Question: Package version of Bioconductor cannot be unloaded, Error in unloadNamespace(package),help!!
0
gravatar for naf
29 days 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....

ADD COMMENTlink written 29 days 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 Please try BiocManager::valid(), it will show any out-of-date or missing packages.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.

ADD REPLYlink modified 29 days ago • written 29 days ago by shepherl ♦♦ 1.4k

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"

ADD REPLYlink written 29 days ago by naf0

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

ADD REPLYlink written 29 days ago by shepherl ♦♦ 1.4k

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)

rawfiles <- ReadAffy(filenames=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:

getID ILM1A1 BEADSTDEV-A1 AvgNBEADS-A1 Detection-A1

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!

ADD REPLYlink modified 19 days ago • written 19 days ago by naf0

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) -

ADD REPLYlink written 19 days ago by shepherl ♦♦ 1.4k

thanks, I have just posted my question as you suggested

ADD REPLYlink written 19 days ago by naf0
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