Hi, I am trying to install "pdftools" package in R from source, however could not succeeded due to following error. Source file is downloaded from https://cran.r-project.org/web/packages/pdftools/index.html Appreciate for any pointer how to install it properly. I am using R version 3.2.1 (2015-06-18) The loading error : tar: Failed to set default locale During startup - Warning messages: 1: Setting LC_CTYPE failed, using "C" 2: Setting LC_TIME failed, using "C" 3: Setting LC_MESSAGES failed, using "C" 4: Setting LC_MONETARY failed, using "C" * installing *source* package 'pdftools' ... ** package 'pdftools' successfully unpacked and MD5 sums checked Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/local/Cellar/poppler/0.50.0/include/poppler/cpp -I/usr/local/Cellar/poppler/0.50.0/include/poppler Using PKG_LIBS=-L/usr/local/Cellar/poppler/0.50.0/lib -lpoppler-cpp ** libs llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/poppler/0.50.0/include/poppler/cpp -I/usr/local/Cellar/poppler/0.50.0/include/poppler -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/poppler/0.50.0/include/poppler/cpp -I/usr/local/Cellar/poppler/0.50.0/include/poppler -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -c bindings.cpp -o bindings.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/poppler/0.50.0/include/poppler/cpp -I/usr/local/Cellar/poppler/0.50.0/include/poppler -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -c init.cpp -o init.o llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o pdftools.so RcppExports.o bindings.o init.o -L/usr/local/Cellar/poppler/0.50.0/lib -lpoppler-cpp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded During startup - Warning messages: 1: Setting LC_CTYPE failed, using "C" 2: Setting LC_TIME failed, using "C" 3: Setting LC_MESSAGES failed, using "C" 4: Setting LC_MONETARY failed, using "C" Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs/pdftools.so': dlopen(/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs/pdftools.so, 6): Symbol not found: __ZN7poppler14version_stringEv Referenced from: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs/pdftools.so Expected in: flat namespace in /Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs/pdftools.so Error: loading failed Execution halted ERROR: loading failed * removing '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools' * restoring previous '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools'
Could not install Package:pdftools in Mac lion 10.7.5
7 messages · Christofer Bogaso, Jeroen Ooms
How did you install libpoppler? Such errors typically appear when you link to a shared library which was built with another (incompatible) compiler than the one you use for compiling R packages. Note that Mac lion 10.7.5 has been deprecated for 2 over two years; upgrading your OS is highly recommended. On Tue, Dec 27, 2016 at 7:05 PM, Christofer Bogaso
<bogaso.christofer at gmail.com> wrote:
Hi, I am trying to install "pdftools" package in R from source, however could not succeeded due to following error. Source file is downloaded from https://cran.r-project.org/web/packages/pdftools/index.html Appreciate for any pointer how to install it properly. I am using R version 3.2.1 (2015-06-18) The loading error : tar: Failed to set default locale During startup - Warning messages: 1: Setting LC_CTYPE failed, using "C" 2: Setting LC_TIME failed, using "C" 3: Setting LC_MESSAGES failed, using "C" 4: Setting LC_MONETARY failed, using "C" * installing *source* package 'pdftools' ... ** package 'pdftools' successfully unpacked and MD5 sums checked Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/local/Cellar/poppler/0.50.0/include/poppler/cpp -I/usr/local/Cellar/poppler/0.50.0/include/poppler Using PKG_LIBS=-L/usr/local/Cellar/poppler/0.50.0/lib -lpoppler-cpp ** libs llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/poppler/0.50.0/include/poppler/cpp -I/usr/local/Cellar/poppler/0.50.0/include/poppler -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/poppler/0.50.0/include/poppler/cpp -I/usr/local/Cellar/poppler/0.50.0/include/poppler -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -c bindings.cpp -o bindings.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/poppler/0.50.0/include/poppler/cpp -I/usr/local/Cellar/poppler/0.50.0/include/poppler -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -c init.cpp -o init.o llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o pdftools.so RcppExports.o bindings.o init.o -L/usr/local/Cellar/poppler/0.50.0/lib -lpoppler-cpp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded During startup - Warning messages: 1: Setting LC_CTYPE failed, using "C" 2: Setting LC_TIME failed, using "C" 3: Setting LC_MESSAGES failed, using "C" 4: Setting LC_MONETARY failed, using "C" Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs/pdftools.so': dlopen(/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs/pdftools.so, 6): Symbol not found: __ZN7poppler14version_stringEv Referenced from: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs/pdftools.so Expected in: flat namespace in /Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs/pdftools.so Error: loading failed Execution halted ERROR: loading failed * removing '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools' * restoring previous '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools'
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Hi, I have installed poppler as instructed in below site. However, not libpoppler. Let me know if I need to install libpoppler as well, in that case appreciate any pointer how should I install. I know my Mac version is old now, right now I am not in a position to get the most recent version. Thanks, http://macappstore.org/poppler/
On Tue, Dec 27, 2016 at 11:53 PM, Jeroen Ooms <jeroen.ooms at stat.ucla.edu> wrote:
How did you install libpoppler? Such errors typically appear when you link to a shared library which was built with another (incompatible) compiler than the one you use for compiling R packages. Note that Mac lion 10.7.5 has been deprecated for 2 over two years; upgrading your OS is highly recommended. On Tue, Dec 27, 2016 at 7:05 PM, Christofer Bogaso <bogaso.christofer at gmail.com> wrote:
