Re: Missing Rnw(knitr) module

[John Kane]

Hello Murat!
Your idea seems to have worked. The *sudo update R *seems to have worked
but apparently, despite RStudio and RKwark seeming to find knitr  I did a
install.packages("knitr") at root level and R installed it.

LyX seems to be finding knitr now. I just ran a couple of simple-minded
plots with no problem.

I have never had to do anything like this before upgrading. I still think I
have a slightly wonky Ubuntu installation but I can live with it for a
little while.  I am still seriously considering reverting to 16.04 though.

Thank you very,very much.

On 23 August 2017 at 11:10, Murat Yildizoglu  wrote:

> Hi John,
>
> I understand, that is weird indeed. To me
>
> lib = "/usr/lib/R/site-library"' is not writable
> Would you like to use a personal library instead?  (y/n) y
>
> messages seem to indicate that you do not have the necessary
> authorizations for writing to these folders. Have you tried to launch R as
> sudo and try to install knitr and the updates? If this is only an
> authorization issue, that should work, no? Then it would be nice to become
> root and give to the normal user the full writes to these folders.
>
> My two cents.
>
> Murat
>
> 2017-08-23 16:44 GMT+02:00 John Kane :
>
>> Hi Murat,
>> Both RKward and RStudio indicate that they are loading knitr so I think I
>> have it installed but if I try running R from the terminal I get >
>> library(knitr)
>> *Error in library(knitr) : there is no package called ‘knitr’ *so, at
>> present, my response is "I have no idea".
>>
>> I just tried to do a new update.packages() in R and end up getting this
>> weird result
>>
>> lib = "/usr/lib/R/site-library"' is not writable
>> Would you like to use a personal library instead?  (y/n) y
>> Would you like to create a personal library
>> NA
>> to install packages into?
>>
>> I am coming to the conclusion that I don't have a LyX problem, I have an
>> Ubuntu 17.04 upgrade problem. If I can find my old Ubuntu 16.04 usb stick I
>> think I will do a complete clean install and hope for the best.
>>
>> If all goes well, I should have everything reinstalled and running in a
>> few hours. Oh what fun :(
>>
>>
>> On 23 August 2017 at 02:54, Murat Yildizoglu  wrote:
>>
>>> Hi John,
>>> I have not followed the whole thread so, maybe you have already
>>> indicated it : have you also installed the latex package for knitR?
>>>
>>> Prof. Murat Yildizoglu
>>>
>>> Note: Please use the following address as such
>>>
>>> UNIVERSITE DE BORDEAUX
>>> GREThA (UMR CNRS 5113)
>>> MURAT YILDIZOGLU
>>> 16 AVENUE LEON DUGUIT
>>> CS 50057
>>> 33608 PESSAC CEDEX
>>> FRANCE
>>>
>>> Bureau : E-331
>>>
>>> mail: murat.yildizoglu at u-bordeaux.fr
>>>
>>> web:  www.yildizoglu.fr
>>>
>>> Le 22 août 2017 à 21:56 +0200, John Kane , a écrit
>>> :
>>>
>>> Just as a minor follow-up the knitr.module is in usr/share/lux/layouts.
>>> So I have knitr installed in R and the knitr.module in LyX.
>>>
>>> Presumably I'm missing something obvious but what?
>>>
>>> On 22 August 2017 at 11:14, John Kane  wrote:
>>>
 Yes. I really have no idea of where some of those ppa's have come from
 and I may just go in and wipe out anything that's in the file and hope for
 the best.  I can always replace those that I really need.(I hope.)

 Someone else may have another idea that may help also.

 I did discover that I can compile a LaTeX file with knitr---which does
 not work but at least it does not bomb. However, I have no idea what that
 means.

 On 22 August 2017 at 10:55, Jean-Marc Lasgouttes 
 wrote:

> Le 22/08/2017 à 16:35, John Kane a écrit :
>
>> /sudo apt update
>> /
>> Yes, ran it just before I ran the code listed above. I don't remember
>> any warnings but I had someone talking to me as I did it and so I may 
>> have
>> missed one.
>>
>> Bloody hell! I missed the equivalent of an atom bomb going off.
>> Unfortunately I am not sure how to start to approach this for a solution.
>>
>
> That looks bad indeed... I am not sure why you need all these ppas, I
> would try to remove them unless you are sure that you should use them.
>
> I cannot really advise you on how to fix this kind of mess. It is
> probably 2 or 3 commands, but which ones?
>
> JMarc
>
>


