PDF Output with Knitr for Latex Equations - pdf

I am having trouble getting multi-line latex equations to successfully compile when using knitr in R Markdown. When I output as an HTML file it works but when I attempt to output as a PDF I get errors and it will not compile.
The following sample code illustrates the problem. Just change output:html_document to output: pdf_document. You'll see that in HTML output both Test 1 and Test 2 work. But in PDF output only Test 1 successfully compiles.
---
title: "Test"
date: "1/16/2018"
output: html_document
---
## R Markdown
Testing to see if a multi-line latex equation works.
#### Test 1:
$$ f(x) = x^5 + x^3 + x $$
$$ g(x) = y^{x+1} $$
#### Test 2:
\begin{align}
f(x) &= x^5 + x^3 + x \\
g(x) &= y^{x+1}
\end{align}
I am running Mac OS X - High Sierra and R Studio - Version 1.1.383
The following is the error I got:
Rule 'pdflatex': File changes, etc:
Non-existent destination files:
'Untitled.pdf'
------------
Run number 1 of rule 'pdflatex'
------------
------------
Running 'pdflatex -halt-on-error -interaction=batchmode -recorder "Untitled.tex"'
------------
This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
=== TeX engine is 'pdfTeX'
Latexmk: Errors, so I did not complete making targets
Collected error summary (may duplicate other messages):
pdflatex: Command for 'pdflatex' gave return code 1
Refer to 'Untitled.log' for details
Latexmk: Use the -f option to force complete processing,
unless error was exceeding maximum runs of latex/pdflatex.
! Paragraph ended before \align was complete.
<to be read again>
\par
l.112
Error: Failed to compile Untitled.tex. See Untitled.log for more info.
Execution halted

Related

How to run test cases for a binary in Makefile

There is a small project which produces a binary application. The source code is C, I'm using autotools to create the Makefile and build the binary - it works as well.
I would like to run tests cases with that binary. Here is what I did:
SUBDIRS = src
dist_doc_DATA = README
TESTS=
TESTS+=tests/config1.conf
TESTS+=tests/config2.conf
TESTS+=tests/config3.conf
TESTS+=tests/config4.conf
TESTS+=tests/config5.conf
TESTS+=tests/config6.conf
TESTS+=tests/config7.conf
TESTS+=tests/config8.conf
TESTS+=tests/config9.conf
TESTS+=tests/config10.conf
TESTS+=tests/config11.conf
I would like to run these cases as argument with the tool. When I run make check, I got:
make[3]: Entering directory '/home/airween/src/mytool'
FAIL: tests/config1.conf
FAIL: tests/config2.conf
FAIL: tests/config3.conf
which is correct, because those files are simple configurations files.
How can I solve that make check runs my tool with the scripts above, and finally I get a list with number of success, failed, ... tests, like in that case:
============================================================================
Testsuite summary for mytool 0.1
============================================================================
# TOTAL: 11
# PASS: 0
# SKIP: 0
# XFAIL: 0
# FAIL: 11
# XPASS: 0
# ERROR: 0
Edit: so I would like to emulate these runs:
for f in `ls -1 tests/*.conf; do src/mytool ${f}; done
but - of course - I want to see the summary at the end.
Thanks.
The Autotools' built-in test runner expects you to specify the names of executable tests via the make variable TESTS. You cannot just put random filenames in there and expect make or Automake to know what to do with them.
The tests can be built programs, generated scripts, static scripts distributed with the project, or any combination of the above.
How can I solve that make check runs my tool with the scripts above, and finally I get a [test summary report]?
You have acknowledged that your configuration files are not scripts, so stop calling them that! This is in fact the crux of the problem. The easiest solution is probably to create actual executable scripts, one for each case, and name those in your TESTS variable. Each one would run the binary under test with the appropriate configuration file (that is, you're responsible for making them do that if those are the tests you want to perform).
See also the Automake Manual's chapter on tests.
Okay, the solution from here:
tests/Makefile.am:
==================
TEST_EXTENSIONS = .conf
CONF_LOG_COMPILER = ./test-suit.sh
TESTS=
TESTS+=config1.conf
TESTS+=config2.conf
TESTS+=config3.conf
TESTS+=config4.conf
TESTS+=config5.conf
TESTS+=config6.conf
TESTS+=config7.conf
TESTS+=config8.conf
TESTS+=config9.conf
TESTS+=config10.conf
TESTS+=config11.conf
test/test-suit.sh:
==================
#!/bin/sh
CONF=$1
exec ../src/mytool $CONF
And the result:
make check
...
PASS: config1.conf
PASS: config2.conf
PASS: config3.conf
PASS: config4.conf
PASS: config5.conf
PASS: config6.conf
PASS: config7.conf
PASS: config8.conf
PASS: config9.conf
PASS: config10.conf
PASS: config11.conf
============================================================================
Testsuite summary for mytool 0.1
============================================================================
# TOTAL: 11
# PASS: 11
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
This is what I expected.

