I'm having a problem installing 'seqminer'
Please, help me if anyone recognize this problem or been through this.
gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
R version 3.2.5 (2016-04-14) -- "Very, Very Secure Dishes"
R_CPP_interface.cpp: In function ‘SEXPREC* getListElement(SEXP, const char*)’:
R_CPP_interface.cpp:37:8: error: ‘strcmp’ is not a member of ‘std’
R_CPP_interface.cpp:37:8: note: suggested alternative:
/usr/include/string.h:143:12: note: ‘strcmp’
make: *** [R_CPP_interface.o] error 1
ERROR: compilation failed for package ‘seqminer’
* removing ‘/usr/local/lib/R/site-library/seqminer’
* restoring previous ‘/usr/local/lib/R/site-library/seqminer’
The error seems to be related to this issue:
strcmp et. al. not a member of std?
Based on the answer there, possible solutions may include:
install and use an earlier version of gcc (<= 4.1)
download the source, edit R_CPP_interface.cpp to insert #include <cstring>, then install from the local source
I would also file an issue at the project Github repo.
Related
When I tried to install r package "osmdata" (or any other package) with command
install.packages("osmdata")
it failed with error
"GLIBCXX_3.4.29' not found (required by /home...R/x86_64-unknown-linux-gnu-library/4.2/00LOCK-osmdata/00new/osmdata/libs/osmdata.so)
host system is debian, r is installed using package manager Guix.
The error means: osmdata.so was compiled with g++ version 11.1.0 (ABI mapping of GLIBCXX to g++ version is documented here), but the version of libstdc++.so.6 installed on the system is older, and doesn't provide GLIBCXX_3.4.29.
You need to get a version of osmdata.so appropriate for your system, or you need to build it from source, or you need to update your libstdc++.so.6.
P.S. Your question has nothing to do with glibc.
I solved it by installing package r-guix-install from Guix package manager and using this command
guix.install::guix.install("osmdata")
I'd like to keep my OS, R, and R packages up to date. I unknowingly treaded into deep water by upgrading to OSX 10.15.6 and upgrading to R 4.0.2. Currently, Rcpp is failing to compile c++ code, which I believe is causing the CRAN installation for certain packages to fail (e.g. glmmTMB), and is also causing installations from source to fail. I'll describe what I've done and hopefully someone can elucidate a solution.
In a rough order, here's what I've done:
Installed OSX 10.15.6
I don't remember the date but it was fairly recent. I don't know how closely this is related to the problem, I was having issues installing other R packages (e.g. rstan) that needed Rcpp prior to this.
Ran into an issue trying to run some old glmmTMB models
The exact error was identical to this issue. I followed the various solutions on that thread to no avail. Perhaps the most frustrating was when attempting to install from source, which then failed to compile some c++.
This wasn't the first time I had seen similar errors. Something similar happened when I tried installing rstan, so I asked for some help on their repo under a similar issue. Nothing helped.
This was on R 3.6, so I thought maybe it'd be worth updating R and glmmTMB. Before doing this I wanted to install Xcode, as opposed to just the Command Line Developer Tools, in hopes that the installation would ensure I'd have everything clang- and c++ compiler-related squared away.
Installed Xcode to help set a baseline c++ environment
Relatively painless, am able to build and compile fairly simple c++ projects.
Installed R 4.0.2
From the r-project site, I installed R-4.0.2.pkg without issues and with the default install settings. According to the R project Tools site, I was reassured in installing Xcode and continued on to install the GNU Fortran 8.2 installer.
Followed #coatless's guide to installing Rcpp
Discovered this guide and followed each step, except for those related to xcode-select.
Testing Rcpp and RcppArmadillo from the guide
One of the last steps is to test the installation with a simple helloworld.cpp test. This fails with this error (abridged for clarity):
> Rcpp::sourceCpp("~/Documents/BergenLab/nlp_cancer_metaphor/helloworld.cpp")
In file included from helloworld.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadillo.h:31:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include/RcppArmadilloForward.h:26:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/RcppCommon.h:29:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/r/headers.h:67:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/platform/compiler.h:100:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:317:9: error: no member named 'signbit' in the global namespace
using ::signbit;
~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [helloworld.o] Error 1
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include" -I"/Users/alex/Documents/BergenLab/nlp_cancer_metaphor" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c helloworld.cpp -o helloworld.o
Error in Rcpp::sourceCpp("~/Documents/BergenLab/nlp_cancer_metaphor/helloworld.cpp") :
Error 1 occurred building shared library.
Tried to debug Rcpp to no avail
Found some somewhat related reports, such as Packages cannot build from source due to math.h not found, Rcpp doesn't under macOS, math.h not found, Source Cpp file failed due to math.h not found, and Cannot compile R packages with c++ code after updating to macOS Catalina.
