knitr 1.5 / patchDVI 1.9 doesn't seem to generate a concordance acceptable to evince + emacs - pdf

Setup : here is sessionInfo() :
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8
[5] LC_MONETARY=fr_FR.UTF-8 LC_MESSAGES=fr_FR.UTF-8
[7] LC_PAPER=fr_FR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] patchDVI_1.9 knitr_1.5
loaded via a namespace (and not attached):
[1] compiler_3.0.2 evaluate_0.5.1 formatR_0.9 highr_0.2.1 stringr_0.6.2
[6] tcltk_3.0.2 tools_3.0.2
I am trying to get emacs and AucTeX to synchronize my .Rnw source file with evince to go to comiled text from source and back.
I have already checked that the synchronization works fine between a .tex source and a PDF.
My .Rnw file starts with :
\documentclass[a4paper,twoside,12pt]{article}
\synctex=1 %% Should force concordance generation
\pdfcompresslevel=0 %% Should force avoidance of PDF compression, which patchDVI does
\pdfobjcompresslevel=0 %% not handle
<<include=FALSE>>= %% Modificaton of what Sweave2kinitr does
## opts_chunk$set(concordance=TRUE, self.contained=TRUE) ## No possible effect
opts_knit$set(concordance=TRUE, self.contained=TRUE) ## Seems reasonable
#
%% \SweaveOpts{concordance=TRUE} %% That's where inspiration came from
Consider the following log (unrelevant parts edited) :
> options("knitr.concordance")
$knitr.concordance
[1] TRUE
> opts_knit$get("concordance")
[1] TRUE
> knit("IntroStat.Rnw")
processing file: IntroStat.Rnw
|...................... | 33%
ordinary text without R code
|........................................... | 67%
label: unnamed-chunk-1 (with options)
List of 1
$ include: logi FALSE
|.................................................................| 100%
ordinary text without R code
output file: IntroStat.tex
[1] "IntroStat.tex"
> system("pdflatex -synctex=1 IntroStat.tex")
[ Edited irrelevancies ]
SyncTeX written on IntroStat.synctex.gz.
Note : a concordance has *been* generated !!! **
Transcript written on IntroStat.log.
Let's do that again to fix references :
> system("pdflatex -synctex=1 IntroStat.tex")
[ Edited irrelevancies ]
Output written on IntroStat.pdf (1 page, 136907 bytes).
SyncTeX written on IntroStat.synctex.gz.
Note : a concordance has *been* generated *again* !!! **
Transcript written on IntroStat.log.
> patchDVI("IntroStat.pdf")
[1] "0 patches made. Did you set \\SweaveOpts{concordance=TRUE}?"
* This I do not understand *
> patchSynctex("IntroStat.synctex.gz")
[1] "0 patches made. Did you set \\SweaveOpts{concordance=TRUE}?"
* Ditto *
It appears that something in the set of tools does not work as advertized : either dviPatch does not recognize legal concordance \specials or pdflatex dfoes not generate them. It does generate something, however...
I checked that the resulting PDF enables evince to synchronize with the .tex file, but not in the .Rnw file. Furthermore, when the .Rnw file is open in emacs, starting the viewer with 'C-c C-v View" in AucTeX indeed starts the viewer (after requesting to open a server, which I authorize), but the viewers is empty, and i get this :
"TeX-evince-sync-view: Couldn't find the Evince instance for file:///home/charpent/Boulot/Cours/ODF/Chapitres/Ch3-StatMath/IntroStat.Rnw.pdf"
in the "Messages" buffer.
So we have a second problem here.
A third one would be to integrate all of this transparently in the AucTeX production chain, but this is another story...
I'd really like to keep emacs as my main tool for R/\LaTeX/Sage work, rather tha switch to RStudio, which probably won't like much SageTeX and othe various tools I need on a daily/weekly basis...
Any thoughts ?