 --
 John Kane
 Kingston ON Canada

>>>
>>>
>>>
>>> --
>>> John Kane
>>> Kingston ON Canada
>>>
>>>
>>
>>
>> --
>> John Kane
>> Kingston ON Canada
>>
>
>
>
> --
> Prof. Murat Yildizoglu
>
> Université Montesquieu Bordeaux IV
> GREThA (UMR CNRS 5113)
> Avenue Léon Duguit
> 33608 Pessac cedex
> France
>
> Bureau : E-331
>
> mail: murat.yildizoglu at u-bordeaux.fr
>
> web: http://yildizoglu.fr
>



-- 
John Kane
Kingston ON Canada

Re: Missing Rnw(knitr) module

[Dr Eberhard Lisse]

The former has a smaller footprint than inkscape and works very well for me.

ek

On 2017-08-23 12:54 , Kornel Benko wrote:
> Am Mittwoch, 23. August 2017 um 06:30:37, schrieb John Kane 
> 
>> INFO: +checking for "rsvg-convert"...  no
>> INFO: +checking for "inkscape"...  no
> 
> for "rsvg-convert" try
>   # sudo apt-get install librsvg2-bin
> and for "inkscape"
>   # sudo apt-get install inkscape
> 
> When done, reconfigure lyx.
> 
>   Kornel
> 

Re: Missing Rnw(knitr) module

[John Kane]

Blast, forgot to include the text of /etc/apt/sources.list.d/

Contents of /etc/apt/sources.list.d/
---
aims-ubuntu-sagemath-xenial.list
aims-ubuntu-sagemath-xenial.list.distUpgrade
aims-ubuntu-sagemath-xenial.list.save
dropbox.list
dropbox.list.distUpgrade
dropbox.list.save
jasp-uva-ubuntu-jasp-xenial.list
jasp-uva-ubuntu-jasp-xenial.list.distUpgrade
jasp-uva-ubuntu-jasp-xenial.list.save
jonathonf-ubuntu-texlive-2016-zesty.list
jonathonf-ubuntu-texlive-zesty.list
jonathonf-ubuntu-texlive-zesty.list.save
lyx-devel-ubuntu-release-xenial.list
lyx-devel-ubuntu-release-xenial.list.distUpgrade
lyx-devel-ubuntu-release-xenial.list.save
lyx-devel-ubuntu-release-zesty.list
lyx-devel-ubuntu-release-zesty.list.save
marutter-ubuntu-rrutter-zesty.list
marutter-ubuntu-rrutter-zesty.list.save
rkward-devel-ubuntu-rkward-stable-cran-zesty.list
rkward-devel-ubuntu-rkward-stable-cran-zesty.list.save
webupd8team-ubuntu-sublime-text-3-xenial.list
webupd8team-ubuntu-sublime-text-3-xenial.list.distUpgrade
webupd8team-ubuntu-sublime-text-3-xenial.list.save


On 23 August 2017 at 09:01, John Kane  wrote:

> Oh just had a look at my ppa file "/etc/apt/sources.list.d/" and the
> entries seem to have no connection with the errors reported in my last
> post.
>
> Am I missing another ppa file?
>
> On 23 August 2017 at 08:47, John Kane  wrote:
>
>> Tried a purge (looked successful) and a reconfigure.
>>
>> Same error.
>> ##==##
>>
>> An error occurred while running:
>>
>> Rscript --verbose --no-save --no-restore $$s/scripts/lyxknitr.R
>>
>> "/tmp/lyx_tmpdir.SpjIUqEQ9242/lyx_tmpbuf0/""LyXnewfile1.Rnw"
>>
>> "/tmp/lyx_tmpdir.SpjIUqEQ9242/lyx_tmpbuf0/""LyXnewfile1.tex" ISO-8859-15
>>
>> "/home/jrkrideau/"
>>
>> 08:22:12.888: Error while exporting format: PDF (pdflatex)
>>
>> 08:23:02.090: (dialog-toggle progress)
>>
>> ####
>>
>>
>> I does annoy me that I cannot install Inkscape. I am pretty sure I had it
>> installed under Ubuntu 16.04 and an upgrade should not have removed it.
>>
>> Synaptic is showing a couple of unloaded Inkscape dependencies but not
>> the main Inkscape program.
>>
>> I just tried an reload of the synaptic data base and am getting some
>> nasty messages that I have no idea how to interpret. They seem to mirror
>> messages I get when doing a *sudo apt update*.
>>
>> Please see attached screenshot
>>
>>
>>
>> On 23 August 2017 at 08:15, Kornel Benko  wrote:
>>
>>> Am Mittwoch, 23. August 2017 um 07:38:45, schrieb John Kane <
>>> jrkrid...@gmail.com>
>>> > I tried your suggestions.
>>> > librsvg2-bin seems to have installed successfully
>>> >
>>> > Inkscape aborted.
>>> >
>>> > This is weird indeed.  I loaded the ubuntu software gui and it reports
>>> that
>>> > inkscape is, indeed, installed but I cannot launch it.
>>>
>>> I would try to purge inkscape first.
>>>
>>> > On the other hand synaptic is saying that a) it is not installed, and
>>> b) is
>>> > reporting a problem that I don't know how to resolve. Please see
>>> attached
>>> > screenshot.
>>>
>>> I see.
>>> But I think, you even don't need inkscape.
>>>
>>> > I am beginning to wonder if I have a mangeled Ubuntu 17.04
>>> installation or
>>> > a corrupt LyX installation or both
>>> > ##=##
>>> > jrkrideau@jrk-T420:~$ sudo apt-get install inkscape
>>> > Reading package lists... Done
>>> > Building dependency tree
>>> > Reading state information... Done
>>> > Package inkscape is not available, but is referred to by another
>>> package.
>>> > This may mean that the package is missing, has been obsoleted, or
>>> > is only available from another source
>>> >
>>> > E: Package 'inkscape' has no installation candidate
>>> > ##=##
>>> >
>>>
>>> Inkscape is only used by lyx, if it is found.
>>>
>>> Try to reconfigure lyx.
>>>
>>> Kornel
>>
>>
>>
>>
>> --
>> John Kane
>> Kingston ON Canada
>>
>
>
>
> --
> John Kane
> Kingston ON Canada
>