None of the solutions in these answers have helped at all. The only solution which gave me feedback was using installer to install macOS_SDK_headers_for_macOS_10.14.pkg which subsequently gave me installer: Error - the package path specified was invalid (not sure how what the implications of this are).
Installing glmmTMB from source fails
One of the solutions from an above glmmTMB issue recommends installing from source. Here is the error on my attempt:
* installing *source* package ‘glmmTMB’ ...
** package ‘glmmTMB’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/TMB/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -c glmmTMB.cpp -o glmmTMB.o
In file included from glmmTMB.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/TMB/include/TMB.hpp:53:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Dense:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppEigen/include/Eigen/Core:96:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/complex:245:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/cmath:317:9: error: no member named 'signbit' in the global namespace
using ::signbit;
~~^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
13 warnings and 20 errors generated.
make: *** [glmmTMB.o] Error 1
ERROR: compilation failed for package ‘glmmTMB’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/glmmTMB’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/glmmTMB’
Warning in install.packages :
installation of package ‘glmmTMB’ had non-zero exit status
Overall, I'm still unable to run my glmmTMB models (and I presume unable to build rstan as well). Something with my c++ compiler must be off but I'm a c++ beginner and am unsure how to interpret the errors I'm getting. Something's wrong with the header files, but it seems perhaps like it's not due to math.h being missing (like most other posts). It should go without saying but any help would be greatly appreciated!
Edit 1
I've tried to narrow down the error and thus followed each step from #coatless's guide, exactly as listed there and according to the R installation documentation. My exact steps:
Removed gfortran 8.2. Removed ~/.Renviron and ~/.R/Makevars. Unlinked both of these files from Rstudio with unlink().
Ran xcode-select --install, which returned with "use "Software Update" to install updates." Accordingly, softwareupdate --list estimated that nothing needed updating. Regardless, I uninstalled Command Line Tools with sudo rm -rf /Library/Developer/CommandLineTools and installed the Command Line Tools with xcode-select —install. Up to this point everything is working as expected. Small c++ programs are being compiled without issue by both gcc and clang++.
According to the R manual, from https://mac.r-project.org/libs-4/, I installed pcre2-10.34-darwin.17-x86_64.tar.gz, xz-5.2.4-darwin.17-x86_64.tar.gz , and readline-5.2.14-darwin.17-x86_64.tar.gz to /usr/local. No big issues here, although I'm not really sure how to verify that these work as expected.
Restarted an R session in RStudio.
Installed Rcpp and RcppArmadillo with install.packages(c(‘Rcpp’, ‘RcppArmadillo’))
Created a ~/helloworld.cpp with the code from Slide 15 mentioned in the comments.
Running Rcpp::sourceCpp("~/helloworld.cpp") fails with the exact error as mentioned in the body of the post. Similarly evalCpp() fails with a similar error.
After a bit of digging, the issue turned out to be neither glmmTMB, Rcpp, or really anything high-level. From what I understand: When R uses Rcpp to compile c++ code, a certain set of arguments are passed to the system c++ compiler. In my case this compiler was clang++ since I had just installed Xcode. The c++ compiler relies on a set of c++ header files to be included in exactly the right order. Seemed like the order of mine were incorrect, thus causing a slew of errors regarding "missing template definitions."
I looked into changing the order of the includes but couldn't find any straightforward solution. I knew that Rcpp was calling a very specific array of arguments to clang++, so I looked into how that might elucidate an answer. I looked into the manuals for clang++ to figure out what -isysroot and -I meant and felt like they might play a part in reconfiguring how the system header files were being compiled. From one of the threads below I discovered the $(R RHOME)/etc/Makeconf Makefile and proceeded to change the directory of the OSX SDK from what I believe was the Command Line Tools path to the Xcode path. This seemed to solve the issue.
Some threads I used to find this solution: Cannot compile R packages with c++ code after updating to macOS Catalina and Catalina C++: Using <cmath> headers yield error: no member named 'signbit' in the global namespace.
What worked for me:
Note the current header file search
From clang++ -Wp,-v -E -:
#include <...> search starts here:
/usr/local/include
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/11.0.3/include
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks (framework directory)
Note the OSX SDK path
From xcrun --show-sdk-path:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk
Modify the R configuration
With vim $(R RHOME)/etc/Makeconf, changed the CPPFLAGS flag to:
CPPFLAGS = -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk -I/usr/local/include
Notice how this SDK directory is what was found in step 2. This apparently cleans up the location and order of the SDK header file includes.
