Closed leungi closed 4 years ago
Same question as here: https://github.com/bnosac/udpipe/issues/20
keywords_phrases
uses C++11 <regex>
. <regex>
was implemented and released in GCC 4.9.0. So you need to make sure you have at least gcc 4.9.0 for this to work and once you have installed gcc >= 4.9.0 install the udpipe package again.
You can see which version of gcc you have on centos with gcc --version
See also https://stackoverflow.com/questions/12530406/is-gcc-4-8-or-earlier-buggy-about-regular-expressions
Thanks for prompt reply and pointers @jwijffels.
A new issue after upgrading gcc
and g++
- unable to re-install udpipe
as you suggested in #20.
[leungi@ohylpyt1-d ~]$ gcc --version
gcc (GCC) 4.9.3
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
[leungi@ohylpyt1-d ~]$ g++ -v
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/usr/local/gcc493/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../gcc-4.9.3/configure --prefix=/usr/local/gcc493 --program-suffix=49 --enable-languages=c,c++ --disable-libstdcxx-pch --disable-multilib
Thread model: posix
gcc version 4.9.3 (GCC)
[leungi@ohylpyt1-d ~]$ sudo R
[sudo] password for leungi:
Account with conflicting name (leungi) exists locally
R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> install.packages("udpipe")
* installing *source* package âudpipeâ ...
** package âudpipeâ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c rcpp_phrases.cpp -o rcpp_phrases.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c rcpp_udpipe.cpp -o rcpp_udpipe.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c udpipe.cpp -o udpipe.o
udpipe.cpp: In static member function âstatic bool ufal::udpipe::morphodita::gru_tokenizer_trainer::train(unsigned int, unsigned int, bool, unsigned int, unsigned int, unsigned int, float, float, float, float, bool, const std::vector<ufal::udpipe::morphodita::tokenized_sentence>&, const std::vector<ufal::udpipe::morphodita::tokenized_sentence>&, std::ostream&, std::string&)â:
udpipe.cpp:13510:80: error: âto_stringâ was not declared in this scope
return error.assign("Gru tokenizer dimension '").append(to_string(dimension)).append("' is not supported!"), false;
^
udpipe.cpp: In static member function âstatic void ufal::udpipe::parsito::parser_nn_trainer::train(const string&, const string&, bool, const string&, const string&, const ufal::udpipe::parsito::network_parameters&, unsigned int, const std::vector<ufal::udpipe::parsito::tree>&, const std::vector<ufal::udpipe::parsito::tree>&, ufal::udpipe::utils::binary_encoder&)â:
udpipe.cpp:16453:73: error: âto_stringâ was not declared in this scope
embeddings_from_file_comment = "[dim" + to_string(file_dimension) + "->" + to_string(dimension) + "]";
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::parsito::tree_input_format_conllu::next_tree(ufal::udpipe::parsito::tree&)â:
udpipe.cpp:17913:66: error: âto_stringâ was not declared in this scope
return error.assign("Node ID '").append(to_string(node.id)).append("' form '").append(node.form).append("' has too large head: '").append(to_string(node.head)).append("'!"), false;
^
udpipe.cpp: In member function âvirtual void ufal::udpipe::parsito::tree_output_format_conllu::write_tree(const ufal::udpipe::parsito::tree&, std::string&, const ufal::udpipe::parsito::tree_input_format*) constâ:
udpipe.cpp:17947:30: error: âto_stringâ was not declared in this scope
output.append(to_string(i)).push_back('\t');
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::input_format_conllu::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:18218:66: error: âto_stringâ was not declared in this scope
return error.assign("Node ID '").append(to_string(word.id)).append("' form '").append(word.form).append("' has too large head: '").append(to_string(word.head)).append("'!"), false;
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::input_format_horizontal::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:18314:42: error: âto_stringâ was not declared in this scope
s.set_sent_id(to_string(sentence_id++));
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::input_format_vertical::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:18404:42: error: âto_stringâ was not declared in this scope
s.set_sent_id(to_string(sentence_id++));
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::input_format_presegmented_tokenizer::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:18518:42: error: âto_stringâ was not declared in this scope
s.set_sent_id(to_string(sentence_id++));
^
udpipe.cpp: In member function âvoid ufal::udpipe::token::set_token_range(size_t, size_t)â:
udpipe.cpp:19369:58: error: âto_stringâ was not declared in this scope
start_misc_field("TokenRange").append(to_string(start)).append(1, ':').append(to_string(end));
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::morphodita_tokenizer_wrapper::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:19793:42: error: âto_stringâ was not declared in this scope
s.set_sent_id(to_string(sentence_id++));
^
udpipe.cpp: In static member function âstatic bool ufal::udpipe::trainer_morphodita_parsito::train_tagger(const std::vector<ufal::udpipe::sentence>&, const std::vector<ufal::udpipe::sentence>&, const string&, std::ostream&, std::string&)â:
udpipe.cpp:21133:61: error: âto_stringâ was not declared in this scope
model_name = "from_model_" + to_string(++model_index);
^
udpipe.cpp: In static member function âstatic bool ufal::udpipe::trainer_morphodita_parsito::train_parser(const std::vector<ufal::udpipe::sentence>&, const std::vector<ufal::udpipe::sentence>&, const string&, const string&, std::ostream&, std::string&)â:
udpipe.cpp:21194:100: error: âto_stringâ was not declared in this scope
if (embedding_upostag) embeddings.append("universal_tag ").append(to_string(embedding_upostag)).append(" 1\n");
^
udpipe.cpp:21195:88: error: âto_stringâ was not declared in this scope
if (embedding_feats) embeddings.append("feats ").append(to_string(embedding_feats)).append(" 1\n");
^
udpipe.cpp:21196:90: error: âto_stringâ was not declared in this scope
if (embedding_xpostag) embeddings.append("tag ").append(to_string(embedding_xpostag)).append(" 1\n");
^
udpipe.cpp:21198:67: error: âto_stringâ was not declared in this scope
embeddings.append("form ").append(to_string(embedding_form)).append(" ").append(to_string(embedding_form_mincount));
^
udpipe.cpp:21203:69: error: âto_stringâ was not declared in this scope
embeddings.append("lemma ").append(to_string(embedding_lemma)).append(" ").append(to_string(embedding_lemma_mincount));
^
udpipe.cpp:21207:91: error: âto_stringâ was not declared in this scope
if (embedding_deprel) embeddings.append("deprel ").append(to_string(embedding_deprel)).append(" 1\n");
^
make: *** [udpipe.o] Error 1
ERROR: compilation failed for package âudpipeâ
* removing â/usr/lib64/R/library/udpipeâ
* restoring previous â/usr/lib64/R/library/udpipeâ
The downloaded source packages are in
â/tmp/Rtmpp6V9ER/downloaded_packagesâ
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("udpipe") :
installation of package âudpipeâ had non-zero exit status
That looks like you have not compiled the package with C++11 support. Your log does not show g++ -std=c++11
but shows g++ -std=gnu++11
. Maybe because you have 2 compilers in your system and R knows only of the previous compiler (PKG_CXXFLAGS is probably pointing to your old compiler)
Thanks again for prompt reply @jwijffels.
