How to fix Blogdown::serve_site() timeout error? - r-markdown

I have tried the solutions I found online for this, but none of them seem to work...
Even after installing blogdown from github and updating hugo, I get a timeout error.
remotes::install_github('rstudio/blogdown')
blogdown::update_hugo()
That is, when I run blogdown::serve_site I get this error:
Launching the server via the command: C:\Users\Master\AppData\Roaming\Hugo\hugo.exe server --bind 127.0.0.1 -p 4321 --themesDir themes -t hugo-future-imperfect -D -F --navigateToChanged ERROR: The process "10244" not found. Error: It took more than 30 seconds to launch the server. There may be something wrong. The process has been killed. If the site needs more time to be built and launched, set options(blogdown.server.timeout) to a larger value.
Is there another way to fix this?
What is causing this error?
Thanks!

I have the same problem on Kubuntu 20.10. I installed latest blogdown and hugo serveral days ago. I have blogdown 0.21.47 and hugo 0.79.0 on Kubuntu. Finally, I found a method to fix it.
Close Rstudio
Open terminal
Enter directory of your website
Execute hugo server -D
Press Ctrl C to stop
Open Rstudio
Click Addin -> BLOGDOWN -> Serve Site
I don't know why it works or whether it works in your case. Please test it and let us know whether it works.

I am running into the same problem.
blogdown::serve_site()
wont work:
Error: It took more than 30 seconds to launch the server. An error might have occurred with hugo. You may run blogdown::build_site() and see if it gives more info. If the site is very large and needs more time to be built, set options(blogdown.server.timeout) to a larger value.
although blogdown::build_site() works smoothly. The blogdown::serve_site() function works fine for a newly created project/website.
For repository see here.
Not sure if it is a blogdown, hugo or academic theme issue.
sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)
Matrix products: default
locale:
[1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252
[3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C
[5] LC_TIME=Dutch_Netherlands.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] servr_0.20
loaded via a namespace (and not attached):
[1] Rcpp_1.0.5 rstudioapi_0.13 knitr_1.30 magrittr_2.0.1 mnormt_2.0.2 pbivnorm_0.6.0
[7] R6_2.5.0 rlang_0.4.9 tools_4.0.3 tmvnsim_1.0-2 xfun_0.19 htmltools_0.5.0
[13] yaml_2.2.1 digest_0.6.27 lavaan_0.6-7 bookdown_0.21 processx_3.4.5 later_1.1.0.1
[19] promises_1.1.1 ps_1.4.0 evaluate_0.14 rmarkdown_2.5 blogdown_0.21.50 compiler_4.0.3
[25] stats4_4.0.3 jsonlite_1.7.1 httpuv_1.5.4

I had the same problem on. Installing "go" (https://golang.org/doc/install) helped - this was missing after my clean install of big sur.

Related

how to compile Ignite application on CMake?

I did compile Ignite Application successfully.
but The Binary didn't work.
/tmp/tmp.Nw0IPD6ru3/cmake-build-debug-local-container/planet_engine: error while loading shared libraries: libjvm.so: cannot open shared object file: No such file or directory
how can I make to it work?
Also, I compiled C++ Examples successfully. such as ignite-compute-example.
and, I execute that but I got an error message.
An error occurred: JVM library is not found (did you set JAVA_HOME environment variable?)
and I using a nightly release version 2.8.0.20190213 because I couldn't build to version 2.7 in my environment.
I posted environment values down.
IGNITE_HOME=
TERM=xterm-256color
SHELL=/bin/bash
LIBRARY_PATH=/root/jre1.8.0_201/lib/amd64/server:/root/jre1.8.0_201/lib/amd64/
LC_NUMERIC=ko_KR.UTF-8
SSH_TTY=/dev/pts/0
JRE_HOME=/root/jre1.8.0_201
USER=root
LS_COLORS=rs=0:d...
LD_LIBRARY_PATH=/root/jre1.8.0_201/lib/amd64/server:/root/jre1.8.0_201/lib/amd64/
CLASS_PATH=/root/jdk-11.0.2/lib:
LC_TELEPHONE=ko_KR.UTF-8
MAIL=/var/mail/root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/root/jdk-11.0.2/bin
LC_IDENTIFICATION=ko_KR.UTF-8
JAVA_HOME=/root/jdk-11.0.2
LANG=en_US.UTF-8
LC_MEASUREMENT=ko_KR.UTF-8
JDK_HOME=/root/jdk-11.0.2/lib
SHLVL=1
HOME=/root
LOGNAME=root
LESSOPEN=| /usr/bin/lesspipe %s
LESSCLOSE=/usr/bin/lesspipe %s %s
LC_TIME=ko_KR.UTF-8
LC_NAME=ko_KR.UTF-8
_=/usr/bin/env
Thank you for reading. :)
I got it.
I am working on a docker container environment.
and therefore I am using remote build and debug with ssh and gdb.
finally, I found out why it couldn't find libjvm.so and why couldn't read environment values such as JAVA_HOME.
because it is working in gdb for now.
I confirmed that it is working when without gdb.
I will find a solution.
and, if I have been found, I will update the answer.
[Solved]
I share how I make solved that.
I was using an Oracle JDK-11 through source install.
but Ignite C++ client need something different with latest released jdk versions.
Ignite need a directory structure like this
JAVA_HOME/ (as JDK install directory)
- jre/
- lib/
- lib/
...
I solved by apt install openjdk-8-jdk.
openjdk-8-jdk have structure for what Ignite need.
i added JAVA_HOME, IGNITE_HOME, at /etc/environment.
It works finally.
but I got another problem. HAHA
I am so sad.
This also GDB problem..

