Error in UseMethod("rleunpack")
Closed this issue · 4 comments
loganylchen commented
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
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
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
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
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.