R help - Nov 2017 - HTML documentation is not in the expected location

Since I have updated my Linux system, and consequently re-installed R, I 
am unable to see HTML documentation which I used to access via a web 
browser. To be more specific, my R installation is declared to be here:

 > R RHOME
/usr/local/lib/R

However, if I look at a location such as
/usr/local/lib/R/library/base/html

this contains only two entries  	

File: 00Index.html
File: R.css

Clicking on 00Index.html, it shows the full list of entries which one 
expects to see, but clicking on one of them, 'abs' say, inevitably leads
to the message 'File not found'.

The documentation exists (at least in the text form): from within R, 
the command ?abs shows the documentation file. However its HTML version 
is not where I expect it to find ...which is where I did it find for 
many years, until the above-mentioned Linux update.

The current system is as follows:

PRETTY_NAME="Debian GNU/Linux 9 (stretch)"
NAME="Debian GNU/Linux"
VERSION_ID="9"
 > uname -a
Linux tamiso 4.9.0-3-amd64 #1 SMP Debian 4.9.30-2+deb9u2 (2017-06-26) 
x86_64 GNU/Linux

 > cat /etc/debian_version
9.0
 > gcc --version
gcc (Debian 6.3.0-18) 6.3.0 20170516

The current R installation is
R version 3.4.2 (2017-09-28) -- "Short Summer"
but the same problem existed with 3.4.1 after the system update.

When I (re-)install R, everything seems fine; no error messages are 
generated.

Can anyone tell me how to put the HTML documentation files in the right 
place?

Best regards,

Adelchi Azzalini

On 17/11/2017 10:47 AM, Adelchi Azzalini wrote:
> Since I have updated my Linux system, and consequently re-installed R, I
> am unable to see HTML documentation which I used to access via a web
> browser. To be more specific, my R installation is declared to be here:
> 
>   > R RHOME
> /usr/local/lib/R
> 
> However, if I look at a location such as
> /usr/local/lib/R/library/base/html
> 
> this contains only two entries  	
> 
> File: 00Index.html
> File: R.css
> 
> Clicking on 00Index.html, it shows the full list of entries which one
> expects to see, but clicking on one of them, 'abs' say, inevitably
leads
> to the message 'File not found'.
> 
> The documentation exists (at least in the text form): from within R,
> the command ?abs shows the documentation file. However its HTML version
> is not where I expect it to find ...which is where I did it find for
> many years, until the above-mentioned Linux update.
> 
> The current system is as follows:
> 
> PRETTY_NAME="Debian GNU/Linux 9 (stretch)"
> NAME="Debian GNU/Linux"
> VERSION_ID="9"
>   > uname -a
> Linux tamiso 4.9.0-3-amd64 #1 SMP Debian 4.9.30-2+deb9u2 (2017-06-26)
> x86_64 GNU/Linux
> 
>   > cat /etc/debian_version
> 9.0
>   > gcc --version
> gcc (Debian 6.3.0-18) 6.3.0 20170516
> 
> The current R installation is
> R version 3.4.2 (2017-09-28) -- "Short Summer"
> but the same problem existed with 3.4.1 after the system update.
> 
> When I (re-)install R, everything seems fine; no error messages are
> generated.
> 
> Can anyone tell me how to put the HTML documentation files in the right
> place?
> 
By default the documentation is produced on demand, but you can ask to 
produce it all at once.  See section 2.2 of the Installation and 
Administration manual.

Duncan Murdoch

Thanks for the useful clarification. This has solved the issue. I am  puzzled on
why the problem has not shown up for a decade (at least), as I have had the HTML
in place without explicitly asking for it.  However, this is a lesser problem.

Best wishes,

Adelchi

> On 17 Nov 2017, at 17:03, Duncan Murdoch <murdoch.duncan at
gmail.com> wrote:
> 
> On 17/11/2017 10:47 AM, Adelchi Azzalini wrote:
>> Since I have updated my Linux system, and consequently re-installed R,
I
>> am unable to see HTML documentation which I used to access via a web
>> browser. To be more specific, my R installation is declared to be here:
>>  > R RHOME
>> /usr/local/lib/R
>> However, if I look at a location such as
>> /usr/local/lib/R/library/base/html
>> this contains only two entries  	
>> File: 00Index.html
>> File: R.css
>> Clicking on 00Index.html, it shows the full list of entries which one
>> expects to see, but clicking on one of them, 'abs' say,
inevitably leads
>> to the message 'File not found'.
>> The documentation exists (at least in the text form): from within R,
>> the command ?abs shows the documentation file. However its HTML version
>> is not where I expect it to find ...which is where I did it find for
>> many years, until the above-mentioned Linux update.
>> The current system is as follows:
>> PRETTY_NAME="Debian GNU/Linux 9 (stretch)"
>> NAME="Debian GNU/Linux"
>> VERSION_ID="9"
>>  > uname -a
>> Linux tamiso 4.9.0-3-amd64 #1 SMP Debian 4.9.30-2+deb9u2 (2017-06-26)
>> x86_64 GNU/Linux
>>  > cat /etc/debian_version
>> 9.0
>>  > gcc --version
>> gcc (Debian 6.3.0-18) 6.3.0 20170516
>> The current R installation is
>> R version 3.4.2 (2017-09-28) -- "Short Summer"
>> but the same problem existed with 3.4.1 after the system update.
>> When I (re-)install R, everything seems fine; no error messages are
>> generated.
>> Can anyone tell me how to put the HTML documentation files in the right
>> place?
> 
> By default the documentation is produced on demand, but you can ask to
produce it all at once.  See section 2.2 of the Installation and Administration
manual.
> 
> Duncan Murdoch
>