I have been trying to install SomaticSignatures from source after updating to R v.3.3.2 and the latest Biobase, but the package fails to install complaint about failed namespace loading.
Any ideas?

Thank you.

Christos

> library(SomaticSignatures)
Error : object ‘isDevel’ is not exported by 'namespace:BiocInstaller'
Error: package or namespace load failed for ‘SomaticSignatures’
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] VariantAnnotation_1.20.2   Rsamtools_1.26.1           Biostrings_2.42.1        
[4] XVector_0.14.0             SummarizedExperiment_1.4.0 Biobase_2.28.0           
[7] GenomicRanges_1.26.1       GenomeInfoDb_1.10.1        IRanges_2.8.1            
[10] S4Vectors_0.12.1           BiocGenerics_0.20.0       

loaded via a namespace (and not attached):
[1] httr_1.2.1                    splines_3.3.2                 Formula_1.2-1               
[4] shiny_0.14.2                  assertthat_0.1                interactiveDisplayBase_1.12.0
[7] latticeExtra_0.6-28           BSgenome_1.42.0               RSQLite_1.1-1               
[10] lattice_0.20-34               digest_0.6.10                 RColorBrewer_1.1-2          
[13] colorspace_1.3-1              htmltools_0.3.5               httpuv_1.3.3                
[16] Matrix_1.2-7.1                plyr_1.8.4                    XML_3.98-1.5                
[19] biomaRt_2.24.1                zlibbioc_1.20.0               xtable_1.8-2                
[22] scales_0.4.1                  BiocParallel_1.2.22           htmlTable_1.7               
[25] tibble_1.2                    openssl_0.9.5                 ggplot2_2.2.0               
[28] GenomicFeatures_1.26.0        nnet_7.3-12                   lazyeval_0.2.0              
[31] survival_2.40-1               magrittr_1.5                  mime_0.5                    
[34] memoise_1.0.0                 GGally_1.3.0                  foreign_0.8-67              
[37] BiocInstaller_1.18.5          tools_3.3.2                   data.table_1.10.0           
[40] stringr_1.1.0                 munsell_0.4.3                 cluster_2.0.5               
[43] AnnotationDbi_1.36.0          lambda.r_1.1.9                base64_2.0                  
[46] futile.logger_1.4.3           grid_3.3.2                    RCurl_1.95-4.8              
[49] dichromat_2.0-0               bitops_1.0-6                  gtable_0.2.0                
[52] DBI_0.5-1                     reshape_0.8.6                 reshape2_1.4.2              
[55] R6_2.2.0                      GenomicAlignments_1.10.0      gridExtra_2.2.1             
[58] knitr_1.15.1                  rtracklayer_1.34.1            Hmisc_4.0-1                 
[61] futile.options_1.0.0          stringi_1.1.2                 Rcpp_0.12.8                 
[64] rpart_4.1-10                  acepack_1.4.1                

I guess you are not using biocLite() to install your packages; they are a mixture of versions, and in particular BiocInstaller version 1.18.5 is very old -- the current 'release' version is 1.24.0. I suggest you follow the instructions at http://bioconductor.org/install/#troubleshoot-bioconductor-packages to remove and update BiocInstaller, and then to bring your packages into sync with the current version.

I used biocLite in the first place, but my BiocInstaller was too old. I followed the instructions under Troubleshoot BiocInstaller to update BiocInstaller and then re-installed out of date packages. Everything works now.

Thanks for your help, Martin.

Christos