Microarray analysis error

Question

[biology_inform]

# Differential expression analysis with limma 
library(GEOquery) 
library(AnnotationDbi) 
library(BiocFileCache) 
library(affy) 
library(oligo) 
library(Biobase) 
library(arrayQualityMetrics) 
library(splitstackshape) 
library(tidyr) 
library(dplyr) 
setwd("~/Desktop/PC9/") 
celFiles <- list.celfiles()
affyRaw <- read.celfiles(celFiles) 

Loading required package: pd.hugene.2.0.st 
Loading required package: RSQLite 
Failed with error:  ‘Package ‘RSQLite’ version 2.2.14 cannot be unloaded:  Error in unloadNamespace(package) : namespace ‘RSQLite’ is imported by ‘AnnotationDbi’, ‘BiocFileCache’, ‘oligo’ so cannot be unloaded ’ 
Attempting to obtain 'pd.hugene.2.0.st' from BioConductor website. Checking to see if your internet connection works... 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

installing the source package ‘pd.hugene.2.0.st’

trying URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/pd.hugene.2.0.st_3.14.1.tar.gz' Content type 'application/x-gzip' length 101764114 bytes (97.0 MB)
================================================== downloaded 97.0 MB

* installing *source* package ‘pd.hugene.2.0.st’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pd.hugene.2.0.st)

The downloaded source packages are in   ‘/private/var/folders/hr/0x5lrx7s2fg_0hgrw94pdt8c0000gn/T/RtmpaduYYW/downloaded_packages’
Loading required package: pd.hugene.2.0.st
Loading required package: RSQLite
Failed with error:  ‘Package ‘RSQLite’ version 2.2.14 cannot be unloaded:
Error in unloadNamespace(package) : 
  namespace ‘RSQLite’ is imported by ‘AnnotationDbi’, ‘BiocFileCache’, ‘oligo’ so cannot be unloaded ’
 There was a problem during download or installation. Package 'pd.hugene.2.0.st' cannot be loaded. Please, try again.
Error in read.celfiles(celFiles) :  
  The annotation package, pd.hugene.2.0.st, could not be loaded.

This is what I get when I run the code above. There is a problem with "pd.hugene.2.0.st". Is there anyone know how to solve this problem? Thanks in advance.

[Ram]

There is a problem with "pd.hugene.2.0.st"

I don't see anything pointing to that in your log above. What makes you think there's a problem with that package?

[Matthias Zepper]

Loading required package: pd.hugene.2.0.st Loading required package: RSQLite Failed with error: ‘Package ‘RSQLite’ version 2.2.14 cannot be unloaded: Error in unloadNamespace(package) : namespace ‘RSQLite’ is imported by ‘AnnotationDbi’, ‘BiocFileCache’, ‘oligo’ so cannot be unloaded ’ There was a problem during download or installation. Package 'pd.hugene.2.0.st' cannot be loaded. Please, try again.

When you use the oligo package, you e.g. won't need the affy or the AnnotationDbi packages. Please follow the tutorials for the oligo package specifically. Also, only import what you do use - the more the merrier doesn't apply to loading libraries ;-)

[Ram]

Ah, the error was all the way to the right. People need to copy paste properly and add new lines where they make sense. I've reformatted their error message so it's a little more readable.