I tried a few ideas from SO, but to no avail.
May you please guide how to point to desired compiler? 🙏
# trial 1
Sys.setenv("PKG_CXXFLAGS"="-g -std=c++11")
# trial 2
Sys.setenv("PKG_CXXFLAGS"="-std=c++11")
# trial 3
# adapted from {rstan} install
file.remove(M)
dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR)) dir.create(dotR)
M <- file.path(dotR, "Makevars")
file.remove(M)
if (!file.exists(M)) file.create(M)
cat("\nCXX14FLAGS=-O3 -march=native -mtune=native -fPIC",
"CXX14=g++ -std=c++11",
"CXX14FLAGS+= -std=c++11",
"CXX14STD='-std=c++11'", # or clang++ but you may need a version postfix
file = M, sep = "\n", append = TRUE)
Providing support in installing a recent compiler on Red Hat is a bit out-of-scope for this github issue. As you prefer to have 2 C++ compilers on your environment (/usr/local/gcc493 and your default location of g++), you will have to tell which one to use when you install udpipe. What you can do is set the right directives in ~/.R/Makevars. You can find out about these at https://stackoverflow.com/questions/43597632/understanding-the-contents-of-the-makevars-file-in-r-macros-variables-r-ma
Appreciate the pointers 👍
Keeping the 2 compilers wasn't my intention; I wished the older version was overwritten to avoid such headache!
Will close the loop once I confirmed upgrading udpipe
with gcc-4.9.0
solves the issue.
@jwijffels: useful SO guide that was 👍
Followed the guide and managed to set compiler of choice, but still compile error:
[leungi@ohylpyt1-d]$ which g++
/bin/g++
[leungi@ohylpyt1-d]$ cd /bin/
[leungi@ohylpyt1-d /bin]$ find . -maxdepth 1 -type l -ls | grep "g++"
71073498 0 lrwxrwxrwx 1 root root 14 Oct 16 07:51 ./g++ -> /usr/bin/g++49
71073708 0 lrwxrwxrwx 1 root root 25 Oct 16 07:34 ./g++49 -> ../local/gcc493/bin/g++49
> dotR <- file.path(Sys.getenv("HOME"), ".R")
> if (!file.exists(dotR)) dir.create(dotR)
> M <- file.path(dotR, "Makevars")
> if (!file.exists(M)) file.create(M)
[1] TRUE
> cat("\nCXX = g++",
+ "CXX11STD = -std=c++11",
+ file = M, sep = "\n", append = TRUE)
> readLines(M)
[1] ""
[2] "CXX = g++"
[3] "CXX11STD = -std=c++11"
> install.packages("udpipe")
Installing package into â/usr/lib64/R/libraryâ
trying URL 'https://cloud.r-project.org/src/contrib/udpipe_0.8.3.tar.gz'
Content type 'application/x-gzip' length 4750855 bytes (4.5 MB)
==================================================
downloaded 4.5 MB
* installing *source* package âudpipeâ ...
** package âudpipeâ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -m64 -std=c++11 -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
g++ -m64 -std=c++11 -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c rcpp_phrases.cpp -o rcpp_phrases.o
g++ -m64 -std=c++11 -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c rcpp_udpipe.cpp -o rcpp_udpipe.o
g++ -m64 -std=c++11 -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c udpipe.cpp -o udpipe.o
udpipe.cpp: In static member function âstatic bool ufal::udpipe::morphodita::gru_tokenizer_trainer::train(unsigned int, unsigned int, bool, unsigned int, unsigned int, unsigned int, float, float, float, float, bool, const std::vector<ufal::udpipe::morphodita::tokenized_sentence>&, const std::vector<ufal::udpipe::morphodita::tokenized_sentence>&, std::ostream&, std::string&)â:
udpipe.cpp:13510:80: error: âto_stringâ was not declared in this scope
return error.assign("Gru tokenizer dimension '").append(to_string(dimension)).append("' is not supported!"), false;
^
udpipe.cpp: In static member function âstatic void ufal::udpipe::parsito::parser_nn_trainer::train(const string&, const string&, bool, const string&, const string&, const ufal::udpipe::parsito::network_parameters&, unsigned int, const std::vector<ufal::udpipe::parsito::tree>&, const std::vector<ufal::udpipe::parsito::tree>&, ufal::udpipe::utils::binary_encoder&)â:
udpipe.cpp:16453:73: error: âto_stringâ was not declared in this scope
embeddings_from_file_comment = "[dim" + to_string(file_dimension) + "->" + to_string(dimension) + "]";
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::parsito::tree_input_format_conllu::next_tree(ufal::udpipe::parsito::tree&)â:
udpipe.cpp:17913:66: error: âto_stringâ was not declared in this scope
return error.assign("Node ID '").append(to_string(node.id)).append("' form '").append(node.form).append("' has too large head: '").append(to_string(node.head)).append("'!"), false;
^
udpipe.cpp: In member function âvirtual void ufal::udpipe::parsito::tree_output_format_conllu::write_tree(const ufal::udpipe::parsito::tree&, std::string&, const ufal::udpipe::parsito::tree_input_format*) constâ:
udpipe.cpp:17947:30: error: âto_stringâ was not declared in this scope
output.append(to_string(i)).push_back('\t');
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::input_format_conllu::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:18218:66: error: âto_stringâ was not declared in this scope