-- 
John Kane
Kingston ON Canada

Re: Missing Rnw(knitr) module

[John Kane]

Oh just had a look at my ppa file "/etc/apt/sources.list.d/" and the
entries seem to have no connection with the errors reported in my last
post.

Am I missing another ppa file?

On 23 August 2017 at 08:47, John Kane  wrote:

> Tried a purge (looked successful) and a reconfigure.
>
> Same error.
> ##==##
>
> An error occurred while running:
>
> Rscript --verbose --no-save --no-restore $$s/scripts/lyxknitr.R
>
> "/tmp/lyx_tmpdir.SpjIUqEQ9242/lyx_tmpbuf0/""LyXnewfile1.Rnw"
>
> "/tmp/lyx_tmpdir.SpjIUqEQ9242/lyx_tmpbuf0/""LyXnewfile1.tex" ISO-8859-15
>
> "/home/jrkrideau/"
>
> 08:22:12.888: Error while exporting format: PDF (pdflatex)
>
> 08:23:02.090: (dialog-toggle progress)
>
> ####
>
>
> I does annoy me that I cannot install Inkscape. I am pretty sure I had it
> installed under Ubuntu 16.04 and an upgrade should not have removed it.
>
> Synaptic is showing a couple of unloaded Inkscape dependencies but not the
> main Inkscape program.
>
> I just tried an reload of the synaptic data base and am getting some nasty
> messages that I have no idea how to interpret. They seem to mirror messages
> I get when doing a *sudo apt update*.
>
> Please see attached screenshot
>
>
>
> On 23 August 2017 at 08:15, Kornel Benko  wrote:
>
>> Am Mittwoch, 23. August 2017 um 07:38:45, schrieb John Kane <
>> jrkrid...@gmail.com>
>> > I tried your suggestions.
>> > librsvg2-bin seems to have installed successfully
>> >
>> > Inkscape aborted.
>> >
>> > This is weird indeed.  I loaded the ubuntu software gui and it reports
>> that
>> > inkscape is, indeed, installed but I cannot launch it.
>>
>> I would try to purge inkscape first.
>>
>> > On the other hand synaptic is saying that a) it is not installed, and
>> b) is
>> > reporting a problem that I don't know how to resolve. Please see
>> attached
>> > screenshot.
>>
>> I see.
>> But I think, you even don't need inkscape.
>>
>> > I am beginning to wonder if I have a mangeled Ubuntu 17.04 installation
>> or
>> > a corrupt LyX installation or both
>> > ##=##
>> > jrkrideau@jrk-T420:~$ sudo apt-get install inkscape
>> > Reading package lists... Done
>> > Building dependency tree
>> > Reading state information... Done
>> > Package inkscape is not available, but is referred to by another
>> package.
>> > This may mean that the package is missing, has been obsoleted, or
>> > is only available from another source
>> >
>> > E: Package 'inkscape' has no installation candidate
>> > ##=##
>> >
>>
>> Inkscape is only used by lyx, if it is found.
>>
>> Try to reconfigure lyx.
>>
>> Kornel
>
>
>
>
> --
> John Kane
> Kingston ON Canada
>



-- 
John Kane
Kingston ON Canada

Re: Missing Rnw(knitr) module

[John Kane]

Tried a purge (looked successful) and a reconfigure.

