Please help! I am stuck. This was just working last week! S.O.S. Thank you!
> library(oligo)
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’:
anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colnames, colSums,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: oligoClasses
Welcome to oligoClasses version 1.42.0
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: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:base’:
expand.grid
Loading required package: IRanges
Attaching package: ‘IRanges’
The following object is masked from ‘package:grDevices’:
windows
Loading required package: XVector
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Error: package or namespace load failed for ‘oligo’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘digest’
> celpath = "~/Documents/"
> data <- read.celfiles(list.celfiles())
Error in read.celfiles(list.celfiles()) :
could not find function "read.celfiles"
1) I am getting a new error at the end of loading package oligo: Error: package or namespace load failed for ‘oligo’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘digest’
2) And also this is a new error Error in read.celfiles(list.celfiles()) :
could not find function "read.celfiles"
and I never had any problem with the argument 'read.celfiles(list.celfiles())' before
I am also seeing the same error 1) when I try to load my library separately using package 'affy' for the annotation package (miRNA-4_0-st-v1.cdf or pd.mirna.4.0)
Perfect! Problem fixed. I didn't know it would be that easy :) I'm new to Bioinformatics...
Thank you James for answering so quickly!
One of the things you have to learn early on is that most errors spit out informative messages that often direct you to the solution, so it's important to read and try to understand what you are being told. There can be times where you get some cryptic message from some helper function that you won't be able to figure out, but it's nice when you do get an easily interpreted message that you can act on without any help.