I have a distill website. When I try to hit "Build Website" using RStudio I get this error message:
Error: invalid version specification '2021.09.0+351' Execution halted
Exited with status 1.
Both issues are already fixed in development version of distill.
It was previously found by us or reported in Github Issues. Don't hesitate to look there when you have trouble, and also test the development v
This issue
Error: invalid version specification
is caused when you used the last RStudio IDE version.
The blank page issue is caused when using last rmarkdown version.
We'll make a patch release to CRAN very soon, but in the meantime, please install the development version of distill
remotes::install_github("rstudio/distill")
It is not a fully satisfactory answer, but I faced the same issue. Running:
rmarkdown::render_site(encoding = 'UTF-8')
on a terminal/command line window does run the command fully. However, the site is created only with blank pages (even though if you check the html source, the page is there, hidden).
I'm tracing the blank pages to the upgrade of the rmarkdown package, in my case, from 2.8 to 2.11. This brings with it a new dependency of jquerylib which might be a cause of this as well. This has started to happen with the new version of RStudio 2021.09.0 Build 351. This is consistent with the error message you and I got.
I tried to downgrade rmarkdown but every time you knit from RStudio with that version, it forces the upgrade. I think this should be reported as a bug, as it was clearly working before and now there are several issues that all seemed to be linked with all the upgrades (not compiling from inside RStudio, compiling with blank pages).
(I would have added this as a comment rather than a solution, but I do not have enough reputation yet)
Related
Godd morning!
On friday while I was doing some tests using parallel processing (with doParallel, compiler and foreach packages) suddenly I began to have repeteadly the following message
Message error
which traduced says:
"It was not possible to find the access point (or point of entry) to the proccedure deflateSetHeader in the dynamic link library C:PROGRA~1\R\R-3.4~1.2\Tcl\bin64\tcl86.dll "
The R version I was using when it started was the prior 3.3.3
I thought that, may be I didn't realize any inconsistency with that version and the packages I mentioned.
I reinstalled everything (R - the most recent version and RStudio, also, the most recent version) and the problem continues even in its most basic installation state (with no extra package installed). And now the message appears even when I just open RStudio but I'm not running anything.
Is anyone having this trouble? how can I solve it?
If any other info is needed I'll be glad to give you. I appreciate any help sice it's been a long weekend trying to solve it.
The issue got resolved by reinstalling R and R studio latest update. Currently using this version
RStudio-1.1.383
R-3.4.2-win
enter image description here
Knitr / Rmarkdown Execution halted
When I run Knitr and Rmarkdown, even with the knitr example scripts, I get the below error message.
Error in system(paste(shQuote(pandoc_path), "--version"), intern = TRUE) :
'"C:/Program Files/RStudio/bin/pandoc/pandoc"' not found
Calls: <Anonymous> ... get_pandoc_version -> with_pandoc_safe_environment -> force -> system Execution halted
I have installed and loaded knitr and rmarkdown from the libraries and alternatively using dev tools to get the most recent versions from github.
As it was working previously and I haven't changed any settings, I was wondering whether it might be due to the new R release and whether that has caused this?
I have tried uploading pandoc to the specific location it requested in the error but the online guidance was difficult to follow so didn't move into folder just it case it made it worst, as it was not required before I was confused as to why it was an error?
Not sure what else to try out, I have googled, stackflowed and explored knitr and pandoc webpages for any clues but with not success.
If anyone knows how to fix this as soon as possible I would be very grateful!!
I know this is a very old question, but I had the exact same issue, where knitting an Rmd file worked perfectly yesterday, and today, stopped working with the identical error message above. Even knitting the default Rmd starter document failed.
It's possible that a Windows patch was applied by our IS folks that may have broken something, as I had not changed my setup at all.
Doing a Sys.which('pandoc') suggested that it was looking in the wrong place (a user-specific location).