Reinstall glmmTMB from source
I was still seeing a FreeADFunObject error when trying to fit a glmmTMB model, so I went back to this GH thread and followed the first suggestion: to reinstall from source. This wasn't working before since I needed a properly set up c++ configuration, which I fixed in the last two steps.
Hence, install.packages("glmmTMB", type="source") installed without issue and I can now build and fit glmmTMB models.
For posterity's sake:
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
In any R package I try to install, I get the following error message:
ld: library not found for -lintl
collect2: error: ld returned 1 exit status
make: *** [utf8.so] Error 1
I'm not sure how to make this a reprex, but I am running:
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin19.5.0 (64-bit)
Running under: macOS Catalina 10.15.5
What does this error message (ld: library not found for -lintl) mean and how can I fix it to be able to install R packages (the packages I have tried are texreg and lme4)? Thank you.
Edit: I apologize, I thought I had included this with my post. I am not missing gettext (as per Link error installing Rcpp "library not found for -lintl"), and I followed the instructions to export the LPDFLAGS and CPPFLAGS so that they are linked.
As best I can tell, the problem is the ~/.R/Makevars file, which currently looks like this, where I've commented out things I've added to it based on googling.
CC=/usr/local/Cellar/gcc/9.3.0_1/bin/gcc-9
CXX=/usr/local/Cellar/gcc/9.3.0_1/bin/g++-9
CXX11=/usr/local/Cellar/gcc/9.3.0_1/bin/g++-9
CXX14=/usr/local/Cellar/gcc/9.3.0_1/bin/g++-9
cxx17=/usr/local/cellar/gcc/9.3.0_1/bin/g++-9
cxx1X=/usr/local/cellar/gcc/9.3.0_1/bin/g++-9
LDFLAGS=-L/usr/local/Cellar/gcc/9.3.0_1/lib
#FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0
#CC=/usr/local/clang4/bin/clang
#CXX=/usr/local/clang4/bin/clang++
#CXX1X=/usr/local/clang4/bin/clang++
#CXX98=/usr/local/clang4/bin/clang++
#CXX11=/usr/local/clang4/bin/clang++
#CXX14=/usr/local/clang4/bin/clang++
#CXX17=/usr/local/clang4/bin/clang++
#LDFLAGS=-L/usr/local/clang4/lib
Apparently, I needed to remove all the lines from ~/.R/Makevars and I was able to install lme4. I did get some warnings, but library(lme4) works.
If you're using a mac with an Apple Silicon chip (like the M1), then you can try adding this to ~/.R/Makevars:
CFLAGS=-I/opt/homebrew/include
CPPFLAGS=-I/opt/homebrew/include
CXXFLAGS=-I/opt/homebrew/include
CXX11FLAGS=-I/opt/homebrew/include
LDFLAGS=-L/opt/homebrew/lib
This allows R to find the needed libraries. You will need to first ensure you have the needed compilers and dependencies installed. You can usually do this with brew.
I am using a Linux system x86_64-redhat-linux-gnu-library with a CentOS server.
The R version is 3.4.1
When installing the package "pdftools" I get the following error :
Error in .shlib_internal(args) :
C++11 standard requested but CXX11 is not defined
Has anyone encountered the problem?
Doing the following worked for me:
Under /usr/lib64/R/etc there are 2 Makeconf files:
Makeconf
Makeconf.rpmnew
Backup the 'Makeconf' file and replace it with the contents of 'Makeconf.rpmnew'
Found the solution here (wch's answer):
https://github.com/rstudio/httpuv/issues/82
I'm having trouble installing igraph on R 3.1.0 on OS X Mavericks with XCode 5.1.1. The error message I get is:
ld: illegal text-relocation to '___gmp_binvert_limb_table' in /usr/local/lib/libgmp.a(mp_minv_tab.o) from '___gmpn_divexact_1' in /usr/local/lib/libgmp.a(dive_1.o) for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [igraph.so] Error 1
ERROR: compilation failed for package ‘igraph’
Looking around, I found that I'm not the only one to have this issue and it's not limited to igraph (here and here), but adding CXXFLAGS=-Wno-error=unused-command-line-argument-hard-error-in-future to ~/.R/Makevars didn't help. From the error message, it looks like R found the system installation of GMP and not the Macports version, which could conceivably have been built for a different architecture. (Installing from binaries also didn't work for me, with an error message of image not found, but it looks like this is a separate issue.) Has anyone else encountered similar issues?
sessionInfo() gives:
R version 3.1.0 (2014-04-10)
Platform: x86_64-apple-darwin13.0.2 (64-bit)
Thanks in advance!
In case this is helpful to anyone else, here is the solution from Gabor Csardi that worked for me: Try with the binary distribution of R. I had built R from source, and that version didn't work with installing igraph from either source or binary.