Hi everyone,

I was trying to load BiocInstaller in order to install additional packages during my analysis, but this error message keeps returning:

library(BiocInstaller)

Error in unloadNamespace(package) :
  namespace 'BiocInstaller' is imported by 'affy', 'oligoClasses' so cannot be unloaded
Error in library(BiocInstaller) :
  Package 'BiocInstaller' version 1.18.1 cannot be unloaded

My sessionInfo() is as follows:

R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.3 (Yosemite)

locale:
[1] C

attached base packages:
 [1] stats4    graphics  grDevices utils     datasets  parallel  compiler
 [8] stats     methods   base     

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0      
 [2] BSgenome_1.36.0                        
 [3] rtracklayer_1.28.2                     
 [4] Biostrings_2.36.0                      
 [5] XVector_0.8.0                          
 [6] hgu133plus2cdf_2.16.0                  
 [7] TxDb.Hsapiens.UCSC.hg19.knownGene_3.1.2
 [8] GenomicFeatures_1.20.0                 
 [9] GenomicRanges_1.20.3                   
[10] magrittr_1.5                           
[11] hgu133plus2frmavecs_1.5.0              
[12] hgu133plus2barcodevecs_1.6.0           
[13] hgu133plus2.db_3.1.2                   
[14] org.Hs.eg.db_3.1.2                     
[15] GO.db_3.1.2                            
[16] RSQLite_1.0.0                          
[17] DBI_0.3.1                              
[18] AnnotationDbi_1.30.1                   
[19] GenomeInfoDb_1.4.0                     
[20] IRanges_2.2.1                          
[21] S4Vectors_0.6.0                        
[22] frma_1.20.0                            
[23] affy_1.46.0                            
[24] Biobase_2.28.0                         
[25] BiocGenerics_0.14.0                    
[26] RColorBrewer_1.1-2                     
[27] dplyr_0.4.1                            
[28] reshape2_1.4.1                         
[29] ggplot2_1.0.1                          

loaded via a namespace (and not attached):
 [1] Rcpp_0.11.6             Rsamtools_1.20.1        assertthat_0.1         
 [4] digest_0.6.8            foreach_1.4.2           plyr_1.8.2             
 [7] futile.options_1.0.0    BiocInstaller_1.18.2    oligoClasses_1.30.0    
[10] zlibbioc_1.14.0         lazyeval_0.1.10         preprocessCore_1.30.0  
[13] proto_0.3-10            splines_3.2.0           BiocParallel_1.2.1     
[16] stringr_1.0.0           RCurl_1.95-4.6          bit_1.1-12             
[19] biomaRt_2.24.0          munsell_0.4.2           oligo_1.32.0           
[22] ff_2.2-13               codetools_0.2-11        XML_3.98-1.1           
[25] GenomicAlignments_1.4.1 MASS_7.3-40             bitops_1.0-6           
[28] grid_3.2.0              gtable_0.1.2            scales_0.2.4           
[31] stringi_0.4-1           affyio_1.36.0           futile.logger_1.4.1    
[34] lambda.r_1.1.7          iterators_1.0.7         tools_3.2.0            
[37] colorspace_1.2-6        affxparser_1.40.0    

I was wondering if there is anyway that I can load BiocInstaller halfway through my analysis without having to re-start a new R process?

Thanks a ton!

Jeremy

You have something weird going on with your installation. The error says you cannot unload BiocInstaller 1.18.1, yet you have BiocInstaller 1.18.2 loaded via namespace. You might want to restart R, load BiocInstaller, and then run biocValid() to see what's up.