Hi, I am trying to install "pdftools" package in R from source, however could not succeeded due to following error. Source file is downloaded from https://cran.r-project.org/web/packages/pdftools/index.html Appreciate for any pointer how to install it properly. I am using R version 3.2.1 (2015-06-18) The loading error : tar: Failed to set default locale During startup - Warning messages: 1: Setting LC_CTYPE failed, using "C" 2: Setting LC_TIME failed, using "C" 3: Setting LC_MESSAGES failed, using "C" 4: Setting LC_MONETARY failed, using "C" * installing *source* package 'pdftools' ... ** package 'pdftools' successfully unpacked and MD5 sums checked Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/local/Cellar/poppler/0.50.0/include/poppler/cpp -I/usr/local/Cellar/poppler/0.50.0/include/poppler Using PKG_LIBS=-L/usr/local/Cellar/poppler/0.50.0/lib -lpoppler-cpp ** libs llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/poppler/0.50.0/include/poppler/cpp -I/usr/local/Cellar/poppler/0.50.0/include/poppler -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -c RcppExports.cpp -o RcppExports.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/poppler/0.50.0/include/poppler/cpp -I/usr/local/Cellar/poppler/0.50.0/include/poppler -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -c bindings.cpp -o bindings.o llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/Cellar/poppler/0.50.0/include/poppler/cpp -I/usr/local/Cellar/poppler/0.50.0/include/poppler -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include" -fPIC -mtune=core2 -g -O2 -c init.cpp -o init.o llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o pdftools.so RcppExports.o bindings.o init.o -L/usr/local/Cellar/poppler/0.50.0/lib -lpoppler-cpp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs ** R ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded During startup - Warning messages: 1: Setting LC_CTYPE failed, using "C" 2: Setting LC_TIME failed, using "C" 3: Setting LC_MESSAGES failed, using "C" 4: Setting LC_MONETARY failed, using "C" Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs/pdftools.so': dlopen(/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs/pdftools.so, 6): Symbol not found: __ZN7poppler14version_stringEv Referenced from: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs/pdftools.so Expected in: flat namespace in /Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs/pdftools.so Error: loading failed Execution halted ERROR: loading failed * removing '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools' * restoring previous '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools'
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On Tue, Dec 27, 2016 at 7:27 PM, Christofer Bogaso
<bogaso.christofer at gmail.com> wrote:
I have installed poppler as instructed in below site. However, not libpoppler. Let me know if I need to install libpoppler as well, in that case appreciate any pointer how should I install.
No that's the same thing. It's difficult for me to debug this since you're using such an old version of OSX and R. Chances are poppler simply doesn't work on such an old system. But one thing you could try is manually installing the mavericks binary package. Download this file to your system: https://cran.r-project.org/bin/macosx/mavericks/contrib/3.2/pdftools_1.0.tgz And then install it in R using: install.packages('~/Downloads/pdftools_1.0.tgz', repos = NULL) If you're lucky it works :)
It giving below error :(
install.packages('/Users/ARR/pdftools_1.0.tgz', repos = NULL)
tar: Failed to set default locale
On Wed, Dec 28, 2016 at 12:35 AM, Jeroen Ooms <jeroen.ooms at stat.ucla.edu> wrote:
On Tue, Dec 27, 2016 at 7:27 PM, Christofer Bogaso <bogaso.christofer at gmail.com> wrote:
I have installed poppler as instructed in below site. However, not libpoppler. Let me know if I need to install libpoppler as well, in that case appreciate any pointer how should I install.
No that's the same thing. It's difficult for me to debug this since you're using such an old version of OSX and R. Chances are poppler simply doesn't work on such an old system. But one thing you could try is manually installing the mavericks binary package. Download this file to your system: https://cran.r-project.org/bin/macosx/mavericks/contrib/3.2/pdftools_1.0.tgz And then install it in R using: install.packages('~/Downloads/pdftools_1.0.tgz', repos = NULL) If you're lucky it works :)
On Tue, Dec 27, 2016 at 8:09 PM, Christofer Bogaso
<bogaso.christofer at gmail.com> wrote:
It giving below error :(
install.packages('/Users/ARR/pdftools_1.0.tgz', repos = NULL)
tar: Failed to set default locale
I think that is an unrelated problem on your system. See: http://stackoverflow.com/questions/3907719/how-to-fix-tar-failed-to-set-default-locale-error But if you didn't get any other error the installation might have succeeded? Try loading the package: library(pdftools) If that works you might be OK.
I fix one problem and another problem pops up. After fixing default locale, I am getting below error when I try loading pdftools :
install.packages('/Users/ARR/pdftools_1.0.tgz', repos = NULL)
library(pdftools)
Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs/pdftools.so': dlopen(/Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs/pdftools.so, 6): Symbol not found: ___exp10 Referenced from: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs/pdftools.so Expected in: /usr/lib/libSystem.B.dylib in /Library/Frameworks/R.framework/Versions/3.2/Resources/library/pdftools/libs/pdftools.so In addition: Warning message: package ?pdftools? was built under R version 3.2.5 Error: package or namespace load failed for ?pdftools?
On Wed, Dec 28, 2016 at 12:51 AM, Jeroen Ooms <jeroen.ooms at stat.ucla.edu> wrote:
On Tue, Dec 27, 2016 at 8:09 PM, Christofer Bogaso <bogaso.christofer at gmail.com> wrote:
It giving below error :(
install.packages('/Users/ARR/pdftools_1.0.tgz', repos = NULL)
tar: Failed to set default locale
I think that is an unrelated problem on your system. See: http://stackoverflow.com/questions/3907719/how-to-fix-tar-failed-to-set-default-locale-error But if you didn't get any other error the installation might have succeeded? Try loading the package: library(pdftools) If that works you might be OK.