Maybe this https://github.com/jan-glx/patchKnitrSynctex will help. I tried it on a simple file, and it does work.
As for the second and third problems, I have this script (note that I source the above code from jan-glx; modify path accordingly):
#!/bin/bash
FILE=$1
BASENAME=$(basename $FILE .Rnw)
Rscript -e 'library(knitr); opts_knit$set("concordance" = TRUE); knit("'$1'")'
pdflatex --synctex=1 --file-line-error --shell-escape "${1%.*}"
Rscript -e "source('~/Sources/patchKnitrSynctex.R'); patchKnitrSynctex('${1%.*}.tex')"
ln -s $BASENAME.synctex.gz $BASENAME.Rnw.synctex.gz
ln -s $BASENAME.pdf $BASENAME.Rnw.pdf
The links are my kludgy way of getting around the "Couldn't find the instance (...) ".
If you have your .Rnw in an Emacs buffer, go to a shell buffer, and call that script. When finished, C-c C-v from Emacs will open your configured PDF viewer (okular in my case). In the PDF, shift + left mouse click (okular at least) will bring you to the right place in the Emacs .Rnw buffer.
This is not ideal: if you jump to an error, it goest to the .tex, not the .Rnw. And I'd like to be able to invoke it via C-c C-c or similar (but I don't know how ---elisp ignorance).

Related

How to interact with a subprocess through its stdin, stdout, stderr in Smalltalk?

This Python code shows how to call some process in Windows 10 and to send to it string commands, to read its string responses through stdin, stdout pipes of the process:
Python 3.8.0 (tags/v3.8.0:fa919fd, Oct 14 2019, 19:37:50) [MSC v.1916 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from subprocess import *
>>> p = Popen("c:/python38/python.exe", stdin=PIPE, stdout=PIPE)
>>> p.stdin.write(b"print(1+9)\n")
11
>>> p.communicate()
(b'10\r\n', None)
>>>
As you can see the python.exe process returned 10 as an answer to print(1+9). Now I want to do the same in Pharo (or Squeak): in Windows 10 OS - I suppose something similar, i.e. short, simple, understandable, really working.
I installed OSProcess, ProcessWrapper (they were missing in Pharo, also its strange that I got warning that they are not marked for Pharo 8.0 and were not checked to work in Pharo 8.0, but OK), and I tried ProcessWrapper, PipeableOSProcess (copy-pasted different snippets from the Web), etc - with zero success! The results were:
nothing happens, python.exe was not started
VM errors console was opened (white console in the bottom of the Pharo, which is controlled with F2 menu)
different exceptions
etc
Would somebody show me simple working example how to start a process and to to send it commands, read answers, then send again, and so on in some loop - I plan to have such communication in a detached thread and to use it as some service, because Pharo, Smalltalk in general is missing most bindings, so then I will use subprocess communication like in "good" old days...
I know how to call a command and to get its output:
out := LibC resultOfCommand: 'dir ', aDir.
but I am talking about another scenario: a communication with a running process interactively (for example, with SSH or similar like in the example above - python.exe).
PS. Maybe it's possible to do it with LibC #pipe:mode even?
Let me start with that the PipeableOsProcess is probably broken on Windows. I have tried it and it just opened a command line and nothing else (it does not freeze my Pharo 8). The whole OSProcess does not work correctly in my eyes.
So I took a shot at LibC which is supposed to not work with Windows.
I’m a module defining access to standard LibC. I’m available under Linux and OSX, but not under Windows for obvious reasons :)
Next is to say that Python's Windows support is probably much better than Pharo's.
The solution, which is more like a workaround using files, is to use LibC and #runCommand: (I tried to come up with a similar example as you had shown above):
| count command result outputFile errorFile |
count := 9+1. "The counting"
command := 'echo ', count asString. "command run at the command line"
outputFile := 'output'. "a file into which the output is redirected"
errorFile := 'error'. "a file where the error output is redirected "
result := LibC runCommand: command, "run the command "
' >', outputFile, "redirect the output to output file"
' 2>', errorFile.
"reading back the value from output file"
outputFile asFileReference contents lines.
"reading back the value from the error file - which is empty in this case"
errorFile asFileReference contents lines.