Same error.
##==##

An error occurred while running:

Rscript --verbose --no-save --no-restore $$s/scripts/lyxknitr.R

"/tmp/lyx_tmpdir.SpjIUqEQ9242/lyx_tmpbuf0/""LyXnewfile1.Rnw"

"/tmp/lyx_tmpdir.SpjIUqEQ9242/lyx_tmpbuf0/""LyXnewfile1.tex" ISO-8859-15

"/home/jrkrideau/"

08:22:12.888: Error while exporting format: PDF (pdflatex)

08:23:02.090: (dialog-toggle progress)

####


I does annoy me that I cannot install Inkscape. I am pretty sure I had it
installed under Ubuntu 16.04 and an upgrade should not have removed it.

Synaptic is showing a couple of unloaded Inkscape dependencies but not the
main Inkscape program.

I just tried an reload of the synaptic data base and am getting some nasty
messages that I have no idea how to interpret. They seem to mirror messages
I get when doing a *sudo apt update*.

Please see attached screenshot



On 23 August 2017 at 08:15, Kornel Benko  wrote:

> Am Mittwoch, 23. August 2017 um 07:38:45, schrieb John Kane <
> jrkrid...@gmail.com>
> > I tried your suggestions.
> > librsvg2-bin seems to have installed successfully
> >
> > Inkscape aborted.
> >
> > This is weird indeed.  I loaded the ubuntu software gui and it reports
> that
> > inkscape is, indeed, installed but I cannot launch it.
>
> I would try to purge inkscape first.
>
> > On the other hand synaptic is saying that a) it is not installed, and b)
> is
> > reporting a problem that I don't know how to resolve. Please see attached
> > screenshot.
>
> I see.
> But I think, you even don't need inkscape.
>
> > I am beginning to wonder if I have a mangeled Ubuntu 17.04 installation
> or
> > a corrupt LyX installation or both
> > ##=##
> > jrkrideau@jrk-T420:~$ sudo apt-get install inkscape
> > Reading package lists... Done
> > Building dependency tree
> > Reading state information... Done
> > Package inkscape is not available, but is referred to by another package.
> > This may mean that the package is missing, has been obsoleted, or
> > is only available from another source
> >
> > E: Package 'inkscape' has no installation candidate
> > ##=##
> >
>
> Inkscape is only used by lyx, if it is found.
>
> Try to reconfigure lyx.
>
> Kornel




-- 
John Kane
Kingston ON Canada

Re: Missing Rnw(knitr) module

[Kornel Benko]

Am Mittwoch, 23. August 2017 um 07:38:45, schrieb John Kane 

> I tried your suggestions.
> librsvg2-bin seems to have installed successfully
> 
> Inkscape aborted.
> 
> This is weird indeed.  I loaded the ubuntu software gui and it reports that
> inkscape is, indeed, installed but I cannot launch it.

I would try to purge inkscape first.

> On the other hand synaptic is saying that a) it is not installed, and b) is
> reporting a problem that I don't know how to resolve. Please see attached
> screenshot.

I see.
But I think, you even don't need inkscape.

> I am beginning to wonder if I have a mangeled Ubuntu 17.04 installation or
> a corrupt LyX installation or both
> ##=##
> jrkrideau@jrk-T420:~$ sudo apt-get install inkscape
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> Package inkscape is not available, but is referred to by another package.
> This may mean that the package is missing, has been obsoleted, or
> is only available from another source
> 
> E: Package 'inkscape' has no installation candidate
> ##=##
> 

Inkscape is only used by lyx, if it is found.

Try to reconfigure lyx.

Kornel

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Re: Missing Rnw(knitr) module

[John Kane]

That screenshot is rather small. Perhaps this cropped one will be better

On 23 August 2017 at 07:38, John Kane  wrote:

