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5 months ago by
naf0
naf0 wrote:

I am getting desperate trying to install a package.

I am not extremely experienced in BioConductor packages.

The R version I am using is 3.5.2 and I have a mac High Sierra, version 10.13.6.

I want to analyse microarray data generated by the Affymetrix platform.

I am using a series of installation commands and at the end of all this I get the constant error comment:

Error in value[[3L]](cond) :
Package ‘S4Vectors’ version 0.18.3 cannot be unloaded:
Error in unloadNamespace(package) : namespace ‘S4Vectors’ is imported by ‘IRanges’, ‘genefilter’, ‘Biostrings’, ‘AnnotationDbi’, ‘XVector’ so cannot be unloaded.


I am using the following commands:

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("XVector", version = "3.8")
BiocManager::install("S4Vectors", version = "3.8")
BiocManager::install("matrixStats", version = "3.8")
BiocManager::install("limma", version = "3.8")
BiocManager::install("gcrma", version = "3.8")

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("hgu133plus2.db", version = "3.8")

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("IRanges", version = "3.8")

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("genefilter", version = "3.8")

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Biostrings", version = "3.8")

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("AnnotationDbi", version = "3.8")

library(limma)
library(gcrma)
library(hgu133plus2.db)


The line "library(hgu133plus2.db)" is the one creating the error message. Could anyone help me please? I am wasting so much time trying to find the right package update for the right versions of R....

written 5 months ago by naf0

Can you please show the results of the commands with the full error messages so we can better assist. Please try BiocManager::valid(), it will show any out-of-date or missing packages. Run any commands it recommends. If you are still having trouble after that, then try running BiocManager::install("hgu133plus2.db") and report any ERROR messages it gives. Please also include the results from running sessionInfo( ) .

Also, just so you are aware, once you doif (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") once, BiocManager is installed and doesn't need to be run again. You only need to do the install commands for all the packages after.

magic to get such a prompt reply! Thank you.

I removed the countless "install.packages("BiocManager")" commands that I had written, removed all the packages from BioConductor once again and ran a new Rstudio session once again and...it works!! Thanks a lot for your support.

I however still don't have a clue why I was getting the message :

"Error in value[3L] : Package ‘S4Vectors’ version 0.18.3 cannot be unloaded: Error in unloadNamespace(package) : namespace ‘S4Vectors’ is imported by ‘IRanges’, ‘genefilter’, ‘Biostrings’, ‘AnnotationDbi’, ‘XVector’ so cannot be unloaded"

It might have somehow gotten a mixed version of install. That's why we recommend running BiocManager::valid() when there are errors to check for mismatches. Glad its working. Cheers

Hello shepherl,

I am analysing Affymetryx and Illumina data from the MACQ project for the moment. I used the following commands to read and preprocess (normalisation, background correction,..) the Affymetry CEL files:

files <- list.files('DONNEES-AFFYMETRIX/')

files <- paste0('DONNEES-AFFYMETRIX/',files)

expressionset <- gcrma(rawfiles)

I don't know what commands to use to read AND preprocess ILLUMINA file (eg. ILM1A1.txt ) downloaded from NCBI:

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE5350:

I started with the same commands as for the Affymetrix cell files;namely

files <- list.files('DONNEES-ILLUMINA/')

files <- paste0('DONNEES-ILLUMINA/',files)

and tried to read the files with "read.ilmn" but with no success; the file content looks like this:

GI10047089-S 59.4 3.3 45 0.8431114 GI10047091-S 90.4 3.1 50 0.99802241 GI10047093-S 539.8 13.5 43 1 GI10047099-S 563.6 21.2 32 1

I read about the existence of "rsn" "ssn" "lumiR" and "lumiR.batch" for preprocessing( normalisation...) but couldn't use them as I can't read the data to start with. I have spent quite a long time searching the internet for answers but couldn't find any. Could you perhaps help me with that?? It would be really great!

It would probably be better to open a new support site issue for this - There are many users that analyze this type of data and may be able to answer quicker (as I would have to reach this) -