I am new to posting in the stack overflow community so I am sorry if this the wrong place. I have recently downloaded the newest version of R (4.2.1.) and Rstudio (2022.07.1 Build 554). I was testing out an older previous document that knitted perfectly using the 'papaja' package and now a code chunk will not work (that worked previously) and provides this error message:
Error in compileCode(f, code, language = language, verbose = verbose) :
C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file425c5d805023.o:file425c5d805023.cpp:(.text$_ZN3tbb8internal26task_scheduler_observer_v3D0Ev[_ZN3tbb8internal26task_scheduler_observer_v3D0Ev]+0x1d): undefined reference to tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file425c5d805023.o:file425c5d805023.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x1d): undefined reference to tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file425c5d805023.o:file425c5d805023.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x3a): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'C:\rtools42\x86_64-w64-mingw32.static.posix\bin/ld.exe: file425c5d805023.o:file425c5d805023.cpp:(.text$_ZN3tbb10interface
Error in sink(type = "output") : invalid connection
I have the rtools42 and this worked with my previous version of R and Rstudio so I am not sure how to fix this. Help!
There are problems with the compatibility of R4.2, RTools42 and Rstan. For me, it worked to install the preview of rstan 2.26.x:
Remove an existing rstan:
remove.packages("rstan")
if (file.exists(".RData")) file.remove(".RData")
Install preview version of packages:
install.packages("StanHeaders", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
install.packages("rstan", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
You can verify your installation with the example model:
example(stan_model, package = "rstan", run.dontrun = TRUE)
References:
rstan/wiki/Configuring-C---Toolchain-for-Windows
rstan/wiki/RStan-Getting-Started
rstan-fit-error
Related
I need biomaRT but it is not installing. How do I fix this?
BiocManager::install("biomaRt")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://mirror.las.iastate.edu/CRAN
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10)
Warning message:
package(s) not installed when version(s) same as current; use force = TRUE to re-install: 'biomaRt'
This doesn't look like an error. The relevant part of the message is
package(s) not installed when version(s) same as current; use force = TRUE to re-install: 'biomaRt'
Essentially, this is saying "You've already got the biomaRt package installed and it's the same version as in Bioconductor, so you don't need to do anything."
You should be able to load biomaRt with: library(biomaRt).
I am trying to use package glmmTMB. When I call library(glmmTMB) this is the error message:
">library(glmmTMB)
Error: package or namespace load failed for ‘glmmTMB’ in inDL(x, as.logical(local), as.logical(now), ...):
function 'Rcpp_precious_remove' not provided by package 'Rcpp'
In addition: Warning messages:
1: package ‘glmmTMB’ was built under R version 4.0.5
2: In checkMatrixPackageVersion() :
Package version inconsistency detected.
TMB was built with Matrix version 1.3.4
Current Matrix version is 1.2.18
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
I have tried using install.packages('TMB', type = 'source') with no luck. Any ideas?
It's a FAQ -- search for 'Rcpp_precious_remove' not provided by package 'Rcpp'.
In short you are mixing a NEWER compilatio nof something that was built with Rcpp 1.0.7 present with an older installed version which lacks the symbol.
Fix: install.packages("Rcpp") to get the newer Rcpp. And I generally recommend regular update.packages() runs to avoid these issues.
I am attempting to set up a new Stack project on NixOS with GHCJS as the compiler following the instructions at http://docs.haskellstack.org/en/stable/ghcjs.html
I have included in my stack.yaml file the following lines of code (all on one line because tab spaces seem to give issues):
# Compiler specifying the GHCJS compiler for this project (using improved base).
compiler: ghcjs-0.2.0.20151230.3_ghc-7.10.2
compiler-check: match-exact
setup-info:
ghcjs: source:
ghcjs-0.2.0.20151230.3_ghc7.10.2:
url: "https://github.com/nrolland/ghcjs/releases/download/v.0.2.0.20151230.3/ghcjs-0.2.0.20151230.3.tar.gz"
and I have retrieved the following error message when I ran stack setup
Could not parse '/home/lorkaan/pandocJS/stack.yaml':
InvalidYaml (Just (YamlParseException {yamlProblem = "mapping values are not allowed in this context", yamlContext = "", yamlProblemMark = YamlMark {yamlIndex = 487, yamlLine = 12, yamlColumn = 17}}))
See https://github.com/commercialhaskell/stack/blob/release/doc/yaml_configuration.md.