Updating RStudio did not help. Adding the following to my Rmd file also did not work:
Sys.setenv(RSTUDIO_PANDOC="PATH_TO_MY_PANDOC_BIN")
What eventually worked was a subset of the response by Ivo Fugers:
install.packages('installr')
install.pandoc()
(I wasn't paying close attention but think I allowed it to uninstall another version of pandoc.) After a system restart, knitting is working again.
Hope this helps folks in the future, as it seems to be a problem that still sporadically recurs.
I had a similar problem in a Statistical Computing class. A solution that worked for some of my classmates (including myself) is installing a few version of MikTex (takes about an hour). Otherwise, this is a solution that our teacher gave us:
So here is a possible strategy when you end up with a pandoc error, or when your Latex Equations do not show up in the 'markup':
Step 1
Re-install pandoc manually in your R console:
installing/loading the package:
if(!require(installr)) { install.packages("installr"); require(installr)} #load / install+load installr
Installing pandoc
install.pandoc()
Step 2
Download the the self-extracting protext.exe file from http://www.tug.org/protext/ . Install MikTex from this .exe file using the default settings...
2a. Make sure you allow Protext to install packages on the fly without asking permission.
Step 3
Look at https://tex.stackexchange.com/questions/81739/the-memory-dump-file-could-not-be-found , not the solution. Change the persmissions of all users in
C:\Users\YourUsername\AppData\Local\Temp
and
C:\Program Files\MikTex 2.9\
to full control.
How to do this? Go to C:\Users\YourUsername\AppData\Local , and right click on the folder Temp. Go to properties --> Security... and make sure all users listed there (even the trusted install) will have full control acces.
I faced the exact same problem yesterday and shocked because everything was working until day before yesterday. I was finishing my project in R markdown and it started throwing error.
Without having much help, I just have upgraded my RStudio to its latest version (0.98.1091). It took less than 10 minutes and everything started working as it was. I believe this sudden chocking was due to Windows patch update, but not 100% sure.
change your file name "C:/Program Files/RStudio/bin/pandoc/pandoc" into
"C:/ProgramFiles/RStudio/bin/pandoc/pandoc" or something else.
It doesn't allow space in the file address (like Program Files).
I just installed 2.1 RC1 bundle on windows 7
Each time I try to save a document (also when I first open Lyx), I get this message
LyX-210RC1-Bundle-1.exe
why this happens? Do I need to configure something else? I had Lyx 2.0 before, but I uninstalled that before installing Lyx 2.1
I also got this message. For me, this is what I think was going on:
The first execution of Lyx very quietly (i.e., in the background) performs package updates for MiKTeX. Afterwards, it actually launches Lyx.
However, if you launch a second invocation of Lyx immediately after the first (since nothing has yet displayed), it will launch w/o the packages it requires and result in the message that you see.
I suppose if MiKTeX was not / improperly installed, you could also encounter this issue.
#scottkosty is right--this should not happen and having downloaded the latest version of LyX 2.1.1. I had the same problem (NOTE: I am, however, working on a Mac). These are the steps I took to finally get things working in my case:
If you have the above issues working on a Mac with OS X try the following:
1. reinstall latest version MacTeX at: [https://tug.org/mactex/][1]
2. install latest version of LyX: 2.1.1. (see: [http://www.lyx.org/Download][2])
3. Tools --> Reconfigure.
4. Restart, check: Document --> Settings --> Document Classes: these should now be available.
i had a similar problem but I believe I sorted it. If you can get someone to send you their 'templates' folder (i just put my one from my old laptop on googledrive), then go to lyx, go preferences, go paths, and then set the path to go to the location of your new templates folder. I then restarted it and it worked! Hope it helps :)
I am working on installing collective.sendaspdf on a Plone 4.2.4 server.
This add-on provides two extra document action buttons, one "Send as PDF" and the other "View as PDF"
After following instructions on the packages pypi page. I get the following traceback when trying to click one of the aformentioned document action links:
Exception AttributeError: AttributeError("'_DummyThread' object has no attribute
'_Thread__block'",) in <module 'threading' from '/home/dan/Plone/Python-2.7/lib/python2.7
/threading.pyc'> ignored
2013-02-13 14:04:50 ERROR collective.sendaspdf Running wkhtmltopdf failed. Please check that you
use a version compatible with your OS and the version is 0.9.