return error.assign("Node ID '").append(to_string(word.id)).append("' form '").append(word.form).append("' has too large head: '").append(to_string(word.head)).append("'!"), false;
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::input_format_horizontal::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:18314:42: error: âto_stringâ was not declared in this scope
s.set_sent_id(to_string(sentence_id++));
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::input_format_vertical::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:18404:42: error: âto_stringâ was not declared in this scope
s.set_sent_id(to_string(sentence_id++));
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::input_format_presegmented_tokenizer::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:18518:42: error: âto_stringâ was not declared in this scope
s.set_sent_id(to_string(sentence_id++));
^
udpipe.cpp: In member function âvoid ufal::udpipe::token::set_token_range(size_t, size_t)â:
udpipe.cpp:19369:58: error: âto_stringâ was not declared in this scope
start_misc_field("TokenRange").append(to_string(start)).append(1, ':').append(to_string(end));
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::morphodita_tokenizer_wrapper::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:19793:42: error: âto_stringâ was not declared in this scope
s.set_sent_id(to_string(sentence_id++));
^
udpipe.cpp: In static member function âstatic bool ufal::udpipe::trainer_morphodita_parsito::train_tagger(const std::vector<ufal::udpipe::sentence>&, const std::vector<ufal::udpipe::sentence>&, const string&, std::ostream&, std::string&)â:
udpipe.cpp:21133:61: error: âto_stringâ was not declared in this scope
model_name = "from_model_" + to_string(++model_index);
^
udpipe.cpp: In static member function âstatic bool ufal::udpipe::trainer_morphodita_parsito::train_parser(const std::vector<ufal::udpipe::sentence>&, const std::vector<ufal::udpipe::sentence>&, const string&, const string&, std::ostream&, std::string&)â:
udpipe.cpp:21194:100: error: âto_stringâ was not declared in this scope
if (embedding_upostag) embeddings.append("universal_tag ").append(to_string(embedding_upostag)).append(" 1\n");
^
udpipe.cpp:21195:88: error: âto_stringâ was not declared in this scope
if (embedding_feats) embeddings.append("feats ").append(to_string(embedding_feats)).append(" 1\n");
^
udpipe.cpp:21196:90: error: âto_stringâ was not declared in this scope
if (embedding_xpostag) embeddings.append("tag ").append(to_string(embedding_xpostag)).append(" 1\n");
^
udpipe.cpp:21198:67: error: âto_stringâ was not declared in this scope
embeddings.append("form ").append(to_string(embedding_form)).append(" ").append(to_string(embedding_form_mincount));
^
udpipe.cpp:21203:69: error: âto_stringâ was not declared in this scope
embeddings.append("lemma ").append(to_string(embedding_lemma)).append(" ").append(to_string(embedding_lemma_mincount));
^
udpipe.cpp:21207:91: error: âto_stringâ was not declared in this scope
if (embedding_deprel) embeddings.append("deprel ").append(to_string(embedding_deprel)).append(" 1\n");
^
make: *** [udpipe.o] Error 1
ERROR: compilation failed for package âudpipeâ
* removing â/usr/lib64/R/library/udpipeâ
* restoring previous â/usr/lib64/R/library/udpipeâ
The downloaded source packages are in
â/tmp/Rtmpnx42Mk/downloaded_packagesâ
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("udpipe") :
installation of package âudpipeâ had non-zero exit status
Did you set the exact location of CXX11 in your makevars file (e.g. your local/gcc493/bin/g++49 path)
@jwijffels , thanks for your continued support.
I tried your suggestion to explicitly set g++49
path, but still no go. I also tried with c++49
, which is available in /usr/local/gcc493/bin
, but same outcome.
[leungi@ohylpyt1-d bin]$ pwd
/usr/local/gcc493/bin
[leungi@ohylpyt1-d bin]$ ls -ls
total 3280
800 -rwxr-xr-x. 1 root root 816792 Nov 20 2017 c++49
800 -rwxr-xr-x. 1 root root 815128 Nov 20 2017 cpp49
800 -rwxr-xr-x. 1 root root 816792 Nov 20 2017 g++49
796 -rwxr-xr-x. 1 root root 814104 Nov 20 2017 gcc49
28 -rwxr-xr-x. 1 root root 25184 Nov 20 2017 gcc-ar49
28 -rwxr-xr-x. 1 root root 25120 Nov 20 2017 gcc-nm49
28 -rwxr-xr-x. 1 root root 25120 Nov 20 2017 gcc-ranlib49
[leungi@ohylpyt1-d bin]$ R
> dotR <- file.path(Sys.getenv("HOME"), ".R")
> if (!file.exists(dotR)) dir.create(dotR)
> M <- file.path(dotR, "Makevars")
> if (!file.exists(M)) file.create(M)
[1] TRUE
> cat("\nCXX11 = /usr/local/gcc493/bin/g++49", "CXX11STD = -std=c++11", file = M, sep = "\n", append = TRUE)
> readLines(M)
[1] "" "CXX11 = /usr/local/gcc493/bin/g++49"
[3] "CXX11STD = -std=c++11"
> install.packages("udpipe")
Installing package into â/usr/lib64/R/libraryâ
(as âlibâ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/udpipe_0.8.3.tar.gz'
Content type 'application/x-gzip' length 4750855 bytes (4.5 MB)
==================================================
downloaded 4.5 MB
* installing *source* package âudpipeâ ...