Switching the system does not work

I had the following situation: I'm in a live user mode debugging session and I wanted to show the win32k!_W32Process structure. Unfortunately, win32k is a kernel mode SYS file, so the symbols are not available in the user mode session.
I know that I can always load a DLL, EXE or SYS as a dump file and then inspect the symbols. Usually I would do that via File/Open Crash Dump.
This time, I wanted to show the participants of a debugging workshop that it's possible to debug multiple systems at the same time, so I opened the Win32K.sys via WinDbg's command prompt:
0:003> |
. 0 id: 10fc attach name: [...]\NetHeaps.exe
0:003> .opendump C:\Windows\winsxs\[...]\win32k.sys
Loading Dump File [C:\Windows\winsxs\[...]\win32k.sys]
Opened 'C:\Windows\winsxs\[...]\win32k.sys'
||0:0:003>
As we can now see, we have 2 systems and I'm currently on the live debugging system:
||0:0:003> ||
. 0 Live user mode: <Local>
1 Image file: C:\Windows\winsxs\[...]\win32k.sys
I thought I could switch to the other system now, but that does not work:
||0:0:003> ||1s
^ Illegal debuggee error in '||1s'
I would not have worried too much, but it can't find the symbols of win32k in this case:
||0:0:003> .reload
Reloading current modules
...........................
||0:0:003> dt win32k!_W32Process
Symbol win32k!_W32Process not found.
The problem is not in the || command, it's in the .opendump command.
The help says:
After you use the .opendump command, you must use the g (Go) command to finish loading the dump file.
Be aware that this will also run your live process. Therefore, freeze the threads first (~*f) and unfreeze later (~*u).
After that you can switch the system and display the type:
||1:1:004> ||
0 Live user mode: <Local>
. 1 Image file: C:\Windows\winsxs\[...]\win32k.sys
||1:1:004> dt _W32Process
win32k!_W32PROCESS
+0x000 Process : Ptr64 _EPROCESS
+0x008 RefCount : Uint4B
+0x00c W32PF_Flags : Uint4B
[...]

Setting the photometric interpretation tag for a multi-page tiff

While trying to convert a multipage document from a tiff to a pdf, I encountered the following problem:
↪ tiff2pdf 0271.f1.tiff -o 0271.f1.pdf
tiff2pdf: No support for 0271.f1.tiff with no photometric interpretation tag.
tiff2pdf: An error occurred creating output PDF file.
Does anybody know what causes this and how to fix it?
This is caused because one or more of the pages in the multi-page tiff does not have the photometric interpretation tag set. This is a required tag, so that means your tiffs are technically invalid (though I bet they work fine anyway).
To fix this, you must identify the page (or pages) that does not have the photometric interpretation set and fix it.
To identify the page, you can simply run something like:
↪ tiffinfo your-file.tiff
This will spit out the info for every page of your tiff. For each good page, you'll see something like:
TIFF Directory at offset 0x105c0 (67008)
Subfile Type: (0 = 0x0)
Image Width: 1760 Image Length: 2639
Resolution: 300, 300 pixels/inch
Bits/Sample: 1
Compression Scheme: CCITT Group 4
**Photometric Interpretation: min-is-white**
FillOrder: msb-to-lsb
Orientation: row 0 top, col 0 lhs
Samples/Pixel: 1
Rows/Strip: 2639
Planar Configuration: single image plane
Software: ScanFix(TM) Enhanced ImageGear Version: 11.00.024
DateTime: Mon Oct 31 15:11:07 2005
Artist: 1996-2001 AccuSoft Co., All rights reserved
If you have a bad page, it'll lack the photometric interpretation section, and you can fix it with:
↪ tiffset -d $page-number -s 262 0 your-file.tiff
Note that the value of zero is the default for the photometric interpretation key, which is 262. You can see the other values for this key at the link above.
If your tiff has a lot of pages (like mine does), you may not be able to easily identify the bad page by eye. In that case, you can take a brute force approach, setting the photometric interpretation for all pages to the default value.
# First, split the tiff into many one-page files
↪ tiffsplit your-file.tiff
# Then, set the photometric interpretation to the default for all pages
↪ find . -name '*.tiff' -exec tiffset -s 262 0 '{}' \;
# Then rejoin the pages
↪ tiffcp *.tiff -o out-file.tiff
Lot of dummy work, but gets the job done.

