Error in library(oligo) : package or namespace load failed for ‘oligoClasses’
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tanya • 0
@tanya-24893
Last seen 7 weeks ago

Hi, Can you please help me with using Oligo package. I am using Oligo Package to read celfiles. I donwloaded the data from GEOquery and now want to read the celfiles. But reading celfiles using read.celfiles gives an error. So I thought maybe its linked with the error that comes with loading the oligo library. I have included the code and the following errors. Code should be placed in three backticks as shown below

library(oligo)
Loading required package: oligoClasses
Error: package or namespace load failed for ‘oligoClasses’:
 object 'maxindex' not found whilst loading namespace 'ff'
Error: package ‘oligoClasses’ could not be loaded

rawData<- read.celfiles(celfiles)
Error in read.celfiles(celfiles) : could not find function "read.celfiles" 

sessionInfo( )
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocGenerics_0.34.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6                lattice_0.20-41             prettyunits_1.1.1           Rsamtools_2.4.0             Biostrings_2.56.0          
 [6] assertthat_0.2.1            digest_0.6.25               BiocFileCache_1.12.0        R6_2.4.1                    GenomeInfoDb_1.24.2        
[11] stats4_4.0.2                RSQLite_2.2.0               httr_1.4.2                  pillar_1.4.4                zlibbioc_1.34.0            
[16] rlang_0.4.9                 GenomicFeatures_1.40.1      progress_1.2.2              curl_4.3                    rstudioapi_0.13            
[21] blob_1.2.1                  S4Vectors_0.26.1            Matrix_1.2-18               BiocParallel_1.22.0         stringr_1.4.0              
[26] RCurl_1.98-1.2              bit_1.1-15.2                biomaRt_2.44.4              DelayedArray_0.14.0         compiler_4.0.2             
[31] rtracklayer_1.48.0          pkgconfig_2.0.3             askpass_1.1                 openssl_1.4.1               tidyselect_1.1.0           
[36] SummarizedExperiment_1.18.1 tibble_3.0.1                GenomeInfoDbData_1.2.3      IRanges_2.22.2              matrixStats_0.56.0         
[41] XML_3.99-0.3                crayon_1.3.4                dplyr_1.0.0                 dbplyr_1.4.4                GenomicAlignments_1.24.0   
[46] bitops_1.0-6                rappdirs_0.3.1              grid_4.0.2                  lifecycle_0.2.0             DBI_1.1.0                  
[51] magrittr_1.5                stringi_1.4.6               XVector_0.28.0              affyio_1.58.0               xml2_1.3.2                 
[56] ellipsis_0.3.1              generics_0.0.2              vctrs_0.3.1                 tools_4.0.2                 bit64_0.9-7                
[61] Biobase_2.48.0              glue_1.4.1                  purrr_0.3.4                 hms_0.5.3                   AnnotationDbi_1.50.3       
[66] GenomicRanges_1.40.0        memoise_1.1.0
R oligoClasses Oligoclass Bioconductor Oligo • 97 views
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I have installed oligoClasses but to no avail, It is still showing the same error above. I tried installing ff from CRAN but its not available for the R version I am using.

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This type of error usually means that you are mixing Bioconductor packages from different releases. Try

BiocManager::version()  # Should be "3.12"
BiocManager::valid()  # should return TRUE, or installation instructions to make the  installation valid

ff is available under 'Windows binaries' at https://cran.r-project.org/package=ff, so probably R is trying to tell you something else; posting the full installation attempt and message would help.

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