** package âudpipeâ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/usr/local/gcc493/bin/g++49 -std=c++11 -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
/usr/local/gcc493/bin/g++49 -std=c++11 -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c rcpp_phrases.cpp -o rcpp_phrases.o
/usr/local/gcc493/bin/g++49 -std=c++11 -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c rcpp_udpipe.cpp -o rcpp_udpipe.o
/usr/local/gcc493/bin/g++49 -std=c++11 -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c udpipe.cpp -o udpipe.o
udpipe.cpp: In static member function âstatic bool ufal::udpipe::morphodita::gru_tokenizer_trainer::train(unsigned int, unsigned int, bool, unsigned int, unsigned int, unsigned int, float, float, float, float, bool, const std::vector<ufal::udpipe::morphodita::tokenized_sentence>&, const std::vector<ufal::udpipe::morphodita::tokenized_sentence>&, std::ostream&, std::string&)â:
udpipe.cpp:13510:80: error: âto_stringâ was not declared in this scope
return error.assign("Gru tokenizer dimension '").append(to_string(dimension)).append("' is not supported!"), false;
^
udpipe.cpp: In static member function âstatic void ufal::udpipe::parsito::parser_nn_trainer::train(const string&, const string&, bool, const string&, const string&, const ufal::udpipe::parsito::network_parameters&, unsigned int, const std::vector<ufal::udpipe::parsito::tree>&, const std::vector<ufal::udpipe::parsito::tree>&, ufal::udpipe::utils::binary_encoder&)â:
udpipe.cpp:16453:73: error: âto_stringâ was not declared in this scope
embeddings_from_file_comment = "[dim" + to_string(file_dimension) + "->" + to_string(dimension) + "]";
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::parsito::tree_input_format_conllu::next_tree(ufal::udpipe::parsito::tree&)â:
udpipe.cpp:17913:66: error: âto_stringâ was not declared in this scope
return error.assign("Node ID '").append(to_string(node.id)).append("' form '").append(node.form).append("' has too large head: '").append(to_string(node.head)).append("'!"), false;
^
udpipe.cpp: In member function âvirtual void ufal::udpipe::parsito::tree_output_format_conllu::write_tree(const ufal::udpipe::parsito::tree&, std::string&, const ufal::udpipe::parsito::tree_input_format*) constâ:
udpipe.cpp:17947:30: error: âto_stringâ was not declared in this scope
output.append(to_string(i)).push_back('\t');
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::input_format_conllu::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:18218:66: error: âto_stringâ was not declared in this scope
return error.assign("Node ID '").append(to_string(word.id)).append("' form '").append(word.form).append("' has too large head: '").append(to_string(word.head)).append("'!"), false;
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::input_format_horizontal::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:18314:42: error: âto_stringâ was not declared in this scope
s.set_sent_id(to_string(sentence_id++));
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::input_format_vertical::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:18404:42: error: âto_stringâ was not declared in this scope
s.set_sent_id(to_string(sentence_id++));
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::input_format_presegmented_tokenizer::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:18518:42: error: âto_stringâ was not declared in this scope
s.set_sent_id(to_string(sentence_id++));
^
udpipe.cpp: In member function âvoid ufal::udpipe::token::set_token_range(size_t, size_t)â:
udpipe.cpp:19369:58: error: âto_stringâ was not declared in this scope
start_misc_field("TokenRange").append(to_string(start)).append(1, ':').append(to_string(end));
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::morphodita_tokenizer_wrapper::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:19793:42: error: âto_stringâ was not declared in this scope
s.set_sent_id(to_string(sentence_id++));
^
udpipe.cpp: In static member function âstatic bool ufal::udpipe::trainer_morphodita_parsito::train_tagger(const std::vector<ufal::udpipe::sentence>&, const std::vector<ufal::udpipe::sentence>&, const string&, std::ostream&, std::string&)â:
udpipe.cpp:21133:61: error: âto_stringâ was not declared in this scope
model_name = "from_model_" + to_string(++model_index);
^
udpipe.cpp: In static member function âstatic bool ufal::udpipe::trainer_morphodita_parsito::train_parser(const std::vector<ufal::udpipe::sentence>&, const std::vector<ufal::udpipe::sentence>&, const string&, const string&, std::ostream&, std::string&)â:
udpipe.cpp:21194:100: error: âto_stringâ was not declared in this scope
if (embedding_upostag) embeddings.append("universal_tag ").append(to_string(embedding_upostag)).append(" 1\n");
^
udpipe.cpp:21195:88: error: âto_stringâ was not declared in this scope
if (embedding_feats) embeddings.append("feats ").append(to_string(embedding_feats)).append(" 1\n");
^
udpipe.cpp:21196:90: error: âto_stringâ was not declared in this scope
if (embedding_xpostag) embeddings.append("tag ").append(to_string(embedding_xpostag)).append(" 1\n");
^
udpipe.cpp:21198:67: error: âto_stringâ was not declared in this scope
embeddings.append("form ").append(to_string(embedding_form)).append(" ").append(to_string(embedding_form_mincount));
^
udpipe.cpp:21203:69: error: âto_stringâ was not declared in this scope
embeddings.append("lemma ").append(to_string(embedding_lemma)).append(" ").append(to_string(embedding_lemma_mincount));
^
udpipe.cpp:21207:91: error: âto_stringâ was not declared in this scope
if (embedding_deprel) embeddings.append("deprel ").append(to_string(embedding_deprel)).append(" 1\n");
^
make: *** [udpipe.o] Error 1
ERROR: compilation failed for package âudpipeâ
* removing â/usr/lib64/R/library/udpipeâ
* restoring previous â/usr/lib64/R/library/udpipeâ
The downloaded source packages are in
â/tmp/RtmpM14MzT/downloaded_packagesâ
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("udpipe") :
installation of package âudpipeâ had non-zero exit status
Have you also tried with CXX11STD = -std=c++0x
Thanks for prompt reply; still no go.
