[Bioc-devel] biocLite misbehavior?

[Kasper Daniel Hansen]

Vince, you might also want to report

capabilities()["libcurl"]

Kasper

On Fri, Aug 21, 2015 at 12:10 PM, Martin Morgan <mtmorgan at fredhutch.org>
wrote:

> 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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>>
>>
>
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