Re: [R] Somewhat obscure bug in R 3.4.0 building from source

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Re: [R] Somewhat obscure bug in R 3.4.0 building from source

Duncan Murdoch-2
On 21/05/2017 10:30 AM, Peter Carbonetto wrote:
> Hi,
>
> I uncovered a bug in installing R 3.4.0 from source in Linux, following the
> standard procedure (configure; make; make install). Is this an appropriate
> place to report this bug? If not, can you please direct me to the
> appropriate place?

Generally R-devel is better; I've responded there.

>
> The error occurs only when I do "make clean" followed by "make" again; make
> works the first time.
>
> The error is a failure to build NEWS.pdf:
>
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
>   pdflatex is not available
> Calls: <Anonymous> -> texi2pdf -> texi2dvi
> Execution halted
> make[1]: *** [NEWS.pdf] Error 1
> make: [docs] Error 2 (ignored)
>
> and can be reproduced wit the following sequence:
>
> ./configure
> make
> make clean
> make

We usually don't build in the source directory; see the second
recommendation in the admin manual section 2.1.  So it's possible
there's a bug triggered when you do that.  Can you try building in a
separate directory?

Duncan Murdoch

>
> This suggests to me that perhaps "make clean" is not working.
>
> I'm happy to provide more details so that you are able to reproduce the bug.
>
> Thanks,
>
> Peter Carbonetto, Ph.D.
> Computational Staff Scientist, Statistics & Genetics
> Research Computing Center
> University of Chicago
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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Re: [R] Somewhat obscure bug in R 3.4.0 building from source

Peter Dalgaard-2
Inline below...

> On 21 May 2017, at 20:57 , Duncan Murdoch <[hidden email]> wrote:
>
> On 21/05/2017 10:30 AM, Peter Carbonetto wrote:
>> Hi,
>>
>> I uncovered a bug in installing R 3.4.0 from source in Linux, following the
>> standard procedure (configure; make; make install). Is this an appropriate
>> place to report this bug? If not, can you please direct me to the
>> appropriate place?
>
> Generally R-devel is better; I've responded there.
>
>>
>> The error occurs only when I do "make clean" followed by "make" again; make
>> works the first time.
>>
>> The error is a failure to build NEWS.pdf:
>>
>> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
>>  pdflatex is not available
>> Calls: <Anonymous> -> texi2pdf -> texi2dvi
>> Execution halted
>> make[1]: *** [NEWS.pdf] Error 1
>> make: [docs] Error 2 (ignored)
>>
>> and can be reproduced wit the following sequence:
>>
>> ./configure
>> make
>> make clean
>> make
>
> We usually don't build in the source directory; see the second recommendation in the admin manual section 2.1.  So it's possible there's a bug triggered when you do that.  Can you try building in a separate directory?

Notice that the error is that "pdflatex" is missing from your setup. We do, for the benefit of users with defective TeX installations supply a pre-built NEWS.pdf (and NEWS.html too) in the source tarballs. However, they are technically make targets and make clean will wipe them; in that case, you had better have the tools to rebuild them!

-pd

>
> Duncan Murdoch
>
>>
>> This suggests to me that perhaps "make clean" is not working.
>>
>> I'm happy to provide more details so that you are able to reproduce the bug.
>>
>> Thanks,
>>
>> Peter Carbonetto, Ph.D.
>> Computational Staff Scientist, Statistics & Genetics
>> Research Computing Center
>> University of Chicago
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: [hidden email]  Priv: [hidden email]

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Re: [R] Somewhat obscure bug in R 3.4.0 building from source

Peter Carbonetto
Hi Peter, Duncan & Bert,

Thank you kindly for the responses.

Indeed, doc/NEWS.pdf is included in the source distribution, and then
removed upon "make clean".

I thought that it might be useful to report this for your benefit, but on
closer inspection it appears that I'm getting errors that arise due to
incompatibilities in my texlive and texinfo installations. This is the
error I get when trying to build NEWS.pdf using "R CMD Rd2pdf":

R CMD Rd2pdf --output=NEWS.pdf NEWS.Rd
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
  Running 'texi2dvi' on 'Rd2.tex' failed.
Messages:
/software/texinfo-6.3-el7-x86_64/bin/texi2dvi: TeX neither supports
-recorder nor outputs \openout lines in its log file
Output:

I'm not sure what to make of this error exactly but perhaps it is
introduced by the latest version of texinfo (which seems to be a recurring
issue based on reading the help for texi2dvi in R):

texi2dvi --version
texi2dvi (GNU Texinfo 6.3) 7353

Peter

On Sun, May 21, 2017 at 5:07 PM, Peter Dalgaard <[hidden email]> wrote:

