Not sure anyone will be able to help with this, but I can no longer install packages from bioc-devel using a current R-devel and biocLite() on my OSX Yosemite 10.10.5. I can still install from the command line `R CMD INSTALL` and `install.packages()`. Here is the error - the package lazyeval is just an example of a commonly used package from CRAN so I can show that install.packages works, but it seems to happen for all CRAN, Bioconductor, or Github packages. I don't have any problems when using R 3.3.2 patched + Bioc 3.4.
> biocLite("lazyeval") BioC_mirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.25.3), R Under development (unstable) (2017-01-26 r72035). Installing package(s) ‘lazyeval’ *Error in readRDS(dest) : error reading from connection* Note that the problem isn't there with `install.packages()`: > install.packages("lazyeval") ##successful install Following some advice from stackoverflow <http://stackoverflow.com/questions/6473831/readrdsfile-in-r> and rstudio <https://support.rstudio.com/hc/en-us/community/posts/203864278-Error-in-readRDS-pfile-error-reading-from-connection-when-updating-loading-installing-packages> for people who've had the same error in R, I tried starting from a fresh install (and didn't see any zero-size rds files in my R library), and am still having the problem *only* when using biocLite (not install.packages or R CMD INSTALL). Just to show this is a fresh installation (I have only installed R-devel from https://r.research.att.com/, then done `> source(" https://www.bioconductor.org/biocLite.R")`): > dir(.libPaths()) [1] "AnnotationDbi" "base" "BH" "Biobase" [5] "BiocGenerics" "BiocInstaller" "boot" "class" [9] "cluster" "codetools" "compiler" "datasets" [13] "DBI" "digest" "foreign" "graphics" [17] "grDevices" "grid" "IRanges" "KernSmooth" [21] "lattice" "lazyeval" "MASS" "Matrix" [25] "memoise" "methods" "mgcv" "nlme" [29] "nnet" "parallel" "plogr" "Rcpp" [33] "rpart" "RSQLite" "S4Vectors" "spatial" [37] "splines" "stats" "stats4" "survival" [41] "tcltk" "tools" "translations" "utils" One other strange thing I've noticed - using my primary user account I got one good call to biocLite after the fresh install of R-devel, then all subsequent calls produced this error. The good call installed Bioconductor in a system directory for all users. Then starting as another user without write access to the system package library, that user got one good call which created a user directory library, and I could use to run biocLite("lazyeval") locally, but then subsequent calls to biocLite failed for that user too. biocValid() and session info: > biocValid() [1] TRUE > sessionInfo() R Under development (unstable) (2017-01-26 r72035) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X Yosemite 10.10.5 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] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.25.3 loaded via a namespace (and not attached): [1] compiler_3.4.0 tools_3.4.0 tcltk_3.4.0 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel