[Bioc-devel] biocLite misbehavior?

[Martin Morgan]

On 08/21/2015 09:01 AM, Vincent Carey wrote:
> install.packages works on the given machine ... seems to be latest source
> version
>
> of BiocInstaller.  perhaps related to https conversion?

yeah, that's what is trying to be done; I can't reproduce this. Is this with R 
--vanilla or equivalent? Can you step through the following and report output?

             con <- file(fl <- tempfile(), "a")
             xx <- close(file("https://bioconductor.org"))
             flush(con)
             length(readLines(fl))

if the second line causes problems can you run the file() and close() parts 
separately?

Thanks, Martin

>> biocLite()
>
>
> Enter a frame number, or 0 to exit
>
>
> 1: biocLite()
>
> 2: .isCurrentBiocInstaller()
>
> 3: .getContribUrl(biocVersion())
>
> 4: biocinstallRepos(version = biocVersion)
>
> 5: getOption("BioC_mirror", sprintf("%s//bioconductor.org", .protocol()))
>
> 6: sprintf("%s//bioconductor.org", .protocol())
>
> 7: .protocol()
>
> 8: close(con)
>
> 9: close.connection(con)
>
>
> Selection: 0
>
>> sessionInfo()
>
> R version 3.2.2 Patched (2015-08-18 r69117)
>
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> Running under: CentOS release 6.6 (Final)
>
>
> locale:
>
>   [1] LC_CTYPE=en_US.ISO8859-1    LC_NUMERIC=C
>
>   [3] LC_TIME=en_US.ISO8859-1     LC_COLLATE=en_US.ISO8859-1
>
>   [5] LC_MONETARY=en_US.ISO8859-1 LC_MESSAGES=C
>
>   [7] LC_PAPER=C                  LC_NAME=C
>
>   [9] LC_ADDRESS=C                LC_TELEPHONE=C
>
> [11] LC_MEASUREMENT=C            LC_IDENTIFICATION=C
>
>
> attached base packages:
>
> [1] stats     graphics  grDevices datasets  utils     tools     methods
>
> [8] base
>
>
> other attached packages:
>
> [1] knitr_1.10.5          weaver_1.35.0         codetools_0.2-14
>
> [4] digest_0.6.8          BiocInstaller_1.19.11
>
>>
>
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>
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