I'm updating the renv folder from a project in order to adjust the libraries, but it seems I'm having a permission problem. After running renv::init() and trying to installing manually the remaining libraries using install.packages() I always get the message
Error: failed to retrieve 'https://cran.rstudio.com/bin/windows/contrib/4.2/ipeadatar_0.1.6.zip' [error code 23]
1: curl: (23) Failure writing output to destination
2: curl: (23) Failure writing output to destination
Using .libPath() I can see that the renv was created in the "AppData" hidden folder
1] "C:/Users/André Ferreira/AppData/Local/R/cache/R/renv/library/MacroBRA_Wrld-09789847/R-4.2/x86_64-w64-mingw32"
So checking my permissions, I couldn't see anything wrong. Any thoughts about this problem? The thing it's that when I open my .Rmd file and try to knit, I receive the same message "1: curl: (23) Failure writing output to destination", now from rmarkdown retrieve installation, so it may be a configuration/permission problem.
Adding "C:\rtools42\usr\bin" and "C:\Program Files\R\R-4.2.1\bin" in the environment variable didn't help.
As I could see, opening an empty file from rstudio, I could use install.packages() without problem.
Although this doesn't solve the problem directly, you can also instruct renv to use a different library path with something like:
# use a project-local library path
RENV_PATHS_LIBRARY = renv/library
in your project's .Renviron file. Depending on your environment, you might also consider placing the library path in an alternate location.
See https://rstudio.github.io/renv/articles/packages.html#r-cmd-build-and-the-project-library for more details.
Related
R CMD check packagename_0.1.1.tar.gz --as-cran produces a WARNING if badges are present in README.md. This causes consequences like travis CI to fail (since it treats warnings as errors)
Is there a workaround to get the check to pass without removing the badges?
Here is an example of the WARNING I see
* checking top-level files ... WARNING
Conversion of ‘README.md’ failed:
pandoc: Could not fetch https://www.r-pkg.org/badges/version/bigrquery
TlsExceptionHostPort (HandshakeFailed (Error_Misc "user error (unexpected type received. expecting handshake and got: Alert [(AlertLevel_Fatal,HandshakeFailure)])")) "www.r-pkg.org" 443
Related: pandoc: Could not fetch http://www.r-pkg.org/badges/version/package TlsExceptionHostPort (HandshakeFailed
This is a workaround to embed (static) badges in pages. They do not auto-update. The purpose is to avoid offline derived errors.
Take a look at readme files in:
https://gitlab.com/ferroao/idiogramFISH. This also handles errors while installing with devtools in windows, a process that does not have online connectivity (see vignette index.Rmd). Look at DESCRIPTION also if you want to see dependencies and vignette builders.
Generate the .md from the .Rmd (Rmarkdown).
Months on, I discovered the problem. When I installed anaconda, it changed the version of pandoc my system used - which pandoc should return something like /usr/local/bin/pandoc (and not like /Users/st/anaconda3/bin/pandoc).
In my case, I edited by .bash_profile to exclude ananconda, closed and reopened the terminal and everything worked. (I also reinstalled pandoc from here, but I don't think that had anything to do with fixing it - it did show me the default installation location though)
I am trying to build PhantomJS 2.0 on Windows from the c:\fastio\phantomjs\phantomjs directory. For some reason, the build process fails after a while, with 2 errors (see error message below):
1) It tries to access "C:fastiophantomjsphantomjssrcqtqtbasebinmoc.exe". Obviously, the backslash characters between directory names are somehow getting stripped away deep in the build process - possibly a mismatch between Windows-style "\" and Linux-style "/" (but this is only a guess).
2) There's another error, "Failed to read names from file: C:/fastio/phantomjs/phantomjs/src/qt/qtwebkit/Source/WebCore/mathml/mathtags.in".
If I remove sh.exe from the PATH, the build still gets to this point, and only error #2 appears, leading me to think that error #2 is the real problem here.
Here is the full error message (as far as I can tell this is happening while building WebKit):
sh: C:fastiophantomjsphantomjssrcqtqtbasebinmoc.exe: command not found
Failed to read names from file: C:/fastio/phantomjs/phantomjs/src/qt/qtwebkit/Source/WebCore/mathml/mathtags.in at C:/fastio/phantomjs/phantomjs/src/qt/qtwebkit/Source/WebCore/dom/make_names.pl line 315.
NMAKE : fatal error U1077: 'C:\Users\Eugene\AppData\Local\GitHub\PortableGit_c2ba306e536fdf878271f7fe636a147ff37326ad\bin\perl.EXE' : return code '0x7f'
Stop.
(By the way, I saw this question but I'm already past the issues described there, my error is happening later in the build process.)
How can I make this work?
Full logs below:
Console output:
http://pastebin.com/btMeNPz4
QT build log file build_qt_4-285-20-0859.log:
http://pastebin.com/LUEJz7E0
WebKit build log file build_webkit_4-285-20_0859.log:
http://pastebin.com/494TivXF
PhantomJS build log file build_phantomjs_4-285-20_0859.log:
Empty
Looks like I found the solution myself, here were my steps:
Remove as much as possible from the PATH leaving only the entries critical to the build process
Most importantly, remove all GitHub's git directories from the PATH
Install GIT separately (not from GitHub but from git-scm.com), add its cmd directory only (not its bin directory) to the PATH
Install ActivePerl separately, add it to the PATH
It's moving past the error I asked about with the steps above (still not sure if it will finish the build successfully, it's taking a while).
