Question: New Error in library(oligo) Reading in CEL files
0
gravatar for majeskea
11 months ago by
majeskea0
majeskea0 wrote:

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)

oligo package • 240 views
ADD COMMENTlink modified 11 months ago by James W. MacDonald51k • written 11 months ago by majeskea0
Answer: New Error in library(oligo) Reading in CEL files
1
gravatar for James W. MacDonald
11 months ago by
United States
James W. MacDonald51k wrote:

Any time you see an error like

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’

What it means is that you had an error because there isn't a required package called 'digest'. And the fix for that is to install that package!

library(BiocInstaller)

biocLite("digest")

 

ADD COMMENTlink written 11 months ago by James W. MacDonald51k

Perfect! Problem fixed. I didn't know it would be that easy :) I'm new to Bioinformatics...

Thank you James for answering so quickly!

ADD REPLYlink written 11 months ago by majeskea0

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.

ADD REPLYlink written 11 months ago by James W. MacDonald51k
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