Hi, looking for assistance with an issue that’s got me baffled. Im unable to add pdftools package to R in my TLJH environment.
Other R packages have been installed e.g. devtools.
libpoppler-cpp-dev has been installed via terminal.
/opt/tljh/user/lib/R - rwx permissions granted to jupyterhub-users group
installing *source* package ‘pdftools’ ...
** package ‘pdftools’ successfully unpacked and MD5 sums checked
** using staged installation
Using PKG_CFLAGS=-I/usr/include/poppler/cpp -I/usr/include/poppler
Using PKG_LIBS=-lpoppler-cpp
** libs
using C++ compiler: ‘x86_64-conda-linux-gnu-c++ (conda-forge gcc 14.2.0-1) 14.2.0’
x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/opt/tljh/user/lib/R/include" -DNDEBUG -I/usr/include/poppler/cpp -I/usr/include/poppler -DSTRICT_R_HEADERS -DR_NO_REMAP -I'/opt/tljh/user/lib/R/library/Rcpp/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/tljh/user/include -I/opt/tljh/user/include -Wl,-rpath-link,/opt/tljh/user/lib -fvisibility=hidden -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/tljh/user/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=/opt/tljh/user=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o
x86_64-conda-linux-gnu-c++ -std=gnu++17 -I"/opt/tljh/user/lib/R/include" -DNDEBUG -I/usr/include/poppler/cpp -I/usr/include/poppler -DSTRICT_R_HEADERS -DR_NO_REMAP -I'/opt/tljh/user/lib/R/library/Rcpp/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/tljh/user/include -I/opt/tljh/user/include -Wl,-rpath-link,/opt/tljh/user/lib -fvisibility=hidden -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/tljh/user/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=/opt/tljh/user=/usr/local/src/conda-prefix -c bindings.cpp -o bindings.o
x86_64-conda-linux-gnu-c++ -std=gnu++17 -shared -L/opt/tljh/user/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/tljh/user/lib -Wl,-rpath-link,/opt/tljh/user/lib -L/opt/tljh/user/lib -o pdftools.so RcppExports.o bindings.o -lpoppler-cpp -L/opt/tljh/user/lib/R/lib -lR
/opt/tljh/user/bin/../lib/gcc/x86_64-conda-linux-gnu/14.2.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lpoppler-cpp: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [/opt/tljh/user/lib/R/share/make/shlib.mk:10: pdftools.so] Error 1
ERROR: compilation failed for package ‘pdftools’
* removing ‘/opt/tljh/user/lib/R/library/pdftools’
The downloaded source packages are in
‘/tmp/RtmpBQcq2n/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("pdftools") :
installation of package ‘pdftools’ had non-zero exit status
> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-conda-linux-gnu
Running under: Ubuntu 24.04.1 LTS
Matrix products: default
BLAS/LAPACK: /opt/tljh/user/lib/libopenblasp-r0.3.28.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.4.2 tools_4.4.2