On "./configure" of an open source project I get:
user agent OS = Linux
./configure: line 13957: syntax error near unexpected token 0.9.3'
./configure: line 13957: GOBJECT_INTROSPECTION_CHECK(0.9.3)'
make: *** [config.status] Error 2
Ubuntu 12.04 package "gobject-introspection" and "libgirepository1.0-dev" are present. Removing the GOBJECT_INTROSPECTION_CHECK line allows configure to complete, but the project fails a dependency later.
How can I get past this configure step cleanly? Googling for this issue shows bugs filed against numerous OS projects for this same blocking issue, but the usual answer is "install gobject-introspection".
As the OP discovered on his own he had to install the gobject-introspection package to get the m4 macros that were being used.
The error message has the raw macro in it, as configure scripts are generated from configure.in/configure.ac files via m4/etc the fact that the raw macro is in the output file indicates that the macro did not get translated at generation time.
The gobject-introspection m4 files were apparently installed after autogen.sh (or equivalent) was run to generate the configure script. Re-running the autogen.sh script should regenerate the configure script and run the macro correctly.
I'm having trouble roxygenizing a package. It was last working several months ago and I haven't checked since, so not sure if a snippet of code I added broke it, if my system's configuration changed, or if roxygen2 changed.
I've tried calling it through devtools::document, in a --vanilla R sesssion with roxygen2::roxygenize('taRifx') from the directory above it, roxygenize('.') from the project base directory, tried running as root in case it was a permissions thing, etc.
Here's the RStudio version:
==> roxygenize('.', roclets=c('rd'))
* checking for changes ... ERROR
Error in file(con, "r") : cannot open the connection
Package code is here:
https://github.com/gsk3/taRifx
How do I fix this?
You'll need to change line 1242 of the Rfunctions.R file to #examples instead of #example. For proper formatting you'll also need to change the # in email addresses to ##.
I'm trying to get R (running on Windows) to download some packages from the Internet, but the download fails because I can't get it to correctly use the necessary proxy server. The output text when I try the Windows menu option Packages > Install package(s)... and select a CRAN mirror is:
> utils:::menuInstallPkgs()
--- Please select a CRAN mirror for use in this session ---
Warning: unable to access index for repository http://cran.opensourceresources.org/bin/windows/contrib/2.12
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.12
Error in install.packages(NULL, .libPaths()[1L], dependencies = NA, type = type) :
no packages were specified
In addition: Warning message:
In open.connection(con, "r") :
cannot open: HTTP status was '407 Proxy Authentication Required'
I know the address and port of the proxy, and I also know the address of the automatic configuration script. I don't know what the authentication is called, but when using the proxy (in a browser and some other applications), I enter a username and password in a dialog window that pops up.
To set the proxy, I tried each of the following:
Sys.setenv(http_proxy="http://proxy.example.com:8080")
Sys.setenv("http_proxy"="http://proxy.example.com:8080")
Sys.setenv(HTTP_PROXY="http://proxy.example.com:8080")
Sys.setenv("HTTP_PROXY"="http://proxy.example.com:8080")
For authentication, I similarly tried setting the http_proxy_user environment variable to:
ask
user:passwd
Leaving it untouched
Am I using the right commands in the right way?
You have two options:
Use --internet2 or setInternet2(TRUE) and set the proxy details in the control panel, in Internet Options
Do not use either --internet2 or setInternet2(FALSE), but specify the environment variables
EDIT: One trick is, you cannot change your mind between 1 and 2, after you have tried it in a session, i.e. if you run the command setInternet2(TRUE) and try to use it e.g. install.packages('reshape2'), should this fail, you cannot then call setInternet2(FALSE). You have to restart the R session.
As of R version 3.2.0, the setInternet2 function can set internet connection settings and change them within the same R session. No need to restart.
When using option 2, one way (which is nice and compact) to specify the username and password is http_proxy="http://user:password#proxy.example.com:8080/"
In the past, I have had most luck with option 2
If you want internet2 to be used everytime you use R you could add the following line to the Rprofile.site file which is located in R.x.x\etc\Rprofile.site
utils::setInternet2(TRUE)
I've solved my trouble editing the file .Renviron as documented in Proxy setting for R.
EDITED
The solutions based on the setInternet2 statement do not work with the recent R versions because setInternet2 is declared defunct.
I'm using the 4.2.1 (on Win 11Pro) while I never had any problems in previous versions .
So to solve the problem need to modify some config files in order to fix the proxy issue not only for packages installation but, in general, also to acced to a remote resource (ie. boundary maps in my case).
The question "Proxy setting for R" collect a lot of solutions. I've found that this one has solved both my problems (packages installation and remote resources) explaining step-by-step how to edit the file .Renviron
Other solutions based on the customization of the file Renviron.site for me doesn't work
install.packages("RCurl")
that will solve your problem.