Using Squeak from a shell

Can I launch Squeak as a REPL (no GUI), where I can enter and evaluate Smalltalk expressions? I know the default image don't allow this. Is there any documentation on how to build a minimum image that can be accessed from a command-line shell?
Here is a (hackish) solution:
First, you need OSProcess, so run this in a Workspace:
Gofer new squeaksource:'OSProcess'; package:'OSProcess';load.
Next, put this in the file repl.st:
OSProcess thisOSProcess stdOut
nextPutAll: 'Welcome to the simple Smalltalk REPL';
nextPut: Character lf; nextPut: $>; flush.
[ |input|
[ input := OSProcess readFromStdIn.
input size > 0 ifTrue: [
OSProcess thisOSProcess stdOut
nextPutAll: ((Compiler evaluate: input) asString;
nextPut: Character lf; nextPut: $>; flush
]
] repeat.
]forkAt: (Processor userBackgroundPriority)
And last, run this command:
squeak -headless path/to/squeak.image /absolute/path/to/repl.st
You can now have fun with a Smalltalk REPL. Dont forget to type in the command:
Smalltalk snapshot:true andQuit:true
if you want to save your changes.
Now, onto the explanation of this solution:
OSProcess is a package that allows to run other processes, read from stdin, and write to stdout and stderr. You can access the stdout AttachableFileStream with OSProcess thisOSProcess (the current process, aka squeak).
Next, you run an infinite loop at userBackgroundPriority (to let other processes run). In this infinite loop, you use Compiler evaluate: to execute the input.
And you run this in a script with a headless image.
As of Pharo 2.0 (and 1.3/1.4 with the fix described below), there are no more hacks necessary. The following snippet will turn your vanilla Pharo image into a REPL server...
From https://gist.github.com/2604215:
"Works out of the box in Pharo 2.0. For prior versions (definitely works in 1.3 and 1.4), first file in https://gist.github.com/2602113"
| command |
[
command := FileStream stdin nextLine.
command ~= 'exit' ] whileTrue: [ | result |
result := Compiler evaluate: command.
FileStream stdout nextPutAll: result asString; lf ].
Smalltalk snapshot: false andQuit: true.
If you want the image to always be a REPL, put the code in a #startup: method; otherwise, pass the script at the command line when you want REPL mode, like:
"/path/to/vm" -headless "/path/to/Pharo-2.0.image" "/path/to/gistfile1.st"
Please visit:
http://map.squeak.org/package/2c3b916b-75e2-455b-b25d-eba1bbc94b84
and Run Smalltalk on server without GUI?
The project http://www.squeaksource.com/SecureSqueak.html includes a REPL package that may provide much of what you are looking for.