Once again, I tried various options of CXX11
- g++
, /usr/local/gcc493/bin/c++49
- with same outcome.
> dotR <- file.path(Sys.getenv("HOME"), ".R")
> if (!file.exists(dotR)) dir.create(dotR)
> M <- file.path(dotR, "Makevars")
> file.remove(M)
[1] TRUE
> if (!file.exists(M)) file.create(M)
[1] TRUE
> cat("\nCXX11 = /usr/local/gcc493/bin/g++49", "CXX11STD = -std=c++0x", file = M, sep = "\n", append = TRUE)
> readLines(M)
[1] "" "CXX11 = /usr/local/gcc493/bin/g++49"
[3] "CXX11STD = -std=c++0x"
> install.packages("udpipe")
Installing package into â/usr/lib64/R/libraryâ
(as âlibâ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/udpipe_0.8.3.tar.gz'
Content type 'application/x-gzip' length 4750855 bytes (4.5 MB)
==================================================
downloaded 4.5 MB
* installing *source* package âudpipeâ ...
** package âudpipeâ successfully unpacked and MD5 sums checked
** using staged installation
** libs
/usr/local/gcc493/bin/g++49 -std=c++0x -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
/usr/local/gcc493/bin/g++49 -std=c++0x -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c rcpp_phrases.cpp -o rcpp_phrases.o
/usr/local/gcc493/bin/g++49 -std=c++0x -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c rcpp_udpipe.cpp -o rcpp_udpipe.o
/usr/local/gcc493/bin/g++49 -std=c++0x -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c udpipe.cpp -o udpipe.o
udpipe.cpp: In static member function âstatic bool ufal::udpipe::morphodita::gru_tokenizer_trainer::train(unsigned int, unsigned int, bool, unsigned int, unsigned int, unsigned int, float, float, float, float, bool, const std::vector<ufal::udpipe::morphodita::tokenized_sentence>&, const std::vector<ufal::udpipe::morphodita::tokenized_sentence>&, std::ostream&, std::string&)â:
udpipe.cpp:13510:80: error: âto_stringâ was not declared in this scope
return error.assign("Gru tokenizer dimension '").append(to_string(dimension)).append("' is not supported!"), false;
^
udpipe.cpp: In static member function âstatic void ufal::udpipe::parsito::parser_nn_trainer::train(const string&, const string&, bool, const string&, const string&, const ufal::udpipe::parsito::network_parameters&, unsigned int, const std::vector<ufal::udpipe::parsito::tree>&, const std::vector<ufal::udpipe::parsito::tree>&, ufal::udpipe::utils::binary_encoder&)â:
udpipe.cpp:16453:73: error: âto_stringâ was not declared in this scope
embeddings_from_file_comment = "[dim" + to_string(file_dimension) + "->" + to_string(dimension) + "]";
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::parsito::tree_input_format_conllu::next_tree(ufal::udpipe::parsito::tree&)â:
udpipe.cpp:17913:66: error: âto_stringâ was not declared in this scope
return error.assign("Node ID '").append(to_string(node.id)).append("' form '").append(node.form).append("' has too large head: '").append(to_string(node.head)).append("'!"), false;
^
udpipe.cpp: In member function âvirtual void ufal::udpipe::parsito::tree_output_format_conllu::write_tree(const ufal::udpipe::parsito::tree&, std::string&, const ufal::udpipe::parsito::tree_input_format*) constâ:
udpipe.cpp:17947:30: error: âto_stringâ was not declared in this scope
output.append(to_string(i)).push_back('\t');
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::input_format_conllu::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:18218:66: error: âto_stringâ was not declared in this scope
return error.assign("Node ID '").append(to_string(word.id)).append("' form '").append(word.form).append("' has too large head: '").append(to_string(word.head)).append("'!"), false;
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::input_format_horizontal::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:18314:42: error: âto_stringâ was not declared in this scope
s.set_sent_id(to_string(sentence_id++));
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::input_format_vertical::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:18404:42: error: âto_stringâ was not declared in this scope
s.set_sent_id(to_string(sentence_id++));
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::input_format_presegmented_tokenizer::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:18518:42: error: âto_stringâ was not declared in this scope
s.set_sent_id(to_string(sentence_id++));
^
udpipe.cpp: In member function âvoid ufal::udpipe::token::set_token_range(size_t, size_t)â:
udpipe.cpp:19369:58: error: âto_stringâ was not declared in this scope
start_misc_field("TokenRange").append(to_string(start)).append(1, ':').append(to_string(end));
^
udpipe.cpp: In member function âvirtual bool ufal::udpipe::morphodita_tokenizer_wrapper::next_sentence(ufal::udpipe::sentence&, std::string&)â:
udpipe.cpp:19793:42: error: âto_stringâ was not declared in this scope
s.set_sent_id(to_string(sentence_id++));
^
udpipe.cpp: In static member function âstatic bool ufal::udpipe::trainer_morphodita_parsito::train_tagger(const std::vector<ufal::udpipe::sentence>&, const std::vector<ufal::udpipe::sentence>&, const string&, std::ostream&, std::string&)â:
udpipe.cpp:21133:61: error: âto_stringâ was not declared in this scope
model_name = "from_model_" + to_string(++model_index);
^
udpipe.cpp: In static member function âstatic bool ufal::udpipe::trainer_morphodita_parsito::train_parser(const std::vector<ufal::udpipe::sentence>&, const std::vector<ufal::udpipe::sentence>&, const string&, const string&, std::ostream&, std::string&)â:
udpipe.cpp:21194:100: error: âto_stringâ was not declared in this scope
if (embedding_upostag) embeddings.append("universal_tag ").append(to_string(embedding_upostag)).append(" 1\n");
^
udpipe.cpp:21195:88: error: âto_stringâ was not declared in this scope
if (embedding_feats) embeddings.append("feats ").append(to_string(embedding_feats)).append(" 1\n");
^
udpipe.cpp:21196:90: error: âto_stringâ was not declared in this scope
if (embedding_xpostag) embeddings.append("tag ").append(to_string(embedding_xpostag)).append(" 1\n");
^
udpipe.cpp:21198:67: error: âto_stringâ was not declared in this scope
embeddings.append("form ").append(to_string(embedding_form)).append(" ").append(to_string(embedding_form_mincount));
^
udpipe.cpp:21203:69: error: âto_stringâ was not declared in this scope
embeddings.append("lemma ").append(to_string(embedding_lemma)).append(" ").append(to_string(embedding_lemma_mincount));
^
udpipe.cpp:21207:91: error: âto_stringâ was not declared in this scope
if (embedding_deprel) embeddings.append("deprel ").append(to_string(embedding_deprel)).append(" 1\n");
^
make: *** [udpipe.o] Error 1
ERROR: compilation failed for package âudpipeâ
* removing â/usr/lib64/R/library/udpipeâ
* restoring previous â/usr/lib64/R/library/udpipeâ
The downloaded source packages are in
â/tmp/RtmpjnFp4l/downloaded_packagesâ
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("udpipe") :
installation of package âudpipeâ had non-zero exit status
The best is to look on stackoverflow on the error you are getting namely to_string was not declared in this scope
. It looks like your compiler does not support C++11. I don't have a redhat system to test myself.
