Question: Could not access the Bioconductor repository
0
gravatar for maxininfa
12 days ago by
maxininfa0
maxininfa0 wrote:

Hi! I'm following the ArrayExpress vignette to analyze an experiment, but can't follow through when I need to download the annotation package pd.hg.u133.plus.2

> library(oligo)
> data = read.celfiles(list)
Loading required package: pd.hg.u133.plus.2
Attempting to obtain 'pd.hg.u133.plus.2' from BioConductor website.
Checking to see if your internet connection works...
Could not access the Bioconductor repository.
Please check your internet connection.
Error in read.celfiles(list) : 
  The annotation package, pd.hg.u133.plus.2, could not be loaded.
In addition: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘pd.hg.u133.plus.2’
2: In readLines(biocURL) :
  URL 'http://www.bioconductor.org/main.html': status was 'Couldn't connect to server'

This already happened trying to do it through the ArrayExpress package:

> library(ArrayExpress)
Warning message:
closing unused connection 3 (http://www.bioconductor.org/main.html) 
> AEset = ArrayExpress("E-GEOD-18670")
*** Im omitting showing the correct download of all the data to keep it short, but trust me it did ***
ArrayExpress: Reading pheno data from SDRF
ArrayExpress: Reading data files
Loading required package: pd.hg.u133.plus.2
Attempting to obtain 'pd.hg.u133.plus.2' from BioConductor website.
Checking to see if your internet connection works...
Could not access the Bioconductor repository.
Please check your internet connection.
Error in oligo::read.celfiles(filenames = file.path(path, unique(files))) : 
  The annotation package, pd.hg.u133.plus.2, could not be loaded.
In addition: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘pd.hg.u133.plus.2’
2: In readLines(biocURL) :
  URL 'http://www.bioconductor.org/main.html': status was 'Couldn't connect to server'
Error in readAEdata(path = path, files = dataFiles, dataCols = dataCols,  : 
  Unable to read cel files in/tmp/RtmpNoPLTF
Error in ae2bioc(mageFiles = expFiles, dataCols = dataCols, drop = drop) : 
  ArrayExpress: Unable to read assay data

I followed this suggestion but didn't change.

I do have internet access, and I'm able to install packages.

Is this because of I'm behind a proxy? I downloaded the pd.hg.u133.plus.2 from the ArrayExpress site. If any of you knows how to incorporate it so I can carry on with my analysis I would be extremely grateful.

> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
 [1] LC_CTYPE=en_US.UTF-8      
 [2] LC_NUMERIC=C              
 [3] LC_TIME=es_AR.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=es_AR.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=es_AR.UTF-8      
 [8] LC_NAME=C                 
 [9] LC_ADDRESS=C              
[10] LC_TELEPHONE=C            
[11] LC_MEASUREMENT=es_AR.UTF-8
[12] LC_IDENTIFICATION=C       
attached base packages:
[1] stats4    parallel  stats    
[4] graphics  grDevices utils    
[7] datasets  methods   base     
other attached packages:
[1] ArrayExpress_1.38.0
[2] oligo_1.42.0       
[3] Biostrings_2.46.0  
[4] XVector_0.18.0     
[5] IRanges_2.12.0     
[6] S4Vectors_0.16.0   
[7] Biobase_2.38.0     
[8] oligoClasses_1.40.0
[9] BiocGenerics_0.24.0
loaded via a namespace (and not attached):
 [1] Rcpp_0.12.19              
 [2] compiler_3.4.4            
 [3] BiocInstaller_1.28.0      
 [4] GenomeInfoDb_1.14.0       
 [5] bitops_1.0-6              
 [6] iterators_1.0.10          
 [7] tools_3.4.4               
 [8] zlibbioc_1.24.0           
 [9] digest_0.6.17             
[10] bit_1.1-14                
[11] RSQLite_2.1.1             
[12] memoise_1.1.0             
[13] preprocessCore_1.40.0     
[14] lattice_0.20-38           
[15] ff_2.2-14                 
[16] Matrix_1.2-15             
[17] foreach_1.4.4             
[18] DelayedArray_0.4.1        
[19] DBI_1.0.0                 
[20] yaml_2.2.0                
[21] GenomeInfoDbData_1.0.0    
[22] affxparser_1.50.0         
[23] bit64_0.9-7               
[24] grid_3.4.4                
[25] XML_3.98-1.16             
[26] limma_3.34.9              
[27] blob_1.1.1                
[28] codetools_0.2-15          
[29] matrixStats_0.54.0        
[30] GenomicRanges_1.30.3      
[31] splines_3.4.4             
[32] SummarizedExperiment_1.8.1
[33] RCurl_1.95-4.11           
[34] affyio_1.48.0
ADD COMMENTlink modified 12 days ago by James W. MacDonald49k • written 12 days ago by maxininfa0
Answer: Could not access the Bioconductor repository
2
gravatar for James W. MacDonald
12 days ago by
United States
James W. MacDonald49k wrote:

Update to R-3.5.2, and re-install Bioconductor. We don't support old versions, and it works fine with the current versions of R/BioC:

> library(BiocManager)
> BiocManager::install("pd.hg.u133.plus.2")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.0 (2018-04-23)
Installing package(s) 'pd.hg.u133.plus.2'
installing the source package 'pd.hg.u133.plus.2'

trying URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u133.plus.2_3.12.0.tar.gz'
Content type 'application/x-gzip' length 24799467 bytes (23.7 MB)
downloaded 23.7 MB

* installing *source* package 'pd.hg.u133.plus.2' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pd.hg.u133.plus.2'
    finding HTML links ... done
    pkg                                     html  
    probeSequences                          html  
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (pd.hg.u133.plus.2)
ADD COMMENTlink written 12 days ago by James W. MacDonald49k

Thx! I did install it, the sad part is that ArrayExpress isn't supported on 3.5. I hope I can install 3.4 in parallel and access the package.

ADD REPLYlink modified 11 days ago • written 11 days ago by maxininfa0

Your statement that ArrayExpress is not supported on 3.5 (I guess you mean R-3.5.0, or similar) is not correct.

ADD REPLYlink written 11 days ago by Martin Morgan ♦♦ 22k
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