> I tried your suggestions.
> librsvg2-bin seems to have installed successfully
>
> Inkscape aborted.
>
> This is weird indeed.  I loaded the ubuntu software gui and it reports
> that inkscape is, indeed, installed but I cannot launch it.
>
> On the other hand synaptic is saying that a) it is not installed, and b)
> is reporting a problem that I don't know how to resolve. Please see
> attached screenshot.
>
> I am beginning to wonder if I have a mangeled Ubuntu 17.04 installation or
> a corrupt LyX installation or both
> ##=##
> jrkrideau@jrk-T420:~$ sudo apt-get install inkscape
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> Package inkscape is not available, but is referred to by another package.
> This may mean that the package is missing, has been obsoleted, or
> is only available from another source
>
> E: Package 'inkscape' has no installation candidate
> ##=##
>
>
>
> On 23 August 2017 at 06:54, Kornel Benko  wrote:
>
>> Am Mittwoch, 23. August 2017 um 06:30:37, schrieb John Kane <
>> jrkrid...@gmail.com>
>> > INFO: +checking for "rsvg-convert"...  no
>> > INFO: +checking for "inkscape"...  no
>>
>> for "rsvg-convert" try
>> # sudo apt-get install librsvg2-bin
>> and for "inkscape"
>> # sudo apt-get install inkscape
>>
>> When done, reconfigure lyx.
>>
>> Kornel
>
>
>
>
> --
> John Kane
> Kingston ON Canada
>



-- 
John Kane
Kingston ON Canada

Re: Missing Rnw(knitr) module

[Kornel Benko]

Am Mittwoch, 23. August 2017 um 06:30:37, schrieb John Kane 

> INFO: +checking for "rsvg-convert"...  no
> INFO: +checking for "inkscape"...  no

for "rsvg-convert" try
# sudo apt-get install librsvg2-bin
and for "inkscape"
# sudo apt-get install inkscape

When done, reconfigure lyx.

Kornel

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Re: Missing Rnw(knitr) module

[John Kane]

I'd be happy to do. Please see attached file.

Thanks

On 22 August 2017 at 21:32, Scott Kostyshak  wrote:

> On Tue, Aug 22, 2017 at 03:56:24PM -0400, John Kane wrote:
> > Just as a minor follow-up the knitr.module is in usr/share/lux/layouts.
> So
> > I have knitr installed in R and the knitr.module in LyX.
> >
> > Presumably I'm missing something obvious but what?
>
> Can you send your configure log? That's always useful for issues like
> these.
>
> Scott
>



-- 
John Kane
Kingston ON Canada
INFO: checking for a Latex2e program...
INFO: +checking for "latex"...  yes
INFO: checking for a DVI postprocessing program...
INFO: +checking for "pplatex"...  no
INFO: checking for pLaTeX, the Japanese LaTeX...
INFO: +checking for "platex"...  yes
DEBUG: Add to RC:
\converter platex   dvi   "platex"   "latex=platex"


DEBUG: Add to RC:
\converter latex  dvi"latex"	"latex"


INFO: checking for a java interpreter...
INFO: +checking for "java"...  yes
INFO: checking for a perl interpreter...
INFO: +checking for "perl"...  yes
INFO: checking for a Tgif viewer and editor...
INFO: +checking for "tgif"...  no
DEBUG: Add to RC:
\Format tgif  "obj, tgo" Tgif "" "auto"	"auto"	"vector"	"application/x-tgif"


INFO: checking for a FIG viewer and editor...
INFO: +checking for "xfig"...  no
INFO: +checking for "jfig3-itext.jar"...  no
INFO: +checking for "jfig3.jar"...  no
DEBUG: Add to RC:
\Format figfig FIG"" "auto"	"auto"	"vector"	"application/x-xfig"


INFO: checking for a Dia viewer and editor...
INFO: +checking for "dia"...  no
DEBUG: Add to RC:
\Format diadia DIA"" "auto"	"auto"	"vector,zipped=native", "application/x-dia-diagram"


INFO: checking for an OpenDocument drawing viewer and editor...
INFO: +checking for "libreoffice"...  yes
DEBUG: Add to RC:
\Format odg"odg, sxd" "OpenDocument drawing"   "" "libreoffice"	"libreoffice"	"vector,zipped=native"	"application/vnd.oasis.opendocument.graphics"


DEBUG: Add to RC:
\editor_alternatives odg "libreoffice"
\viewer_alternatives odg "libreoffice"


INFO: +checking for "lodraw"...  yes
DEBUG: Add to RC:
\editor_alternatives odg "lodraw"
\viewer_alternatives odg "lodraw"


INFO: +checking for "ooffice"...  no
INFO: +checking for "oodraw"...  no
INFO: +checking for "soffice"...  yes
DEBUG: Add to RC:
\editor_alternatives odg "soffice"
\viewer_alternatives odg "soffice"


INFO: checking for a Grace viewer and editor...
INFO: +checking for "xmgrace"...  no
DEBUG: Add to RC:
\Format agragr Grace  "" "auto"	"auto"	"vector"	""


INFO: checking for a FEN viewer and editor...
INFO: +checking for "xboard"...  no
DEBUG: Add to RC:
\Format fenfen FEN"" "auto"	"auto"	""	""


