[R] update.packages() behavior

Bennet Fauber bennet at umich.edu
Tue Sep 8 03:43:11 CEST 2015

I am not seeing an option with

$ ./configure --help

to include libcurl.  The Release Notes say:

It is now easier to use secure downloads from https:// URLs on builds
which support them: no longer do non-default options need to be
selected to do so. In particular, packages can be installed from
repositories which offer https:// URLs, and those listed by
setRepositories() now do so (for some of their mirrors).

Support for https:// URLs is available on Windows, and on other
platforms if support for libcurl was compiled in and if that supports
the https protocol (system installations can be expected to do). So
https:// support can be expected except on rather old OSes (an example
being OS X ‘Snow Leopard’, where a non-system version of libcurl can
be used).

Is RHEL6 a 'rather old OS'?  Do I need to compile and include a newer
version of libcurl?

Or, perhaps, I am using a mirror that doesn't support this, even
though I chose one from the presented list?

Thanks,  -- bennet

On Mon, Sep 7, 2015 at 5:09 PM, Uwe Ligges
<ligges at statistik.tu-dortmund.de> wrote:
> Right R-3.2.2 has the new default, but requires, for example, libcurl
> suppport in order to be able to deal with https. See the reelase Notes.
> Otherwise, http works as before.
> Best,
> Uwe Ligges
> On 07.09.2015 17:08, Bennet Fauber wrote:
>> I recently compiled and installed R 3.2.2 on an RHEL 6.5 system.  Upon
>> installation, I tried
>> $ R-3.2.2/bin/R
>> R version 3.2.2 (2015-08-14) -- "Fire Safety"
>> ....
>>> update.packages()
>> --- Please select a CRAN mirror for use in this session ---
>> Error in download.file(url, destfile = f, quiet = TRUE) :
>>    unsupported URL scheme
>> HTTPS CRAN mirror
>> ....
>> Selection: 14
>> Warning: unable to access index for repository
>> https://cran.mtu.edu/src/contrib
>> However, choosing '18: (HTTP mirrors)', which then presents a
>> different menu of download location choices, and selecting one of
>> those seems to work, as does specifically naming a http URL, e.g.,
>> update.packages(repos = "http://cran.mtu.edu/").
>> Is the defaulting to the https URL-type a new behavior?  Did I miss
>> including some library, so https is not included?
>> My configure line was
>> $ ./configure --prefix=/tmp/bennet/local --mandir=/tmp/bennet/local/man \
>>     --enable-R-shlib --without-x \
>>     --with-blas="-L/usr/cac/rhel6/intel-xe-2015/mkl/lib/intel64
>> -lmkl_gf_lp64 -lmkl_sequential -lmkl_core"
>> and I have
>> $ rpm -qa | grep curl
>> curl-7.19.7-46.el6.x86_64
>> libcurl-devel-7.19.7-46.el6.x86_64
>> libcurl-7.19.7-46.el6.x86_64
>> installed.
>> If https is the default URL-type, is there some configuration I need
>> to do to not get the unsupported URL scheme message?  Is there a way
>> to globally set the URL-type to http instead?
>> I recompiled R 3.1.1 to check, and it doesn't seem to default to https.
>> Sorry if this is covered somewhere, pointers to appropriate
>> documentation will be appreciated.
>> Thanks,  -- bennet
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