[Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

[Martin Morgan]

On 01/29/2017 11:25 PM, Levi Waldron wrote:
> 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*

can you try to find out what file it is trying to read and what function 
call, e.g.,

   options(error=recover)
   biocLite("lazyeval")

That should get the call stack; choose readRDS and look for the 'file' 
variable for the exact file.

Martin

>
> 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
>
>>
>
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>
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