INFO: checking for a SVG viewer and editor...
INFO: +checking for "inkscape"...  no
DEBUG: Add to RC:
\Format svg"svg" SVG"" "auto" "auto"	"vector"	"image/svg+xml"
\Format svgz   "svgz" "SVG (compressed)" "" "auto" "auto"	"vector,zipped=native"	""


INFO: checking for a raster image viewer...
INFO: +checking for "xv"...  no
INFO: +checking for "kview"...  no
INFO: +checking for "gimp-remote"...  no
INFO: +checking for "gimp"...  no
INFO: checking for a raster image editor...
INFO: +checking for "gimp-remote"...  no
INFO: +checking for "gimp"...  no
DEBUG: Add to RC:
\Format bmpbmp BMP"" "auto"	"auto"	""	"image/x-bmp"
\Format gifgif GIF"" "auto"	"auto"	""	"image/gif"
\Format jpg   "jpg, jpeg" JPEG"" "auto"	"auto"	""	"image/jpeg"
\Format pbmpbm PBM"" "auto"	"auto"	""	"image/x-portable-bitmap"
\Format pgmpgm PGM"" "auto"	"auto"	""	"image/x-portable-graymap"
\Format pngpng PNG"" "auto"	"auto"	""	"image/x-png"
\Format ppmppm PPM"" "auto"	"auto"	""	"image/x-portable-pixmap"
\Format tiff   tif TIFF   "" "auto"	"auto"	""	"image/tiff"
\Format xbmxbm XBM"" "auto"	"auto"	""	"image/x-xbitmap"
\Format xpmxpm XPM"" "auto"	"auto"	""	"image/x-xpixmap"


INFO: checking for a text editor...
INFO: +checking for "xemacs"...  no
INFO: +checking for "gvim"...  no
INFO: +checking for "kedit"...  no
INFO: +checking for "kwrite"...  no
INFO: +checking for "kate"...  no
INFO: +checking for "nedit"...  no
INFO: +checking for "gedit"...  yes
DEBUG: Add to RC:
\Format asciichess asc"Plain text (chess output)"  "" ""	"gedit"	""	""
\Format asciiimage asc"Plain text (image)" "" ""	"gedit"	""	""
\Format asciixfig  asc"Plain text (Xfig output)"   "" ""	"gedit"	""	""
\Format dateouttmp"date (output)" "" ""	"gedit"	""	""
\Format docbooksgmlDocBookB  ""	"gedit"	"document,menu=export"	""

Re: Missing Rnw(knitr) module

[Scott Kostyshak]

On Tue, Aug 22, 2017 at 03:56:24PM -0400, John Kane wrote:
> Just as a minor follow-up the knitr.module is in usr/share/lux/layouts. So
> I have knitr installed in R and the knitr.module in LyX.
> 
> Presumably I'm missing something obvious but what?

Can you send your configure log? That's always useful for issues like
these.

Scott


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Re: Missing Rnw(knitr) module

[John Kane]

Just as a minor follow-up the knitr.module is in usr/share/lux/layouts. So
I have knitr installed in R and the knitr.module in LyX.

Presumably I'm missing something obvious but what?

On 22 August 2017 at 11:14, John Kane  wrote:

> Yes. I really have no idea of where some of those ppa's have come from and
> I may just go in and wipe out anything that's in the file and hope for the
> best.  I can always replace those that I really need.(I hope.)
>
> Someone else may have another idea that may help also.
>
> I did discover that I can compile a LaTeX file with knitr---which does not
> work but at least it does not bomb. However, I have no idea what that
> means.
>
> On 22 August 2017 at 10:55, Jean-Marc Lasgouttes 
> wrote:
>
>> Le 22/08/2017 à 16:35, John Kane a écrit :
>>
>>> /sudo apt update
>>> /
>>> Yes, ran it just before I ran the code listed above. I don't remember
>>> any warnings but I had someone talking to me as I did it and so I may have
>>> missed one.
>>>
>>> Bloody hell! I missed the equivalent of an atom bomb going off.
>>> Unfortunately I am not sure how to start to approach this for a solution.
>>>
>>
>> That looks bad indeed... I am not sure why you need all these ppas, I
>> would try to remove them unless you are sure that you should use them.
>>
>> I cannot really advise you on how to fix this kind of mess. It is
>> probably 2 or 3 commands, but which ones?
>>
>> JMarc
>>
>>
>
>
> --
> John Kane
> Kingston ON Canada
>



-- 
John Kane
Kingston ON Canada

Re: Missing Rnw(knitr) module

[John Kane]

Yes. I really have no idea of where some of those ppa's have come from and
I may just go in and wipe out anything that's in the file and hope for the
best.  I can always replace those that I really need.(I hope.)