Additionally, I tried removing the setup-info field because Stack was complaining about it, leaving my stack.yaml file like:
# Compiler specifying the GHCJS compiler for this project (using improved base).
compiler: ghcjs-0.2.0.20151230.3_ghc-7.10.2
compiler-check: match-exact
which produces this output with the stack setup command:
Warning: /home/lorkaan/pandocJS/stack.yaml: Unrecognized field in ProjectAndConfigMonoid: compiler
Preparing to install GHC to an isolated location.
This will not interfere with any system-level installation.
Already downloaded.
The following executables are missing and must be installed: make
Does anybody have any idea why this would be happening?
the first error is because of a basic syntax error in your YAML configuration. The correct version would be:
setup-info:
ghcjs:
source:
ghcjs-0.2.0.20151230.3_ghc7.10.2:
url: "https://github.com/nrolland/ghcjs/releases/download/v.0.2.0.20151230.3/ghcjs-0.2.0.20151230.3.tar.gz"
The second error is because of exactly what it says: you are lacking the make utility. You need to use your Linux distribution's package management system to install make. Since I don't know which distribution you are on, I can only recommend simply executing the $ make command and seeing if the environment is smart enough to point out which package it can be found in. Ubuntu typically does that. Then it's only a matter of apt-get install-ing the package, or possibly yum install-ing on e.g. CentOS and Fedora, etc.
P.S. questions like yours normally get a downvote for not having shown sufficient effort in diagnosing the problem (or for putting 2 totally separate problems under a single question) but I'm giving you the benefit of the doubt and just hoping you'll be tidier next time.
I'm integrating C check framework for my project and I was able to run
autoreconf --install
successfully without any errors.
But when I integrate the C check framework, I'm getting an error and warnings that doesn't make sense.
Here is the error I'm getting
src/Makefile.am:7: warning: variable 'main_LDADD' is defined but no program or
src/Makefile.am:7: library has 'main' as canonical name (possible typo)
tests/Makefile.am:2: error: 'SHELLTESTS_PROGRAMS' is used but 'SHELLTESTSdir' is undefined
tests/Makefile.am:3: warning:variable 'ShellTests_SOURCES' is defined but no program or
tests/Makefile.am:3: library has 'ShellTests' as canonical name (possible typo)
tests/Makefile.am:5: warning: variable ShellTests_LDADD' is defined but no program or
tests/Makefile.am:5:library has 'ShellTests' as canonical name (possible typo)
autoreconf:automake failed with exit status: 1
I've followed the C check example source code, the difference between that and my project is that my class uses other class' methods.
Anyways, this is the Makefile.am under my tests/ that is causing 'havoc' on building the project
TESTS = shelltests
SHELLTESTS_PROGRAMS = shelltests
ShellTests_SOURCES = ShellTests.c $(top_builddir)/src/Shell.h $(top_builddir)/src/Parser.h $(top_builddir)/src/JobControl.h
ShellTests_CFLAGS = #CHECK_CFLAGS#
ShellTests_LDADD = $(top_builddir)/src/libshell.la #CHECK_LIBS#
This is the file structure for my project
src -
Parser.h, Parser.c, Shell.h, Shell.c, Job.h, Job.c, Makefile.am
tests -
ShellTests.c Makefile.am
And this is the code in Makefile.am under src.
lib_LTLIBRARIES = libshell.la
libshell_la_SOURCES = Shell.c Shell.h Parser.h Parser.c JobControl.h JobControl.c
bin_programs = main
main_sources = Main.c
main_LDADD = libshell.la
I followed this user's advice to see if it removes the error: What directory should I use for "error: 'extra_PROGRAMS' is used but 'extradir' is undefined"?
Alas, it does not.
I've tried building the example project - the one that you get when you download under examples, to see if I'm missing anything. But it's not able to build on my machine.
I'm on Mac OS X Mavericks (10.9)
Autoconf 2.69
Automake 1.15
Libtool 2.4.6
Check 0.9.14
I did a couple of things to build this project successfully. I first followed what I outlined here: Check framework example giving me error when running './configure'
Then I followed c check frameworks' naming conventions for the tests source files.
Thanks for the help guys, it gave me some ideas on what the cause of compilation errors.
this is Ajit.
I tried downloading the trial version of monotouch from the website but all the links were broken.
So I downloaded the following by digging from google.
()MonoDevelop-3.0.3.5
()MonoFramework-MRE-2.10.9_11.macos10.xamarin.x86.dmg
(*)Monotouch-eval-5.1.0.pkg
but after doing so when I run a sample ios app from the xamarin website only then it fails to build -> not being able to compile to native code.