Nano hacks: most useful tiny programs you've coded or come across

It's the first great virtue of programmers. All of us have, at one time or another automated a task with a bit of throw-away code. Sometimes it takes a couple seconds tapping out a one-liner, sometimes we spend an exorbitant amount of time automating away a two-second task and then never use it again.
What tiny hack have you found useful enough to reuse? To make go so far as to make an alias for?
Note: before answering, please check to make sure it's not already on favourite command-line tricks using BASH or perl/ruby one-liner questions.
i found this on dotfiles.org just today. it's very simple, but clever. i felt stupid for not having thought of it myself.
###
### Handy Extract Program
###
extract () {
if [ -f $1 ] ; then
case $1 in
*.tar.bz2) tar xvjf $1 ;;
*.tar.gz) tar xvzf $1 ;;
*.bz2) bunzip2 $1 ;;
*.rar) unrar x $1 ;;
*.gz) gunzip $1 ;;
*.tar) tar xvf $1 ;;
*.tbz2) tar xvjf $1 ;;
*.tgz) tar xvzf $1 ;;
*.zip) unzip $1 ;;
*.Z) uncompress $1 ;;
*.7z) 7z x $1 ;;
*) echo "'$1' cannot be extracted via >extract<" ;;
esac
else
echo "'$1' is not a valid file"
fi
}
Here's a filter that puts commas in the middle of any large numbers in standard input.
$ cat ~/bin/comma
#!/usr/bin/perl -p
s/(\d{4,})/commify($1)/ge;
sub commify {
local $_ = shift;
1 while s/^([ -+]?\d+)(\d{3})/$1,$2/;
return $_;
}
I usually wind up using it for long output lists of big numbers, and I tire of counting decimal places. Now instead of seeing
-rw-r--r-- 1 alester alester 2244487404 Oct 6 15:38 listdetail.sql
I can run that as ls -l | comma and see
-rw-r--r-- 1 alester alester 2,244,487,404 Oct 6 15:38 listdetail.sql
This script saved my career!
Quite a few years ago, i was working remotely on a client database. I updated a shipment to change its status. But I forgot the where clause.
I'll never forget the feeling in the pit of my stomach when I saw (6834 rows affected). I basically spent the entire night going through event logs and figuring out the proper status on all those shipments. Crap!
So I wrote a script (originally in awk) that would start a transaction for any updates, and check the rows affected before committing. This prevented any surprises.
So now I never do updates from command line without going through a script like this. Here it is (now in Python):
import sys
import subprocess as sp
pgm = "isql"
if len(sys.argv) == 1:
print "Usage: \nsql sql-string [rows-affected]"
sys.exit()
sql_str = sys.argv[1].upper()
max_rows_affected = 3
if len(sys.argv) > 2:
max_rows_affected = int(sys.argv[2])
if sql_str.startswith("UPDATE"):
sql_str = "BEGIN TRANSACTION\\n" + sql_str
p1 = sp.Popen([pgm, sql_str],stdout=sp.PIPE,
shell=True)
(stdout, stderr) = p1.communicate()
print stdout
# example -> (33 rows affected)
affected = stdout.splitlines()[-1]
affected = affected.split()[0].lstrip('(')
num_affected = int(affected)
if num_affected > max_rows_affected:
print "WARNING! ", num_affected,"rows were affected, rolling back..."
sql_str = "ROLLBACK TRANSACTION"
ret_code = sp.call([pgm, sql_str], shell=True)
else:
sql_str = "COMMIT TRANSACTION"
ret_code = sp.call([pgm, sql_str], shell=True)
else:
ret_code = sp.call([pgm, sql_str], shell=True)
I use this script under assorted linuxes to check whether a directory copy between machines (or to CD/DVD) worked or whether copying (e.g. ext3 utf8 filenames -> fusebl
k) has mangled special characters in the filenames.
#!/bin/bash
## dsum Do checksums recursively over a directory.
## Typical usage: dsum <directory> > outfile
export LC_ALL=C # Optional - use sort order across different locales
if [ $# != 1 ]; then echo "Usage: ${0/*\//} <directory>" 1>&2; exit; fi
cd $1 1>&2 || exit
#findargs=-follow # Uncomment to follow symbolic links
find . $findargs -type f | sort | xargs -d'\n' cksum
Sorry, don't have the exact code handy, but I coded a regular expression for searching source code in VS.Net that allowed me to search anything not in comments. It came in very useful in a particular project I was working on, where people insisted that commenting out code was good practice, in case you wanted to go back and see what the code used to do.
I have two ruby scripts that I modify regularly to download all of various webcomics. Extremely handy! Note: They require wget, so probably linux. Note2: read these before you try them, they need a little bit of modification for each site.
Date based downloader:
#!/usr/bin/ruby -w
Day = 60 * 60 * 24