Someone else may have another idea that may help also.

I did discover that I can compile a LaTeX file with knitr---which does not
work but at least it does not bomb. However, I have no idea what that
means.

On 22 August 2017 at 10:55, Jean-Marc Lasgouttes  wrote:

> Le 22/08/2017 à 16:35, John Kane a écrit :
>
>> /sudo apt update
>> /
>> Yes, ran it just before I ran the code listed above. I don't remember any
>> warnings but I had someone talking to me as I did it and so I may have
>> missed one.
>>
>> Bloody hell! I missed the equivalent of an atom bomb going off.
>> Unfortunately I am not sure how to start to approach this for a solution.
>>
>
> That looks bad indeed... I am not sure why you need all these ppas, I
> would try to remove them unless you are sure that you should use them.
>
> I cannot really advise you on how to fix this kind of mess. It is probably
> 2 or 3 commands, but which ones?
>
> JMarc
>
>


-- 
John Kane
Kingston ON Canada

Re: Missing Rnw(knitr) module

[John Kane]

*sudo apt update*
Yes, ran it just before I ran the code listed above. I don't remember any
warnings but I had someone talking to me as I did it and so I may have
missed one.

Bloody hell! I missed the equivalent of an atom bomb going off.
Unfortunately I am not sure how to start to approach this for a solution.

These errors do not look good.  Am I running into coflicting ppa's

Err:12 http://ppa.launchpad.net/jonathonf/texlive-2016/ubuntu zesty Release
  404  Not Found
Err:13 https://cran.utstat.utoronto.ca//bin/linux/ubuntu zesty/ Release
  server certificate verification failed. CAfile:
/etc/ssl/certs/ca-certificates.crt
CRLfile: none
Err:14 http://ppa.launchpad.net/jonathonf/texlive/ubuntu zesty Release
  404  Not Found

Nor does this

E: The repository 'https://launchpad.net/~rkward-devel/+archive/ubuntu/
rkward-stable-cran

zesty Release' does not have a Release file.
N: Updating from such a repository can't be done securely, and is therefore
disabled by default.

#---
-###
rkrideau@jrk-T420:~$ sudo apt update
[sudo] password for jrkrideau:
Get:1 http://archive.ubuntu.com/ubuntu zesty-updates InRelease [89.2 kB]
Get:2 http://security.ubuntu.com/ubuntu zesty-security InRelease [89.2
kB]
Ign:3 http://ppa.launchpad.net/jonathonf/texlive-2016/ubuntu zesty
InRelease
Hit:4 http://archive.canonical.com/ubuntu zesty
InRelease
Ign:5 http://ppa.launchpad.net/jonathonf/texlive/ubuntu zesty
InRelease
Hit:6 http://ppa.launchpad.net/lyx-devel/release/ubuntu zesty
InRelease
Hit:7 http://archive.ubuntu.com/ubuntu zesty InRelease

Hit:8 http://ppa.launchpad.net/marutter/rrutter/ubuntu zesty InRelease
Ign:9 https://cran.utstat.utoronto.ca//bin/linux/ubuntu zesty/ InRelease
Get:10 http://archive.ubuntu.com/ubuntu zesty-backports InRelease [89.2 kB]
Hit:11 http://ppa.launchpad.net/rkward-devel/rkward-stable-cran/ubuntu
zesty InRelease
Err:12 http://ppa.launchpad.net/jonathonf/texlive-2016/ubuntu zesty Release
  404  Not Found
Err:13 https://cran.utstat.utoronto.ca//bin/linux/ubuntu zesty/ Release
  server certificate verification failed. CAfile:
/etc/ssl/certs/ca-certificates.crt
CRLfile: none
Err:14 http://ppa.launchpad.net/jonathonf/texlive/ubuntu zesty Release
  404  Not Found
Ign:15 https://launchpad.net/~rkward-devel/+archive/ubuntu/rkward-
stable-cran

zesty InRelease
Get:16 http://archive.ubuntu.com/ubuntu zesty-updates/main amd64 DEP-11
Metadata [52.7 kB]
Get:17 http://archive.ubuntu.com/ubuntu zesty-updates/main DEP-11 64x64
Icons [26.3 kB]
Get:18 http://archive.ubuntu.com/ubuntu zesty-updates/universe amd64 DEP-11
Metadata [82.7 kB]
Get:19 http://archive.ubuntu.com/ubuntu zesty-updates/universe DEP-11 64x64
Icons [90.1 kB]
Get:20 http://archive.ubuntu.com/ubuntu zesty-updates/multiverse amd64
DEP-11 Metadata [5,840 B]
Get:21 http://security.ubuntu.com/ubuntu zesty-security/main amd64 DEP-11
Metadata [12.5 kB]
Get:22 http://security.ubuntu.com/ubuntu zesty-security/universe amd64
DEP-11 Metadata [20.7 kB]
Get:23 http://security.ubuntu.com/ubuntu zesty-security/universe DEP-11
64x64 Icons [36.5 kB]
Err:24 https://launchpad.net/~rkward-devel/+archive/ubuntu/rkward-
stable-cran

