Unable to complete pdftools installation Ubuntu 18.04 for R supporting readtext
I read the post How install poppler and was hopeful regarding my own difficulty, but no dice.
I am running R under Anaconda on a Ubuntu 18.04 Precision laptop. I wanted to install readtext (R package) to support some corpora linguistics study and attempted that from R terminal window. I had already installed quanteda without a problem so was surprised when readtext tripped on a pdftools requirement which in turn tripped
cannot find -lpoppler-cppI had already installed and uninstalled libpoppler-cpp-dev several times using
sudo apt-get install -y libpoppler-cpp-devThat installed ok
libpoppler-cpp-dev is already the newest version (0.74.0-bionic0)When I attempt the readtext install from R (again, running under Anaconda, which might be problem), it arrives at the pdftools install and finds the local pkg-config info
- 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/include/poppler/cpp -I/usr/include/poppler Using PKG_LIBS=-lpoppler-cpp
But then cannot find it:
/home/dalton/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: cannot find -lpoppler-cpp collect2: error: ld returned 1 exit status make: *** [/home/dalton/anaconda3/lib/R/share/make/shlib.mk:6: pdftools.so] Error 1 ERROR: compilation failed for package ‘pdftools’
- removing ‘/home/dalton/anaconda3/lib/R/library/pdftools’
When I check pkg-config myself:
pkg-config --cflags --libs poppler-cpp-I/usr/include/poppler/cpp -I/usr/include/poppler -lpoppler-cpp
I indeed find the same information the installer in R finds. When I chased down poppler with a system grep:
ls --recursive | grep -E "poppler"I do not find poppler-cpp, though I find libpoppler-cpp-dev and other libpoppler-cpp files/folders. However, if I interrogate pkg-config:
pkg-config --cflags --libs libpoppler-cpp-devIt tells me
Package libpoppler-cpp-dev was not found in the pkg-config search path. Perhaps you should add the directory containing `libpoppler-cpp-dev.pc' to the PKG_CONFIG_PATH environment variable. No package 'libpoppler-cpp-dev' found.
I used the PPA with backports of Poppler 0.74.0 for Ubuntu 18.04 (Bionic) recommended by @jeroen in the cited SE post above, but it appears there is some confusion between the Ubuntu proper and Anaconda R, since the R install is looking for poppler-cpp, but libpoppler-cpp-dev seems to be the appropriate target. Because I am running R under Anaconda, my system seems unaware of R:
apt-cache policy r-base-corereturns
r-base-core: Installed: (none) Candidate: 3.4.4-1ubuntu1 Version table: 3.4.4-1ubuntu1 500 500 bionic/universe amd64 Packages
I realize this is all somewhat of a mess, but I am hoping someone will recognize an obvious problem and tell me what to hack up, e.g., modify the poppler-cpp.pc to point at the new library or the like.
31 Answer
The solution is to remain within the Anaconda/conda environment, since R is running there and this is a bit of an island within the surrounding Ubuntu sea (if the metaphor is not making you seasick). Just do
conda install -c conda-forge popplerThat took quite a while to finish, since the initial two attemtps to "solve the environment" failed, but conda finally tried another repodata source and succeeded:
package | build
---------------------------|-----------------
certifi-2019.9.11 | py37_0 147 KB conda-forge
conda-4.10.1 | py37h89c1867_0 3.1 MB conda-forge
openjpeg-2.3.1 | h21c5421_1 469 KB conda-forge
poppler-0.65.0 | h581218d_1 1.3 MB
poppler-data-0.4.10 | 0 3.8 MB conda-forge
python_abi-3.7 | 1_cp37m 4 KB conda-forge
------------------------------------------------------------ Total: 8.7 MBetc., ending with the blessed
Executing transaction: done
Then I opened a terminal window and started R:
dalton@dalton-Precision-3541:$ R
R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 The R Foundation for Statistical Computing Platform: x86_64-conda_cos6-linux-gnu (64-bit)
and installed pdftools:
> install.packages("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/include/poppler/cpp -I/usr/include/poppler Using PKG_LIBS=-lpoppler-cpp
etc. For those are interested, the Anaconda library files were in areas like
-lpoppler-cpp -L/home/dalton/anaconda3/lib/R/lib -lR
In other words, after the conda installation of poppler, my R install of pdftools could find poppler-cpp. pdftools completed:
** testing if installed package keeps a record of temporary installation path
- DONE (pdftools)
I then was able to complete my original task of installing readtext, which required poppler and pdftools:
install.packages("readtext")** testing if installed package keeps a record of temporary installation path
- DONE (readtext)
The downloaded source packages are in ‘/tmp/Rtmpxksozx/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done
library(readtext)
All is good with the world, the convoluted world of Anaconda/conda within Ubuntu. It is a great environment for scientific and academic computing, once you figure out how to communicate.
