Welcome to the MapMan Family of Software Forum

Please do not hesitate to register and post your question.

Don't forget to subscribe to your posted message so you get notified on updates.
Every question you post will help others and or enhance the software!

Post a question,   post a bug!

Welcome to the MapMen Family of Software Forum Welcome to the MapMen Family of Software Forum

Using MapMan

plier library error

plier library error
Answer
8/22/13 2:37 PM
Hello,

whenever I try to run any analysis in Robin, I get the following error, despite Biobase and plier being installed on mu machine:


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 object is masked from 'package:stats':

xtabs

The following objects are masked from 'package:base':

Filter, Find, Map, Position, Reduce, anyDuplicated, as.data.frame,
cbind, colnames, duplicated, eval, get, intersect, lapply, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rep.int, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unlist

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")'.

Error in library(plier) : there is no package called 'plier'
Execution halted



I am using
Robin 1.2.4_build656
Scientific Linux Release 6.4
java version 1.6.0_24



How can I resolve this issue?

Thanks!

RE: plier library error
Answer
8/22/13 3:13 PM as a reply to Vladislava Chalei.
Hi Vladislava Chalei,

thanks for your feed back. In order to investigate your problem it would be great if you could
give me a few more details about your system. Which version of R is installed on your linux
machine? Are there maybe several parallel installations of different versions? Please check
the file robin.conf in the .robindata folder that is located in you home directory - it contains
the path to R (among other configuration informations). When you run the R that is configured
for usage with RobiNA in the robin.conf and type

library(plier)

does it work or do you get the error message below?

best greetings,
Marc

RE: plier library error
Answer
8/22/13 3:20 PM as a reply to Marc Lohse.
Hi Marc,

I use R 3.0.1. I have only one R installed. And I did check that plier is installed and runs without errors.

Would you recommend I try running Robin on a Windows machine instead? Or else?

Thanks,
Vlada

RE: plier library error
Answer
8/22/13 3:24 PM as a reply to Vladislava Chalei.
Hi Vlada,

thanks for the information. It a bit strange that you can load the plier library when starting R
manually and RobiNA can't when using the same installation - that said, there might be another
problem ahead anyway. RobiNA was developed and tested with R 2.15.2 - most of the internal
analysis scripts will work with R 3.x as well, but it's not guaranteed (e.g. the RNA-Seq workflow
is sure to break when using R 3.x). Usually, when properly configured, RobiNA works fine under
linux - so i would not recommend using the windows version instead. However, the windows
packages come with an embedded R that has all the needed libraries preinstalled...

cheers,
Marc