Noted.
Just checked a few SO posts, and all points to your suggestion - CXX11STD = -std=c++0x
.
Will keep researching, and update here.
Thanks again.
Update.
I got a new VM that comes with gcc
and g++
>4.9.0, and installed udpipe
fresh; however, still running into same issue.
[leungi@ohylpyt2-d ~]$ g++ -v
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ./configure --disable-multilib --enable-languages=c,c++
Thread model: posix
gcc version 4.9.2 (GCC)
[leungi@ohylpyt2-d ~]$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ./configure --disable-multilib --enable-languages=c,c++
Thread model: posix
gcc version 4.9.2 (GCC)
[leungi@ohylpyt2-d ~]$ R
R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(udpipe)
> packageVersion("udpipe")
[1] â0.8.3â
> data(brussels_reviews_anno, package = "udpipe")
> x <- subset(brussels_reviews_anno, language %in% "fr")
> keywords_phrases(x$xpos, pattern = c("DTNNVBRBJJ"), term = x$token, is_regex = T)
[1] keyword ngram pattern start end
<0 rows> (or 0-length row.names)
How the installation of udpipe was done depends on configuration settings of how you installed R. These setting are something you can retrieve with R CMD config --all
in the shell. And next you need to see if the installation trace of installaing the udpipe package has used your C++11 compiler which contains a recent version of <regex>
Thanks for tip! I'll update with progress.
I'm hitting a wall here.
I realized CXX11STD = -std=gnu++11
based on R CMD config --all
(below), hence I created a custom ~/.R/Makevars
.
I read in a couple of post that even with custom Makevars
, the package's /src/Makevars
takes precedence; I suspect this may be the case here.
[leungi@ohylpyt2-d ~]$ R CMD config --all
CC = gcc -m64 -std=gnu99
CFLAGS = -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic
CPICFLAGS = -fpic
CPP = gcc -m64 -std=gnu99 -E
CPPFLAGS = -I/usr/local/include
CXX = g++ -m64 -std=gnu++11
CXXCPP = g++ -m64 -std=gnu++11 -E
CXXFLAGS = -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic
CXXPICFLAGS = -fpic
CXX98 = g++ -m64
CXX98STD = -std=gnu++98
CXX98FLAGS = -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic
CXX98PICFLAGS = -fpic
CXX11 = g++ -m64
CXX11STD = -std=gnu++11
CXX11FLAGS = -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic
CXX11PICFLAGS = -fpic
CXX14 = g++ -std=c++1y
CXX14STD =
CXX14FLAGS = -O3 -march=native -mtune=native -fPIC -Wno-unused-variable -Wno-unused-function
CXX14PICFLAGS =
CXX17 =
CXX17STD =
CXX17FLAGS =
CXX17PICFLAGSS =
DYLIB_EXT = .so
DYLIB_LD = gcc -m64 -std=gnu99
DYLIB_LDFLAGS = -shared -fopenmp
FC = gfortran -m64
F77 = gfortran -m64
FFLAGS = -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -I/usr/lib64/gfortran/modules
FPICFLAGS = -fpic
FLIBS = -lgfortran -lm -lquadmath
FCFLAGS = -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic
FCPICFLAGS = -fpic
SAFE_FFLAGS = -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -I/usr/lib64/gfortran/modules -msse2 -mfpmath=sse
OBJC = gcc
OBJCFLAGS = -g -O2 -fobjc-exceptions
JAVA = /bin/java
JAVAC = /bin/javac
JAVAH = /bin/javah
JAR = /bin/jar
JAVA_HOME = /usr/lib/jvm/jre
JAVA_LIBS = -L/usr/lib/jvm/jre/lib/amd64/server -ljvm
JAVA_CPPFLAGS = -I/usr/lib/jvm/java/include -I/usr/lib/jvm/java/include/linux
LDFLAGS = -Wl,-z,relro
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = g++ -m64 -std=gnu++11
SHLIB_CXXLDFLAGS = -shared
SHLIB_CXX98LD = g++ -m64 -std=gnu++98
SHLIB_CXX98LDFLAGS = -shared
SHLIB_CXX11LD = g++ -m64 -std=gnu++11
SHLIB_CXX11LDFLAGS = -shared
SHLIB_CXX14LD = g++ -std=c++1y
SHLIB_CXX14LDFLAGS = -shared
SHLIB_CXX17LD =
SHLIB_CXX17LDFLAGS = -shared
SHLIB_EXT = .so
SHLIB_FFLAGS =
SHLIB_LD = gcc -m64 -std=gnu99
SHLIB_LDFLAGS = -shared
TCLTK_CPPFLAGS = -I/usr/include -I/usr/include
TCLTK_LIBS = -L/usr/lib64 -ltcl8.5 -L/usr/lib64 -ltk8.5 -lX11
BLAS_LIBS = -L/usr/lib64/R/lib -lRblas
LAPACK_LIBS = -L/usr/lib64/R/lib -lRlapack
MAKE = make
LIBnn = lib64
Installs with custom ~/.R/Makevars
are successfull, but still facing same issue.