> Inline below...
>
> > On 21 May 2017, at 20:57 , Duncan Murdoch <[hidden email]>
> wrote:
> >
> > On 21/05/2017 10:30 AM, Peter Carbonetto wrote:
> >> Hi,
> >>
> >> I uncovered a bug in installing R 3.4.0 from source in Linux, following
> the
> >> standard procedure (configure; make; make install). Is this an
> appropriate
> >> place to report this bug? If not, can you please direct me to the
> >> appropriate place?
> >
> > Generally R-devel is better; I've responded there.
> >
> >>
> >> The error occurs only when I do "make clean" followed by "make" again;
> make
> >> works the first time.
> >>
> >> The error is a failure to build NEWS.pdf:
> >>
> >> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
> quiet,  :
> >>  pdflatex is not available
> >> Calls: <Anonymous> -> texi2pdf -> texi2dvi
> >> Execution halted
> >> make[1]: *** [NEWS.pdf] Error 1
> >> make: [docs] Error 2 (ignored)
> >>
> >> and can be reproduced wit the following sequence:
> >>
> >> ./configure
> >> make
> >> make clean
> >> make
> >
> > We usually don't build in the source directory; see the second
> recommendation in the admin manual section 2.1.  So it's possible there's a
> bug triggered when you do that.  Can you try building in a separate
> directory?
>
> Notice that the error is that "pdflatex" is missing from your setup. We
> do, for the benefit of users with defective TeX installations supply a
> pre-built NEWS.pdf (and NEWS.html too) in the source tarballs. However,
> they are technically make targets and make clean will wipe them; in that
> case, you had better have the tools to rebuild them!
>
> -pd
>
> >
> > Duncan Murdoch
> >
> >>
> >> This suggests to me that perhaps "make clean" is not working.
> >>
> >> I'm happy to provide more details so that you are able to reproduce the
> bug.
> >>
> >> Thanks,
> >>
> >> Peter Carbonetto, Ph.D.
> >> Computational Staff Scientist, Statistics & Genetics
> >> Research Computing Center
> >> University of Chicago
> >>
> >>      [[alternative HTML version deleted]]
> >>
> >> ______________________________________________
> >> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >>
> >
> > ______________________________________________
> > [hidden email] mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: [hidden email]  Priv: [hidden email]
>
>
>
>
>
>
>
>
>
>

        [[alternative HTML version deleted]]

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Re: [R] Somewhat obscure bug in R 3.4.0 building from source

Prof Brian Ripley
On 22/05/2017 18:16, Peter Carbonetto wrote:

> Hi Peter, Duncan & Bert,
>
> Thank you kindly for the responses.
>
> Indeed, doc/NEWS.pdf is included in the source distribution, and then
> removed upon "make clean".
>
> I thought that it might be useful to report this for your benefit, but on
> closer inspection it appears that I'm getting errors that arise due to
> incompatibilities in my texlive and texinfo installations. This is the
> error I get when trying to build NEWS.pdf using "R CMD Rd2pdf":
>
> R CMD Rd2pdf --output=NEWS.pdf NEWS.Rd
> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  :
>    Running 'texi2dvi' on 'Rd2.tex' failed.
> Messages:
> /software/texinfo-6.3-el7-x86_64/bin/texi2dvi: TeX neither supports
> -recorder nor outputs \openout lines in its log file
> Output:
>
> I'm not sure what to make of this error exactly but perhaps it is
> introduced by the latest version of texinfo (which seems to be a recurring
> issue based on reading the help for texi2dvi in R):
>
> texi2dvi --version
> texi2dvi (GNU Texinfo 6.3) 7353

Please do not speculate (see the posting guide and FAQ).

That version is thoroughly tested.  texinfo troubles were mainly in the
transition to Perl ca 5.[012], and its slow adoption by distros: another
holdback has been the transition to GPL-3-only licensing, AFAIR at 6.0.


>
> Peter
>
> On Sun, May 21, 2017 at 5:07 PM, Peter Dalgaard <[hidden email]> wrote:
>
>> Inline below...
>>
>>> On 21 May 2017, at 20:57 , Duncan Murdoch <[hidden email]>
>> wrote:
>>>
>>> On 21/05/2017 10:30 AM, Peter Carbonetto wrote:
>>>> Hi,
>>>>
>>>> I uncovered a bug in installing R 3.4.0 from source in Linux, following
>> the
>>>> standard procedure (configure; make; make install). Is this an
>> appropriate
>>>> place to report this bug? If not, can you please direct me to the
>>>> appropriate place?
>>>
>>> Generally R-devel is better; I've responded there.
>>>
>>>>
>>>> The error occurs only when I do "make clean" followed by "make" again;
>> make
>>>> works the first time.
>>>>
>>>> The error is a failure to build NEWS.pdf:
>>>>
>>>> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet =
>> quiet,  :
>>>>   pdflatex is not available
>>>> Calls: <Anonymous> -> texi2pdf -> texi2dvi
>>>> Execution halted
>>>> make[1]: *** [NEWS.pdf] Error 1
>>>> make: [docs] Error 2 (ignored)
>>>>
>>>> and can be reproduced wit the following sequence:
>>>>
>>>> ./configure
>>>> make
>>>> make clean
>>>> make
>>>
>>> We usually don't build in the source directory; see the second
>> recommendation in the admin manual section 2.1.  So it's possible there's a
>> bug triggered when you do that.  Can you try building in a separate
>> directory?
>>
>> Notice that the error is that "pdflatex" is missing from your setup. We
>> do, for the benefit of users with defective TeX installations supply a
>> pre-built NEWS.pdf (and NEWS.html too) in the source tarballs. However,
>> they are technically make targets and make clean will wipe them; in that
>> case, you had better have the tools to rebuild them!
>>
>> -pd
>>
>>>
>>> Duncan Murdoch
>>>
>>>>
>>>> This suggests to me that perhaps "make clean" is not working.
>>>>
>>>> I'm happy to provide more details so that you are able to reproduce the
>> bug.
>>>>
>>>> Thanks,
>>>>
>>>> Peter Carbonetto, Ph.D.
>>>> Computational Staff Scientist, Statistics & Genetics
>>>> Research Computing Center
>>>> University of Chicago
>>>>
>>>>       [[alternative HTML version deleted]]
>>>>
>>>> ______________________________________________
>>>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide http://www.R-project.org/
>> posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>
>>> ______________________________________________
>>> [hidden email] mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>> --
>> Peter Dalgaard, Professor,
>> Center for Statistics, Copenhagen Business School
>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> Phone: (+45)38153501
>> Office: A 4.23
>> Email: [hidden email]  Priv: [hidden email]
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>


--
Brian D. Ripley,                  [hidden email]
Emeritus Professor of Applied Statistics, University of Oxford

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