Exception AttributeError: AttributeError("'_DummyThread' object has no attribute
'_Thread__block'",) in <module 'threading' from '/home/dan/Plone/Python-2.7/lib/python2.7
/threading.pyc'> ignored
2013-02-13 14:05:55 ERROR collective.sendaspdf Running wkhtmltopdf failed. Please check that you
use a version compatible with your OS and the version is 0.9.
I have tried pinning wkhtmltopdf to the version it requires, under the [versions] heading but that has done nothing for me. I have tried just loading the collective.sendaspdf alone under the eggs section but again, that doesn't work either. I have tried manually downloading them, putting them into my src folder and configuring the develop section accordingly, but that again gives me the same error. I've even tried easy_install but I get the same problems.
The instructions on the pypi page can't be followed to the letter as I believe the url under the [wkhtmltopdf] heading leads to a corrupted archive (i can't use tar, gzip or bunzip2 to extract the files) however he does have zip files contaning the source I have tried manually downloading and using easy_install) but to no avail.
I've been researching the
ERROR collective.sendaspdf Running wkhtmltopdf failed. Please check that you
use a version compatible with your OS and the version is 0.9.
Error message that I'm getting but I don't seem to see any Plone users having difficulty, it seems most people are using this with Rails.
Does anyone know how I can:
Get this to work
Find an alternative way of converting HTML from Plone to a PDF.
I have tried Form2PDF, zopyx.smartpringng, and now collective.sendaspdf (this one I have gotten the furthest with) - except it is falling at the last hurdle
Thanks.
I fear you've failed at the first hurdle: installing wkhtmltopdf. Either visit https://code.google.com/p/wkhtmltopdf/ and follow their instructions for installation, or look there to find the URL for a version compatible with your system
I'm working on getting knitr setup. I installed the latest version of R (2.15.1), Lyx 2.0 including the MiKTex 2.9 distribution, and RStudio 0.96.304 on a Windows 7 Enterprise box. I can get pdflatex output if I open up Lyx and simply view the tutorial, so the basic system is working. I then downloaded the minimal Rnw example saved it in my working directory as testknitr.Snw, opened that file in RStudio, and pressed the compile PDF button. The knitr output completes with a single warning about the parser package, and produces a file testknitr.tex. pdflatex.exe then runs, but fails, and the particular error in the log file seems to be
! LaTeX Error: Environment alltt undefined.
I received the same error when attempting to compile testknitr.tex using TexWorks. I created that file from inside R using knit("testknitr.Rnw") - different extension because of the default in RStudio. I did tell MikTek to update packages automatically when compiling. A bit of research on CTAN suggests that the alltt environment is part of the ltxbase package, which is installed when I look at the package manager. In fact it seems like a pretty core part of the whole thing!
OK - I was reading the comments on the minimal example page, and discovered a workaround to that problem, and that it is a known bug as of 19 hours ago. And yes, I doublechecked that RStudio is set to use knitr, not sweave. I now get a new error:
! LaTeX Error: Command \textquotesingle unavailable in encoding T1.
EDIT: OK! it turns out that error isn't fatal - there's a lovely pdf of the minimal example sitting in the working directory if one takes the time to look. Somewhat alarming that RStudio thinks compilation failed when it didn't?
The workaround, perhaps obvious to an experience LaTex-ie, is to add
\usepackage{alltt}
to the file. According to Yihui's comment this will be fixed in future versions, or now if you want to get the development version from github. I also tested #Yihui's comment above that the line
\usepackage[T1]{fontenc}
could be commented out. This fixes the 2nd issue in the question, and RStudio now treats the compilation as successful, cleaning up (some?) intermediate files and immediately previewing the pdf.