zesty Release
  404  Not Found
Get:25 http://archive.ubuntu.com/ubuntu zesty-backports/universe amd64
DEP-11 Metadata [5,140 B]
Reading package lists... Done
E: The repository 'http://ppa.launchpad.net/jonathonf/texlive-2016/ubuntu
zesty Release' does not have a Release file.
N: Updating from such a repository can't be done securely, and is therefore
disabled by default.
N: See apt-secure(8) manpage for repository creation and user configuration
details.
E: The repository 'https://cran.utstat.utoronto.ca//bin/linux/ubuntu zesty/
Release' does not have a Release file.
N: Updating from such a repository can't be done securely, and is therefore
disabled by default.
N: See apt-secure(8) manpage for repository creation and user configuration
details.
E: The repository 'http://ppa.launchpad.net/jonathonf/texlive/ubuntu zesty
Release' does not have a Release file.
N: Updating from such a repository can't be done securely, and is therefore
disabled by default.
N: See apt-secure(8) manpage for repository creation and user configuration
details.
E: The repository 'https://launchpad.net/~rkward-devel/+archive/ubuntu/
rkward-stable-cran

zesty Release' does not have a Release file.
N: Updating from such a repository can't be done securely, and is therefore
disabled by default.
N: See apt-secure(8) manpage for repository creation and user configuration
details.
jrkrideau@jrk-T420:~$


On 22 August 2017 at 10:35, John Kane  wrote:

>
> *sudo apt update*
> Yes, ran 

Re: Missing Rnw(knitr) module

[Jean-Marc Lasgouttes]

Le 22/08/2017 à 14:31, John Kane a écrit :
But, blast it, I want knitr back. I have a good number of files with 
knitr code and I would hate to have to modify them.  But, at least, we 
now know that LyX is talking to R which is reassuring.


What is your operating system?

JMarc

Re: Missing Rnw(knitr) module

[John Kane]

Thanks  Jean-Marc.

I have reconfigured two or three times.
.
I have not thought of sweave in years.  A plain file, that is no R code,
compiles with sweave loaded. A small knitr file gives an error but that is
to be expected. I'll have to cobble together a sweave example and see what
happens. It should run okay.

I stole a bit of sweave code from Friedrich Leisch's article in R News
https://cran.r-project.org/doc/Rnews/Rnews_2002-3.pdf and it compiles
although not perfectly which is not surprising. It was just a quick and
dirty test.

But, blast it, I want knitr back. I have a good number of files with knitr
code and I would hate to have to modify them.  But, at least, we now know
that LyX is talking to R which is reassuring.

Thanks again,

On 22 August 2017 at 07:51, Jean-Marc Lasgouttes  wrote:

> Le 22/08/2017 à 13:01, John Kane a écrit :
>
>> I recently upgraded to LyX 2.2.3 as I am not doing any production work at
>> the moment and it seemed a good time to explore some of the new features.
>> I have a problem with the Rnw(knitr) module in LyX. LyX is insisting that
>> the knitr package does not exist and the compile aborts.
>> R says knitr is installed and can be loaded. A closer inspection of the
>> “Available” modules list shows that Rnw(knitr) is not listed.
>> If I remove the Rnw(knitr) module from the selected list the file
>> compiles normally.
>>
>
> Two things to try:
> - try to run Tools>Reconfigure
> - check whether Rnw(sweave) (which is bundeled with R) works better.
>
> JMarc
>



-- 
John Kane
Kingston ON Canada

Re: Missing Rnw(knitr) module

[Jean-Marc Lasgouttes]

Le 22/08/2017 à 13:01, John Kane a écrit :
I recently upgraded to LyX 2.2.3 as I am not doing any production work 
at the moment and it seemed a good time to explore some of the new features.
I have a problem with the Rnw(knitr) module in LyX. LyX is insisting 
that the knitr package does not exist and the compile aborts.
R says knitr is installed and can be loaded. A closer inspection of the 
“Available” modules list shows that Rnw(knitr) is not listed.
If I remove the Rnw(knitr) module from the selected list the file 
compiles normally.


Two things to try:
- try to run Tools>Reconfigure
- check whether Rnw(sweave) (which is bundeled with R) works better.

JMarc