Pabot - Unable to run parallel robotframework tests

So, I'm working on a robotframework test project, and the goal is to run several test suites in parallel. For this purpose, pabot was chosen as the solution. I am trying to implement it, but with little success.
My issue is: after installing Pabot (which, I might say, I did by cloning the project and running "setup.py install", instead of using pip, since the corporate proxy I'm behind has proven an obstacle I can't overcome), I created a new directory in the project tree, moved some suites there, and ran:
pabot --processes 2 --outputdir pabot_results Login*.robot
Doing so results in the following error message:
2018-10-10 10:27:30.449000 [PID:9676] [0] EXECUTING Suites.LoginAdmin
2018-10-10 10:27:30.449000 PID:400 EXECUTING Suites.LoginUser
2018-10-10 10:27:30.777000 PID:400 FAILED Suites.LoginUser
2018-10-10 10:27:30.777000 [PID:9676] [0] FAILED Suites.LoginAdmin
WARN: No output files in "pabot_results\pabot_results"
Output:
[ ERROR ] Reading XML source '' failed: invalid mode ('rb') or filename
Try --help for usage information.
Elapsed time: 0 minutes 0.578 seconds
Upon inspecting the stderr file that was generated, I have this message:
Traceback (most recent call last):
File "C:\Python27\Lib\site-packages\robotframework-3.1a2.dev1-py2.7.egg\robot\running\runner.py", line 22, in
from .context import EXECUTION_CONTEXTS
ValueError: Attempted relative import in non-package
Apparently, this has to do with something from the runner.py script, which, if I'm not mistaken, came with the installation of robotframework. Since manually modifying that script does not seem to me the optimal solution, my question is, what am I missing here? Did I forget to do anything while setting this up? Or is this an issue of compatibility between versions?
This project is using Maven as the tool to manage dependencies. The version I am running is 3.5.4. I am using a Windows 10, 64bit system; I have Python 2.7.14, and Robot Framework 3.1a2.dev1. The Pabot version is 0.44. Obviously, I added C:\Python27 and C:\Python27\Scripts to the PATH environment variable.
Edit: I am also using robotframework-maven-plugin version 1.4.0.8, if that happens to be relevant.
Edit 2: added the error messages in text format.
I believe I've come across an issue similar when setting up parallel execution on my machine. Firstly I would confirm that pabot is installed using pip show robotframework-pabot.
Then you should define the directory your results are going to using -d.
I then modified the name of the -o to Output.xml to make it easy to identify.
This is a copy of the code I use. Runs optimally with 8 processes
pabot --processes 8 -d results -o Output.xml Tests
Seems that you stumbled on a bug in the prerelease version of robot framework (3.1a2.dev1).
Please install a release version of robot framework. For example 3.0.4.
Just in case anyone happens to stumble upon this issue in the future:
Since I can't use pip, and I tried a good deal of workarounds that eventually made things more unstable, I ended up saving my project and removing everything Python-related from my system, so as to allow me to install everything from scratch. In a Windows 10, 64bit system, I used:
Python 2.7.14
wxPython 2.8.12.1, win64, unicode, for py27
setuptools 40.2.0 (to allow me to use the easy_install command)
Robot Framework 3.0.4
robotremoteserver 1.1
Selenium2Library 3.0.0
and Pabot version 0.45.
I might add that, when installing the Selenium2Library the way I described above, it eventually tries to download some things from the pip repositories - which, if you have a proxy, will cause you trouble. I solved this problem by browsing https://pypi.org/simple/selenium/, manually downloading the 2.53.6 .tar.gz file, then extracting it and running setup.py install on the command line.
PS: Ideally, though, anyone should be able to use proxy settings from the command line (--proxy http://user:password#server:port) to get pip and then use it; however, for some reason, probably related to network security configurations that I didn't want to lose time with, this didn't work in my case.

