Hi all,

after updating R to 3.4.0 I have a problem reinstalling 1 particular Bioconductor package: clusterProfiler. Do you have any suggestions on what I might do except to download the package .tgz and install manually (which I've already done)?

Thank you.

Here is an error I get:

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> biocLite("clusterProfiler") 
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘clusterProfiler’
trying URL 'https://bioconductor.org/packages/3.5/bioc/bin/macosx/el-capitan/contrib/3.4/clusterProfiler_3.4.0.tgz'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'https://bioconductor.org/packages/3.5/bioc/bin/macosx/el-capitan/contrib/3.4/clusterProfiler_3.4.0.tgz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  cannot open URL 'https://bioconductor.org/packages/3.5/bioc/bin/macosx/el-capitan/contrib/3.4/clusterProfiler_3.4.0.tgz': HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘clusterProfiler’ failed

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] BiocInstaller_1.26.0 dplyr_0.5.0          ggplot2_2.2.1        taxize_0.8.4         myTAI_0.5.0          PSICQUIC_1.14.0      plyr_1.8.4           httr_1.2.1          
 [9] biomaRt_2.32.0       IRanges_2.10.0       S4Vectors_0.14.0     caTools_1.17.1       expm_0.999-2         Matrix_1.2-10        igraph_1.0.1         UniProt.ws_2.16.0   
[17] BiocGenerics_0.22.0  RCurl_1.95-4.8       bitops_1.0-6         RSQLite_1.1-2        R.utils_2.5.0        R.oo_1.21.0          R.methodsS3_1.7.1    downloader_0.4      
[25] data.table_1.10.4   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10         vcd_1.4-3            ape_4.1              lattice_0.20-35      zoo_1.8-0            assertthat_0.2.0     rprojroot_1.2        digest_0.6.12       
 [9] lmtest_0.9-35        foreach_1.4.3        R6_2.2.0             backports_1.0.5      evaluate_0.10        lazyeval_0.2.0       rmarkdown_1.5        gsubfn_0.6-6        
[17] labeling_0.3         proto_1.0.0          stringr_1.2.0        munsell_0.4.3        compiler_3.4.0       htmltools_0.3.6      tcltk_3.4.0          tibble_1.3.0        
[25] lpSolve_5.6.13       codetools_0.2-15     XML_3.98-1.6         reshape_0.8.6        MASS_7.3-47          grid_3.4.0           nlme_3.1-131         jsonlite_1.4        
[33] gtable_0.2.0         DBI_0.6-1            magrittr_1.5         scales_0.4.1         stringi_1.1.5        reshape2_1.4.2       xml2_1.1.1           irr_0.84            
[41] iterators_1.0.8      tools_3.4.0          bold_0.4.0           Biobase_2.36.0       yaml_2.1.14          AnnotationDbi_1.38.0 colorspace_1.3-2     memoise_1.1.0       
[49] knitr_1.15.1  

Can you try again in a new R session? R's install.packages() saves a cache of available packages, and the cache is out-of-date (accessing version 3.4.0 of clusterProfiler, when 3.4.1 is available).

I had a similar problem and a new session couldn't solve it. 

So, just in case someone needs it, I solved the problem by defining the specific repository:

biocLite("clusterProfiler", siteRepos = "https://bioconductor.org/packages/release/bioc/")

It does work in a new R session. That will be useful the next time I have this problem. Thank you.