Various installs
> dotR <- file.path(Sys.getenv("HOME"), ".R")
> if (!file.exists(dotR)) dir.create(dotR)
> M <- file.path(dotR, "Makevars")
> if (file.exists(M)) file.remove(M)
[1] TRUE
> if (!file.exists(M)) file.create(M)
[1] TRUE
> cat("\nCXX = g++",
+ "CXX11STD = -std=c++0x",
+ file = M, sep = "\n", append = TRUE)
> readLines(M)
[1] "" "CXX = g++" "CXX11STD = -std=c++0x"
> install.packages("/home/leungi/R_setup/udpipe_0.8.3.tar.gz", repos = NULL)
Installing package into â/usr/lib64/R/libraryâ
(as âlibâ is unspecified)
* installing *source* package âudpipeâ ...
** package âudpipeâ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -m64 -std=c++0x -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
g++ -m64 -std=c++0x -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c rcpp_phrases.cpp -o rcpp_phrases.o
g++ -m64 -std=c++0x -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c rcpp_udpipe.cpp -o rcpp_udpipe.o
g++ -m64 -std=c++0x -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c udpipe.cpp -o udpipe.o
g++ -m64 -std=c++0x -shared -L/usr/lib64/R/lib -Wl,-z,relro -o udpipe.so RcppExports.o rcpp_phrases.o rcpp_udpipe.o udpipe.o -L/usr/lib64/R/lib -lR
installing to /usr/lib64/R/library/00LOCK-udpipe/00new/udpipe/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package âudpipeâ
finding HTML links ... done
as.data.frame.udpipe_connlu html
as.matrix.cooccurrence html
as_conllu html
as_cooccurrence html
as_phrasemachine html
as_word2vec html
brussels_listings html
brussels_reviews html
brussels_reviews_anno html
cbind_dependencies html
cbind_morphological html
cooccurrence html
document_term_frequencies html
document_term_frequencies_statistics html
document_term_matrix html
dtm_bind html
dtm_colsums html
dtm_cor html
dtm_remove_lowfreq html
dtm_remove_sparseterms html
dtm_remove_terms html
dtm_remove_tfidf html
dtm_reverse html
dtm_tfidf html
keywords_collocation html
keywords_phrases html
keywords_rake html
paste.data.frame html
predict.LDA html
strsplit.data.frame html
txt_collapse html
txt_contains html
txt_freq html
txt_highlight html
txt_next html
txt_nextgram html
txt_previous html
txt_previousgram html
txt_recode html
txt_recode_ngram html
txt_sample html
txt_sentiment html
txt_show html
txt_tagsequence html
udpipe html
udpipe_accuracy html
udpipe_annotate html
udpipe_annotation_params html
udpipe_download_model html
udpipe_load_model html
udpipe_read_conllu html
udpipe_train html
unique_identifier html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (udpipe)
Making 'packages.html' ... done
> library(udpipe)
> packageVersion("udpipe")
[1] â0.8.3â
> data(brussels_reviews_anno, package = "udpipe")
x <- subset(brussels_reviews_anno, language %in% "fr")
keywords_phrases(x$xpos, pattern = c("DTNNVBRBJJ"), term = x$token, is_regex = T)> x <- subset(brussels_reviews_anno, language %in% "fr")
> keywords_phrases(x$xpos, pattern = c("DTNNVBRBJJ"), term = x$token, is_regex = T)
[1] keyword ngram pattern start end
<0 rows> (or 0-length row.names)
> install.packages("udpipe")
Installing package into â/usr/lib64/R/libraryâ
(as âlibâ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/udpipe_0.8.3.tar.gz'
Content type 'application/x-gzip' length 4750855 bytes (4.5 MB)
==================================================
downloaded 4.5 MB
* installing *source* package âudpipeâ ...
** package âudpipeâ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -m64 -std=c++0x -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
g++ -m64 -std=c++0x -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c rcpp_phrases.cpp -o rcpp_phrases.o
g++ -m64 -std=c++0x -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c rcpp_udpipe.cpp -o rcpp_udpipe.o
g++ -m64 -std=c++0x -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c udpipe.cpp -o udpipe.o
g++ -m64 -std=c++0x -shared -L/usr/lib64/R/lib -Wl,-z,relro -o udpipe.so RcppExports.o rcpp_phrases.o rcpp_udpipe.o udpipe.o -L/usr/lib64/R/lib -lR
installing to /usr/lib64/R/library/00LOCK-udpipe/00new/udpipe/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package âudpipeâ
finding HTML links ... done
as.data.frame.udpipe_connlu html
as.matrix.cooccurrence html
as_conllu html
as_cooccurrence html
as_phrasemachine html
as_word2vec html
brussels_listings html
brussels_reviews html
brussels_reviews_anno html
cbind_dependencies html
cbind_morphological html
cooccurrence html
document_term_frequencies html
document_term_frequencies_statistics html
document_term_matrix html
dtm_bind html
dtm_colsums html
dtm_cor html
dtm_remove_lowfreq html
dtm_remove_sparseterms html
dtm_remove_terms html
dtm_remove_tfidf html
dtm_reverse html
dtm_tfidf html
keywords_collocation html
keywords_phrases html
keywords_rake html
paste.data.frame html
predict.LDA html
strsplit.data.frame html
txt_collapse html
txt_contains html
txt_freq html
txt_highlight html
txt_next html
txt_nextgram html
txt_previous html
txt_previousgram html
txt_recode html
txt_recode_ngram html
txt_sample html
txt_sentiment html
txt_show html
txt_tagsequence html
udpipe html
udpipe_accuracy html
udpipe_annotate html
udpipe_annotation_params html
udpipe_download_model html
udpipe_load_model html
udpipe_read_conllu html
udpipe_train html
unique_identifier html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (udpipe)
Making 'packages.html' ... done
The downloaded source packages are in
â/tmp/RtmpXEa4Fl/downloaded_packagesâ
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
> library(udpipe)
> packageVersion("udpipe")
[1] â0.8.3â
> data(brussels_reviews_anno, package = "udpipe")
x <- subset(brussels_reviews_anno, language %in% "fr")
keywords_phrases(x$xpos, pattern = c("DTNNVBRBJJ"), term = x$token, is_regex = T)> x <- subset(brussels_reviews_anno, language %in% "fr")
> keywords_phrases(x$xpos, pattern = c("DTNNVBRBJJ"), term = x$token, is_regex = T)
[1] keyword ngram pattern start end
<0 rows> (or 0-length row.names)
>
> dotR <- file.path(Sys.getenv("HOME"), ".R")
> if (!file.exists(dotR)) dir.create(dotR)
> M <- file.path(dotR, "Makevars")
> if (file.exists(M)) file.remove(M)
[1] TRUE
> if (!file.exists(M)) file.create(M)
[1] TRUE
> cat("\nCXX = g++",
+ "CXX11STD = -std=c++11",
+ file = M, sep = "\n", append = TRUE)
> readLines(M)
[1] "" "CXX = g++" "CXX11STD = -std=c++11"
> install.packages("udpipe")
Installing package into â/usr/lib64/R/libraryâ
(as âlibâ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/udpipe_0.8.3.tar.gz'
Content type 'application/x-gzip' length 4750855 bytes (4.5 MB)
==================================================
downloaded 4.5 MB
* installing *source* package âudpipeâ ...