This is error log.
Building Solution: HelloWorld_iPhone (Debug|iPhoneSimulator)
Building: HelloWorld_iPhone (Debug|iPhoneSimulator)
Performing main compilation...
/Developer/MonoTouch/usr/bin/smcs /noconfig "/out:/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/bin/iPhoneSimulator/Debug/HelloWorld_iPhone.exe" "/r:/Developer/MonoTouch/usr/lib/mono/2.1/System.dll" "/r:/Developer/MonoTouch/usr/lib/mono/2.1/System.Xml.dll" "/r:/Developer/MonoTouch/usr/lib/mono/2.1/System.Core.dll" "/r:/Developer/MonoTouch/usr/lib/mono/2.1/monotouch.dll" /nologo /warn:4 /debug:full /optimize- /codepage:utf8 "/define:DEBUG" /t:exe "/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/Main.cs" "/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/AppDelegate.cs" "/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/HelloWorld_iPhoneViewController.cs" "/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/HelloWorld_iPhoneViewController.designer.cs"
Copying content files
Copying '/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/Images/Icons/57_icon.png' to '/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/bin/iPhoneSimulator/Debug/HelloWorld_iPhone.app/57_icon.png'
Copying '/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/Images/Icons/114_icon.png' to '/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/bin/iPhoneSimulator/Debug/HelloWorld_iPhone.app/114_icon.png'
Copying '/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/Images/Icons/72_icon.png' to '/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/bin/iPhoneSimulator/Debug/HelloWorld_iPhone.app/72_icon.png'
Copying '/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/Images/Icons/29_icon.png' to '/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/bin/iPhoneSimulator/Debug/HelloWorld_iPhone.app/29_icon.png'
Copying '/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/Images/Icons/58_icon.png' to '/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/bin/iPhoneSimulator/Debug/HelloWorld_iPhone.app/58_icon.png'
Copying '/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/Images/Icons/50_icon.png' to '/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/bin/iPhoneSimulator/Debug/HelloWorld_iPhone.app/50_icon.png'
Build complete -- 0 errors, 0 warnings
Compiling to native code
/Developer/MonoTouch/usr/bin/mtouch -v --nomanifest --nosign -sim "/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/bin/iPhoneSimulator/Debug/HelloWorld_iPhone.app" -r "/Developer/MonoTouch/usr/lib/mono/2.1/System.dll" -r "/Developer/MonoTouch/usr/lib/mono/2.1/System.Xml.dll" -r "/Developer/MonoTouch/usr/lib/mono/2.1/System.Core.dll" -r "/Developer/MonoTouch/usr/lib/mono/2.1/monotouch.dll" -debug -nolink -sdk "5.1" "/Users/PBSK/Desktop/HelloWorld_iPhone/HelloWorld_iPhone/bin/iPhoneSimulator/Debug/HelloWorld_iPhone.exe"
This feature is not supported in the evaluation version
No gcc compiler found!
mtouch exited with code 1
---------------------- Done ----------------------
Build: 1 error, 0 warnings
Xcode version is 4.4 and Mac version is 10.7.4.
-Thanks!
but all the links were broken
Please email support#xamarin.com if you have any issues with the website.
Monotouch-eval-5.1.0.pkg
This is an pretty old, beta version of MonoTouch.
MonoTouch 5.2.12 is the current stable release while 5.3.5 is the current unstable release.
No gcc compiler found
This means no C compiler was found. In general you should make sure your MonoDevelop preferences (SDK Locations) are set the point to your Xcode installation directory.
However in this case I think your MonoTouch version is too old to work with Xcode 4.4. Updating your evaluation version to 5.2.12 is the first step you should try to fix this.
Below is the manual installation for MonoTouch evaluation which FINALLY works!:
Download and install packages listed below, in the order given:
1) Mono: http://download.mono-project.com/archive/2.10.9/macos-10-x86/10/MonoFramework-MDK-2.10.9_10.macos10.xamarin.x86.dmg
2) MonoDevelop: http://download.xamarin.com/monodevelop/Mac/MonoDevelop-3.0.dmg
3) Eval MonoTouch: http://download.xamarin.com/priv/d6d0ad447c01dd2bbbbbba829f6e1a/MonoTouch/Mac-eval/monotouch-eval-5.2.11.pkg
For the above mentioned environment this combination works like magic.
Just hope that they'll fix the broken links on their site too or else many other newbies would continue to get discouraged.
Thanks to support people of Xamarin who shared these links.