Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error installing pdftools package on macOS Catalina with Fastr 20.3.0 #180

Open
hsselman opened this issue Feb 18, 2021 · 0 comments
Open
Labels

Comments

@hsselman
Copy link

hsselman commented Feb 18, 2021

I tried installing pdftools using default mirror in GraalVM + FastR 20.3.0. Trying to install on macOS Catalina 10.15.7.

Error installing pdftools:

> install.package('pdftools')
* installing *source* package ‘pdftools’ ...
** package ‘pdftools’ successfully unpacked and MD5 sums checked
** using staged installation
Found pkg-config cflags and libs!
Using PKG_CFLAGS=-I/usr/local/Cellar/poppler/0.74.0/include/poppler/cpp -I/usr/local/Cellar/poppler/0.74.0/include/poppler
Using PKG_LIBS=-L/usr/local/Cellar/poppler/0.74.0/lib -lpoppler-cpp
** libs
".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/bin/safe-forward-g++" -std=gnu++11 -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -I/usr/local/Cellar/poppler/0.74.0/include/poppler/cpp -I/usr/local/Cellar/poppler/0.74.0/include/poppler -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/lib/Rcpp/include" -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c RcppExports.cpp -o RcppExports.o
".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/bin/safe-forward-g++" -std=gnu++11 -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/include" -DNDEBUG -I/usr/local/Cellar/poppler/0.74.0/include/poppler/cpp -I/usr/local/Cellar/poppler/0.74.0/include/poppler -I".../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/lib/Rcpp/include" -O2 -DFASTR -DNO_GNUR  -fvisibility=hidden -fPIC  -O2  -DFASTR -DNO_GNUR  -c bindings.cpp -o bindings.o
.../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/bin/safe-forward-g++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names,-rpath,.../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/lib/,-undefined,dynamic_lookup -L.../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/lib -undefined dynamic_lookup -single_module -multiply_defined suppress -Wl,-rpath,.../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/lib/,-undefined,dynamic_lookup -L.../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/lib -o pdftools.so RcppExports.o bindings.o -L/usr/local/Cellar/poppler/0.74.0/lib -lpoppler-cpp
installing to .../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/lib/00LOCK-pdftools/00new/pdftools/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘pdftools’ in runHook(".onLoad", env, package.lib, package):
 .onLoad failed in loadNamespace() for 'pdftools', details:
  call: .Call("_pdftools_set_error_callback", PACKAGE = "pdftools")
  error: "_pdftools_set_error_callback" not available for .Call() for package "pdftools"
Error: loading failed
> bin/R --vm.version 
openjdk version "11.0.9" 2020-10-20
OpenJDK Runtime Environment GraalVM CE 20.3.0 (build 11.0.9+10-jvmci-20.3-b06)
OpenJDK 64-Bit Server VM GraalVM CE 20.3.0 (build 11.0.9+10-jvmci-20.3-b06, mixed mode, sharing)

Output of R built-in function sessionInfo().

> sessionInfo()
FastR version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin19.6.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   .../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/lib/libRblas.dylib
LAPACK: .../GraalVMWithFastR/20.3.0/graalvm-ce-java11-20.3.0/Contents/Home/languages/R/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     

loaded via a namespace (and not attached):
[1] tools_3.6.1

Do you have anymore suggestions on what I can do? Or is this a bug? I successfully installed GraalVM+FastR 20.3.0 and this package on an Ubuntu 20.04 docker container, so I am quite puzzled right now why it fails in macOS.

@hsselman hsselman added the bug label Feb 18, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

No branches or pull requests

1 participant