bioinformatist / lncpipereporter Goto Github PK

So as to update description ASAP

Hi,
I'm running lncpipe, and the a error always show up when the lncpipeReporter process is running.

The error message is:
"processing file: reporter.Rmd Quitting from lines 51-99 (reporter.Rmd) Error in [.data.table(x, , 2) : Item 1 of j is 2 which is outside the column number range [1,ncol=1] Calls: run_report ... FUN -> determine type -> paste -> [ -> [.data.table Execution halted"
I'm using docker, lastest nextflow and lncpipe versions. I'm not a developer, could someone help me?

Warning message:
package ‘LncPipeReporter’ is not available (for R version 3.4.2)

LncPipeReporter does not support R version 3.4.2? I can't install it in centos.

Hi, what might be reason of getting this error? Thanks in advance.

Command error:

processing file: reporter.Rmd

processing file: ./lncRNA.Rmd
Quitting from lines 27-38 (./lncRNA.Rmd)
Quitting from lines 41-43 (./lncRNA.Rmd)
Error: .onLoad failed in loadNamespace() for 'shiny', details:
call: NULL
error: invalid version specification '1,5'
Execution halted

Hi，this problem occurs when I run testdata in lncpipe. How can I solve it? Thanks in advance.

processing file: ./edger.Rmd
Quitting from lines 9-57 (./edger.Rmd)
Quitting from lines 185-194 (./edger.Rmd)
Error in .rowNamesDF<-(x, value = value) :
duplicate 'row.names' are not allowed
Calls: run_reporter ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<-
In addition: Warning messages:
1: In eval(expr, envir, enclos) : NAs introduced by coercion
2: non-unique values when setting 'row.names':
Execution halted

Hi, I meet an error showed like this ;

Installing 116 packages: acepack, annotate, AnnotationDbi, base64enc, BH, Biobase, BiocGenerics, BiocParallel, bit, bit64, bitops, blob, caTools, checkmate, colorspace, cowplot, crosstalk, data.table, DBI, DelayedArray, dendextend, DEoptimR, DESeq2, diptest, dplyr, DT, edgeR, evaluate, fansi, flexdashboard, flexmix, foreach, formatR, Formula, fpc, futile.logger, futile.options, gclus, gdata, genefilter, geneplotter, GenomeInfoDb, GenomeInfoDbData, GenomicRanges, ggplot2, ggsci, gplots, gridExtra, gtable, gtools, heatmaply, hexbin, highr, Hmisc, htmlTable, htmltools, htmlwidgets, httpuv, IRanges, iterators, kernlab, knitr, labeling, lambda.r, later, latticeExtra, lazyeval, limma, locfit, markdown, matrixStats, mclust, modeltools, munsell, mvtnorm, NOISeq, pillar, pkgconfig, plogr, plotly, plyr, prabclus, promises, qap, RColorBrewer, RcppArmadillo, RCurl, registry, reshape2, rmarkdown, robustbase, RSQLite, S4Vectors, scales, seriation, shiny, snow, sourcetools, stringi, stringr, SummarizedExperiment, tibble, tidyr, tidyselect, tinytex, trimcluster, TSP, utf8, viridis, viridisLite, webshot, xfun, XML, xtable, XVector, zlibbioc
Error in if (type == "binary") { : argument is of length zero
Calls: ... with_rprofile_user -> with_envvar -> force -> force -> i.p
In addition: Warning message:
In is.na(remote_deps$package) :
is.na() applied to non-(list or vector) of type 'NULL'
Execution halted

I found in some discussion. Developers mentioned that the reason is that the pkgtype is not defined. Is there any clue I could fix it?

Thank you!