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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