** package âudpipeâ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -m64 -std=c++11 -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c RcppExports.cpp -o RcppExports.o
g++ -m64 -std=c++11 -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c rcpp_phrases.cpp -o rcpp_phrases.o
g++ -m64 -std=c++11 -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c rcpp_udpipe.cpp -o rcpp_udpipe.o
g++ -m64 -std=c++11 -I"/usr/include/R" -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c udpipe.cpp -o udpipe.o
g++ -m64 -std=c++11 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o udpipe.so RcppExports.o rcpp_phrases.o rcpp_udpipe.o udpipe.o -L/usr/lib64/R/lib -lR
installing to /usr/lib64/R/library/00LOCK-udpipe/00new/udpipe/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package âudpipeâ
finding HTML links ... done
as.data.frame.udpipe_connlu html
as.matrix.cooccurrence html
as_conllu html
as_cooccurrence html
as_phrasemachine html
as_word2vec html
brussels_listings html
brussels_reviews html
brussels_reviews_anno html
cbind_dependencies html
cbind_morphological html
cooccurrence html
document_term_frequencies html
document_term_frequencies_statistics html
document_term_matrix html
dtm_bind html
dtm_colsums html
dtm_cor html
dtm_remove_lowfreq html
dtm_remove_sparseterms html
dtm_remove_terms html
dtm_remove_tfidf html
dtm_reverse html
dtm_tfidf html
keywords_collocation html
keywords_phrases html
keywords_rake html
paste.data.frame html
predict.LDA html
strsplit.data.frame html
txt_collapse html
txt_contains html
txt_freq html
txt_highlight html
txt_next html
txt_nextgram html
txt_previous html
txt_previousgram html
txt_recode html
txt_recode_ngram html
txt_sample html
txt_sentiment html
txt_show html
txt_tagsequence html
udpipe html
udpipe_accuracy html
udpipe_annotate html
udpipe_annotation_params html
udpipe_download_model html
udpipe_load_model html
udpipe_read_conllu html
udpipe_train html
unique_identifier html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (udpipe)
Making 'packages.html' ... done
The downloaded source packages are in
â/tmp/RtmpXEa4Fl/downloaded_packagesâ
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Problem solved, thanks to this SO post.
Steps:
gcc
>= 4.9.0 as per abovelibstdc++.so.6.0.26
file from gcc49-c++-4.9.3-1.el6.x86_64.rpm
/usr/lib64/libstdc++.so.6
to libstdc++.so.6.0.26
; this will provide the needed GLIBCXX 3.4.20
for gcc
gcc
with the correct flags:dotR <- file.path(Sys.getenv("HOME"), ".R")
if (!file.exists(dotR)) dir.create(dotR)
M <- file.path(dotR, "Makevars")
if (file.exists(M)) file.remove(M)
if (!file.exists(M)) file.create(M)
cat("CXX11=/usr/local/bin/g++",
"CXX11STD=-std=c++11",
file = M, sep = "\n", append = TRUE)
install.packages("udpipe")
Successful test
> library(udpipe)
> packageVersion("udpipe")
[1] â0.8.3â
> data(brussels_reviews_anno, package = "udpipe")
> x <- subset(brussels_reviews_anno, language %in% "fr")
> output <- keywords_phrases(x$xpos, pattern = c("DTNNVBRBJJ"), term = x$token, is_regex = T)
> head(output)
keyword ngram pattern start end
1 L' appartement est vraiment parfait 5 DTNNVBRBJJ 473 477
2 Le quartier est tres calme 5 DTNNVBRBJJ 536 540
3 le quartier est vraiment agreable 5 DTNNVBRBJJ 1679 1683
4 L' appartement est tres confortable 5 DTNNVBRBJJ 1809 1813
5 Le logement est tres agreable 5 DTNNVBRBJJ 2280 2284
6 L' appartement est tres agreable 5 DTNNVBRBJJ 3061 3065
Thanks again for your guidance @jwijffels!
Good that you found out how to do it! I will probably need that information also next week :)
The same code works in Windows, but fails in CentOS.
Checked intermediate inputs -
x$phrase_tag
,x$token
- and they're identical in both machines.Windows
Created on 2019-10-15 by the reprex package (v0.2.1)
CentOS
Machine Info