ERROR: Failed to build PhantomJS! Building Qt Base failed

I have Debian Linux(64-bit) in VirtualBox.
Ram: 8Gb (for Debian 4Gb)
CPU: i5-3470
If any other details are needed please tell me.
I have followed instructions written here, and here you can see the console log.
For some reason I am unable to to build phantomjs and I can't understand why its not working... Have searched a lot, but couldn't find any thread which would be about this error.
--- EDIT ---
When I executed this command:
./configure --with-openssl-includes=/usr/include/openssl-1.0/ --with-openssl-libraries=/usr/lib/openssl-1.0/
Output was this:
--with-openssl-includes=/usr/include/openssl-1.0/: invalid command-line switch
--with-openssl-libraries=/usr/lib/openssl-1.0/: invalid command-line switch
The output of the console has changed but I still get errors: https://pastebin.com/wbgi8syg
Looks like you are on stretch (or later) and that you are already aware of the libssl vs libssl1.0 case.
Therefore, if you don't have libssl-dev installed, this line will get you further:
python build.py --qt-config "-I /usr/include/openssl-1.0/ -L /usr/lib/openssl-1.0/"
If you already have it installed and my suggestion doesn't work, you can uninstall libssl-dev for the time to build phantomjs which will likely avoid having to play further with configuration related variables.

Error: could not find function "list_spark_kernels"

I'm following a tutorial to access spark from RStudio on Data Science Experience. However, a function listed in the tutorial is not available:
> list_spark_kernels()
Error: could not find function "list_spark_kernels"
I have the files config.yml and .Rprofile in my home folder:
> dir(all.files = TRUE)
[1] "." ".." ".pki" ".Rhistory" ".Rprofile"
[6] ".rstudio" "config.yml" "ibm-sparkaas-demos" "lost+found" "R"
I've also tried sourcing my .Rprofile but that did not work:
> source(".Rprofile")
> list_spark_kernels()
Error: could not find function "list_spark_kernels"
I tried the list_spark_kernels() function earlier today and it worked fine.
In case, anyone faces list_spark_kernels() not found.
Please remove.packages("sparklyr") from rstudio console and then restart rstudio.
Restart will reinstall sparklyr created for connecting to spark service.
Thanks,
Charles.

Installation of R-package "BH" not possible

I cannot install the R-package BH which I need only to install dplyr afterwards.
The download works but something is wrong with the processing afterwards, as there is no reaction or progress whatsoever. Installation of lubridate (and deinstallation of lubridate) in contrast worked smoothly without any problems.
My output is:
> install.packages("BH")
Installing package into ‘.../R/win-library/3.2’
(as ‘lib’ is unspecified)
versuche URL 'http://cran.univ-paris1.fr/bin/windows/contrib
/3.2/BH_1.58.0-1.zip'
Content type 'application/zip' length 13846684 bytes (13.2 MB)
downloaded 13.2 MB
and then nothing happens.
Any ideas what could be causing this behavior? Are there any prerequisites for the installation of BH?
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
BH, as a sizeable subset of Boost Headers is big, as in really big:
edd#max:~$ du -csm /usr/local/lib/R/site-library/BH/
111 /usr/local/lib/R/site-library/BH/
111 total
edd#max:~$
That is 111 megabytes.
You may simply have run our of patience if your Windows (network share ?) was slow in writing the files.
BH is also widely used by other CRAN packages, and there has not been a package on any of the platforms used by CRAN.
So I suggest you maybe place your R package library onto a local hard drive...
If you have an actual bug report, please consider filing an issue ticket against our BH package.
I had this problem -- there were two parts to my fix.
1/ Download the windows binary from CRAN and save to the hard disk. You then select the menu item: Packages >> Install package(s) from local files…
2/ Edit the utils:::unpackPkgZip function to increase the sleep time – so that my virus checker has time to scan it. To implement this, do the following:
trace(utils:::unpackPkgZip, edit=TRUE)
Look for the line Sys.sleep(0.5), toward the bottom of the body of the function; it's a big package so I went for Sys.sleep(10).
If you are still seeing the error: Warning: unable to move temporary installation, try a longer sleep period.
Note that you won't see the edit if you check utils:::unpackPkgZip; that is the unedited version, and it can be restored via untrace(utils:::unpackPkgZip).
So see the edited version, use body(utils:::unpackPkgZip).