "0.2.2"                          "2.42.0"
                     BiocGenerics                       BiocManager
                         "0.28.0"                          "1.30.4"
                     BiocParallel                       BiocVersion
                         "1.16.2"                           "3.8.0"
                          biomaRt                        Biostrings
                         "2.38.0"                          "2.50.1"
                              bit                             bit64
                         "1.1-14"                           "0.9-7"
                           bitops                              blob
                          "1.0-6"                           "1.1.1"
                       bumphunter                           caTools
                         "1.24.5"                        "1.17.1.1"
                              cli                             clipr
                          "1.0.1"                           "0.4.1"
                       colorspace                            crayon
                          "1.3-2"                           "1.3.4"
                             curl                        data.table
                            "3.2"                          "1.11.8"
                              DBI                      DelayedArray
                          "1.0.0"                           "0.8.0"
               DelayedMatrixStats                            digest
                          "1.4.0"                          "0.6.18"
                            doRNG                         dotCall64
                          "1.7.1"                           "1.0-0"
                            dplyr                             fansi
                          "0.7.8"                           "0.4.0"
     FDb.InfiniumMethylation.hg19                                ff
                          "2.2.0"                          "2.2-14"
                           fields                           foreach
                            "9.6"                           "1.4.4"
                          formatR                     futile.logger
                            "1.5"                           "1.4.3"
                   futile.options                             gdata
                          "1.0.1"                          "2.18.0"
                       genefilter                      GenomeInfoDb
                         "1.64.0"                          "1.18.1"
                 GenomeInfoDbData                 GenomicAlignments
                          "1.2.0"                          "1.18.0"
                  GenomicFeatures                     GenomicRanges
                         "1.34.1"                          "1.34.0"
                         GEOquery                           ggplot2
                         "2.50.4"                           "3.1.0"
                             glue                            gplots
                          "1.3.0"                           "3.0.1"
                        gridExtra                            gtable
                            "2.3"                           "0.2.0"
                           gtools                         HDF5Array
                          "3.8.1"                          "1.10.1"
                              hms                              httr
                          "0.4.2"                           "1.4.0"
                       illuminaio                           IRanges
                         "0.24.0"                          "2.16.0"
                        iterators                          jsonlite
                         "1.0.10"                             "1.6"
                         labeling                          lambda.r
                            "0.3"                           "1.2.3"
                         lazyeval                             limma
                          "0.2.1"                          "3.38.3"
                           locfit                          magrittr
                        "1.5-9.1"                             "1.5"
                             maps                       matrixStats
                          "3.3.0"                          "0.54.0"
                           mclust                           memoise
                          "5.4.2"                           "1.1.0"
                        methylumi                              mime
                         "2.28.0"                             "0.6"
                            minfi                          multtest
                         "1.28.0"                          "2.38.0"
                          munsell                           nor1mix
                          "0.5.0"                           "1.2-3"
                          openssl                      org.Hs.eg.db
                            "1.1"                           "3.7.0"
                           pillar                         pkgconfig
                          "1.3.1"                           "2.0.2"
                         pkgmaker                             plogr
                           "0.27"                           "0.2.0"
                             plyr                    preprocessCore
                          "1.8.4"                          "1.44.0"
                      prettyunits                          progress
                          "1.0.2"                           "1.2.0"
                            purrr                          quadprog
                          "0.2.5"                           "1.5-5"
                               R6                      RColorBrewer
                          "2.3.0"                           "1.1-2"
                             Rcpp                             RCurl
                          "1.0.0"                       "1.95-4.11"
                            readr                          registry
                          "1.3.0"                             "0.5"
                          reshape                          reshape2
                          "0.8.8"                           "1.4.3"
                            rhdf5                          Rhdf5lib
                         "2.26.1"                           "1.4.2"
                            rlang                           RnBeads
                        "0.3.0.1"                           "2.0.0"
                     RnBeads.hg19                          rngtools
                         "1.14.0"                           "1.3.1"
                        Rsamtools                           RSQLite
                         "1.34.0"                           "2.1.1"
                      rtracklayer                         S4Vectors
                         "1.42.1"                          "0.20.1"
                           scales                          siggenes
                          "1.0.0"                          "1.56.0"
                             snow                              spam
                          "0.4-3"                           "2.2-0"
                          stringi                           stringr
                          "1.2.4"                           "1.3.1"
             SummarizedExperiment                            tibble
                         "1.12.0"                           "1.4.2"
                            tidyr                        tidyselect
                          "0.8.2"                           "0.2.5"
TxDb.Hsapiens.UCSC.hg19.knownGene                              utf8
                          "3.2.2"                           "1.1.4"
                      viridisLite                             withr
                          "0.3.0"                           "2.1.2"
                              XML                              xml2
                      "3.98-1.16"                           "1.2.0"
                           xtable                           XVector
                          "1.8-3"                          "0.22.0"
                         zlibbioc                              base
                         "1.28.0"                           "3.5.1"
                             boot                             class
                         "1.3-20"                          "7.3-14"
                          cluster                         codetools
                        "2.0.7-1"                          "0.2-15"
                         compiler                          datasets
                          "3.5.1"                           "3.5.1"
                          foreign                          graphics
                         "0.8-70"                           "3.5.1"
                        grDevices                              grid
                          "3.5.1"                           "3.5.1"
                       KernSmooth                           lattice
                        "2.23-15"                         "0.20-35"
                             MASS                            Matrix
                         "7.3-50"                          "1.2-14"
                          methods                              mgcv
                          "3.5.1"                          "1.8-24"
                             nlme                              nnet
                        "3.1-137"                          "7.3-12"
                         parallel                             rpart
                          "3.5.1"                          "4.1-13"
                          spatial                           splines
                         "7.3-11"                           "3.5.1"
                            stats                            stats4
                          "3.5.1"                           "3.5.1"
                         survival                             tcltk
                         "2.42-3"                           "3.5.1"
                            tools                             utils
                          "3.5.1"                           "3.5.1"

I am not sure if the INFOS I send is exactly your need.

schmic05 commented 5 years ago

Hi @btrspg

I tried reproducing your error, but everything worked well for me within conda. The error is potentially within the "ff" R-package, which uses the "bit" package. You may try to upgrade "ff" in your conda installation and try it again.

If we should really track down the error, we would need very detailed information about your setting, i.e. your operation system, the conda version you are using, the dataset you are using, the option setting used for RnBeads, and general information about your computing infrastructure (since the "ff" package writes files on disk, it might be related to not properly reading/writing to/from disk.

Sorry that I cannot provide an easy solution for your problem.

loganylchen commented 5 years ago

Hi @schmic05, Sorry to reply late. I have re-installed the 'ff' by 

install.packages('https://cran.r-project.org/src/contrib/ff_2.2-14.tar.gz')

and then the RnBeads goes well.

Thanks.