Fromat = "hjlsdahjsd/comics/st%Y%m%d.gif"
t = Time.local(2005, 2, 5)
MWF = [1,3,5]
until t == Time.local(2007, 7, 9)
if MWF.include? t.wday
`wget #{t.strftime(Fromat)}`
sleep 3
end
t += Day
end
Or you can use the number based one:
#!/usr/bin/ruby -w
Fromat = "http://fdsafdsa/comics/%08d.gif"
1.upto(986) do |i|
`wget #{sprintf(Fromat, i)}`
sleep 1
end
Instead of having to repeatedly open files in SQL Query Analyser and run them, I found the syntax needed to make a batch file, and could then run 100 at once. Oh the sweet sweet joy! I've used this ever since.
isqlw -S servername -d dbname -E -i F:\blah\whatever.sql -o F:\results.txt
This goes back to my COBOL days but I had two generic COBOL programs, one batch and one online (mainframe folks will know what these are). They were shells of a program that could take any set of parameters and/or files and be run, batch or executed in an IMS test region. I had them set up so that depending on the parameters I could access files, databases(DB2 or IMS DB) and or just manipulate working storage or whatever.
It was great because I could test that date function without guessing or test why there was truncation or why there was a database ABEND. The programs grew in size as time went on to include all sorts of tests and become a staple of the development group. Everyone knew where the code resided and included them in their unit testing as well. Those programs got so large (most of the code were commented out tests) and it was all contributed by people through the years. They saved so much time and settled so many disagreements!
I coded a Perl script to map dependencies, without going into an endless loop, For a legacy C program I inherited .... that also had a diamond dependency problem.
I wrote small program that e-mailed me when I received e-mails from friends, on an rarely used e-mail account.
I wrote another small program that sent me text messages if my home IP changes.
To name a few.
Years ago I built a suite of applications on a custom web application platform in PERL.
One cool feature was to convert SQL query strings into human readable sentences that described what the results were.
The code was relatively short but the end effect was nice.
I've got a little app that you run and it dumps a GUID into the clipboard. You can run it /noui or not. With UI, its a single button that drops a new GUID every time you click it. Without it drops a new one and then exits.
I mostly use it from within VS. I have it as an external app and mapped to a shortcut. I'm writing an app that relies heavily on xaml and guids, so I always find I need to paste a new guid into xaml...
Any time I write a clever list comprehension or use of map/reduce in python. There was one like this:
if reduce(lambda x, c: locks[x] and c, locknames, True):
print "Sub-threads terminated!"
The reason I remember that is that I came up with it myself, then saw the exact same code on somebody else's website. Now-adays it'd probably be done like:
if all(map(lambda z: locks[z], locknames)):
print "ya trik"
I've got 20 or 30 of these things lying around because once I coded up the framework for my standard console app in windows I can pretty much drop in any logic I want, so I got a lot of these little things that solve specific problems.
I guess the ones I'm using a lot right now is a console app that takes stdin and colorizes the output based on xml profiles that match regular expressions to colors. I use it for watching my log files from builds. The other one is a command line launcher so I don't pollute my PATH env var and it would exceed the limit on some systems anyway, namely win2k.
I'm constantly connecting to various linux servers from my own desktop throughout my workday, so I created a few aliases that will launch an xterm on those machines and set the title, background color, and other tweaks:
alias x="xterm" # local
alias xd="ssh -Xf me#development_host xterm -bg aliceblue -ls -sb -bc -geometry 100x30 -title Development"
alias xp="ssh -Xf me#production_host xterm -bg thistle1 ..."
I have a bunch of servers I frequently connect to, as well, but they're all on my local network. This Ruby script prints out the command to create aliases for any machine with ssh open:
#!/usr/bin/env ruby
require 'rubygems'
require 'dnssd'
handle = DNSSD.browse('_ssh._tcp') do |reply|
print "alias #{reply.name}='ssh #{reply.name}.#{reply.domain}';"
end
sleep 1
handle.stop
Use it like this in your .bash_profile:
eval `ruby ~/.alias_shares`