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.

Fortran runtime error: End of file when reading input data

I'm currently running a code and I'm always getting to the same end. I am trying to read an input file and it returns the error:
Fortran runtime error: End of file
In an other post they said to put in the iostat specifier so now my code looks like this:
INTEGER :: m
INTEGER :: st
Open(Unit = 13,action='read',file='Data_Inp.dat',status='old')
read (13,*, iostat = st) m
write (*,*) st
write (*,*) m
ALLOCATE(winkel(m),energie(m))
Do i = 1,m
read(13,*),winkel(i),energie(i)
End Do
And the input file looks like this:
12
-17.83 -0.019386527878
-15.83 -0.020125057233
-12.83 -0.020653853148
-11.83 -0.020840036028
-9.83 -0.020974157405
-8.83 -0.021056401707
-6.83 -0.021065517811
-5.83 -0.020992571816
-4.83 -0.020867828448
-1.83 -0.02069158012
Now the terminal prints a -1 for iostat and a constantly changing number for m.
If the first read command is causing an error, check for extraneous characters before or after "12" in your input file, especially if you created it on one platform (Windows?) and using it on another platform (Linux? Mac?)

How to set an Icon in NSIS install (CMake)

The documentation for CPACK_PACKAGE_ICON is very limited on cmake wiki page.
The following is not working for me (as per):
set(CPACK_PACKAGE_ICON "${CMAKE_CURRENT_SOURCE_DIR}/images/MyIcon.bmp")
include(CPack)
It leads to:
File: "C:/proj/my_library/images/MyIcon.bmp" -> no files found.
Usage: File [/nonfatal] [/a] ([/r] [/x filespec [...]] filespec [...] |
/oname=outfile one_file_only)
Error in macro MUI_HEADERIMAGE_INIT on macroline 24
Error in macro MUI_GUIINIT on macroline 3
Error in macro MUI_FUNCTION_GUIINIT on macroline 4
Error in macro MUI_INSERT on macroline 11
Error in macro MUI_LANGUAGE on macroline 7
Error in script "C:/proj/bin-win/_CPack_Packages/win32/NSIS/project.nsi" on line 574 -- aborting creation process
So how does one actually set a working icon during the install process of a NSIS installer ? Also what format is actually needed for the icon ?
After some trial-and-error I finally found out two tricks required:
The syntax is actually:
set(CPACK_PACKAGE_ICON "${CMAKE_CURRENT_SOURCE_DIR}/images\\\\MyIcon.bmp")
And the BMP file is restricted to an older format, which is not the default for imagemagick. Eg:
$ file MyIcon.bmp
MyIcon.bmp: PC bitmap, Windows 98/2000 and newer format, 128 x 128 x 24
what is needed is this:
$ convert MyIcon.bmp BMP3:MyIcon2.bmp
$ file MyIcon2.bmp
MyIcon2.bmp: PC bitmap, Windows 3.x format, 128 x 128 x 24
The first representation (Windows 98/2000 and newer format) did not work for me.
For me that command in CMakeLists.txt works fine:
set(CPACK_NSIS_MUI_ICON "${CMAKE_CURRENT_SOURCE_DIR}/images\\\\icon.ico")
I found it here https://cmake.org/cmake/help/v3.0/module/CPackNSIS.html

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

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).