REMP 1.7.1
Yinan Zheng
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/REMP |
| Branch: master |
| Last Commit: a23f642 |
| Last Changed Date: 2019-01-04 13:46:37 -0400 (Fri, 04 Jan 2019) |
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | ERROR | skipped | | |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | [ ERROR ] | skipped | skipped | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data REMP
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* checking for file ‘REMP/DESCRIPTION’ ... OK
* preparing ‘REMP’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘REMP.Rnw’ using Sweave
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall,
clusterEvalQ, clusterExport, clusterMap,
parApply, parCapply, parLapply, parLapplyLB,
parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce,
anyDuplicated, append, as.data.frame, basename,
cbind, colMeans, colSums, colnames, dirname,
do.call, duplicated, eval, evalq, get, grep,
grepl, intersect, is.unsorted, lapply, mapply,
match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rowMeans, rowSums,
rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max,
which.min
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view
with 'browseVignettes()'. To cite Bioconductor,
see 'citation("Biobase")', and for packages
'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: ‘matrixStats’
The following objects are masked from ‘package:Biobase’:
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:matrixStats’:
colMaxs, colMins, colRanges, rowMaxs, rowMins,
rowRanges
The following objects are masked from ‘package:base’:
aperm, apply, rowsum
Loading required package: minfi
Loading required package: Biostrings
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:DelayedArray’:
type
The following object is masked from ‘package:base’:
strsplit
Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.1 2013-03-22
Registered S3 method overwritten by 'openssl':
method from
print.bytes Rcpp
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Loading required package: IlluminaHumanMethylationEPICanno.ilm10b2.hg19
Attaching package: ‘IlluminaHumanMethylationEPICanno.ilm10b2.hg19’
The following objects are masked from ‘package:IlluminaHumanMethylation450kanno.ilmn12.hg19’:
Islands.UCSC, Locations, Manifest, Other,
SNPs.132CommonSingle, SNPs.135CommonSingle,
SNPs.137CommonSingle, SNPs.138CommonSingle,
SNPs.141CommonSingle, SNPs.142CommonSingle,
SNPs.144CommonSingle, SNPs.146CommonSingle,
SNPs.147CommonSingle, SNPs.Illumina
Registered S3 methods overwritten by 'ggplot2':
method from
[.quosures rlang
c.quosures rlang
print.quosures rlang
Illumina 450k Methylation data in beta value detected.
A total of 1715 zero beta values are found.
Fixing zero beta values with the smallest beta value = 0.001 ...
Converting beta value to M value ...
Methylation data grooming is completed.
Start Alu annotation data initialization ... (0 sec.)
Illumina platform: 450k
Done. (42 sec.)
REMParcel has been saved under the directory:
/tmp/RtmpYx25p9/REMP.data.450k
Using random seed = 777
Start RE methylation prediction with FALSE core(s) ... (0 sec.)
Methylation data grooming is completed.
Preparing neighboring CpG information ... (1 sec.)
Predicting sample GM12878 ...
Error: processing vignette 'REMP.Rnw' failed with diagnostics:
chunk 8 (label = rempredict)
Error in ranger::ranger(Methy ˜ ., data = d, mtry = param, num.threads = ncore, :
Error: Invalid value for num.threads
--- failed re-building ‘REMP.Rnw’
SUMMARY: processing the following file failed:
‘REMP.Rnw’
Error: Vignette re-building failed.
Execution halted