Can't compile on Linux CentOS 7

[pvo93]

I'm having trouble compiling the tesseract R package on our research Linux servers. Before starting R, I set CXX11CPP as follows.

export CXX11CPP='g++ -E -std=gnu++17'

However, R seems to ignore it and default to gnu++11. I'm using gcc 8.3.1.

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[Previously saved workspace restored]

install.packages("tesseract") Installing package into ‘/home/biotools/rpackages/R-4.0.3-2020-12-15’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/src/contrib/tesseract_4.1.tar.gz' Content type 'application/x-gzip' length 447439 bytes (436 KB)

downloaded 436 KB

• installing source package ‘tesseract’ ... package ‘tesseract’ successfully unpacked and MD5 sums checked using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/local/biotools/bsi/ver2/include -I/usr/local/biotools/bsi/ver2/include/leptonica
  Using PKG_LIBS=-L/usr/local/biotools/bsi/ver2/lib -ltesseract -lcurl
  Using CXX11CPP: g++ -E -std=gnu++11 ** libs rm -f tesseract.so RcppExports.o tesseract.o g++ -std=gnu++11 -I"/home/biotools/r/R-4.0.3/lib64/R/include" -DNDEBUG -I/usr/local/biotools/bsi/ver2/include -I/usr/local/biotools/bsi/ver2/include/leptonica -I'/home/biotools/rpackages/R-4.0.3-2020-12-15/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biotools/r/R-4.0.3/lib64/R/include" -DNDEBUG -I/usr/local/biotools/bsi/ver2/include -I/usr/local/biotools/bsi/ver2/include/leptonica -I'/home/biotools/rpackages/R-4.0.3-2020-12-15/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c tesseract.cpp -o tesseract.o In file included from /usr/local/biotools/bsi/ver2/include/tesseract/genericvector.h:23, from tesseract.cpp:2: /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h: In member function ‘bool tesseract::TFile::DeSerialize(std::vector&)’: /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:107:15: warning: ‘if constexpr’ only available with -std=c++17 or -std=gnu++17 } else if constexpr (std::is_same_v<T, std::string>) { ^~~~~ /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:107:31: error: ‘is_same_v’ is not a member of ‘std’ } else if constexpr (std::is_same_v<T, std::string>) { ^~~~~ /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:107:31: note: suggested alternative: ‘is_same’ } else if constexpr (std::is_same_v<T, std::string>) { ^~~~~ is_same /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:107:42: error: expected primary-expression before ‘,’ token } else if constexpr (std::is_same_v<T, std::string>) { ^ /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:107:55: error: expected primary-expression before ‘>’ token } else if constexpr (std::is_same_v<T, std::string>) { ^ /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:107:56: error: expected primary-expression before ‘)’ token } else if constexpr (std::is_same_v<T, std::string>) { ^ /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:116:15: warning: ‘if constexpr’ only available with -std=c++17 or -std=gnu++17 } else if constexpr (std::is_class_v) { ^~~~~ /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:116:31: error: ‘is_class_v’ is not a member of ‘std’ } else if constexpr (std::is_class_v) { ^~~~~~ /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:116:31: note: suggested alternative: ‘is_class’ } else if constexpr (std::is_class_v) { ^~~~~~ is_class /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:116:43: error: expected primary-expression before ‘>’ token } else if constexpr (std::is_class_v) { ^ /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:116:44: error: expected primary-expression before ‘)’ token } else if constexpr (std::is_class_v) { ^ /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h: In member function ‘bool tesseract::TFile::Serialize(const std::vector&)’: /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:147:15: warning: ‘if constexpr’ only available with -std=c++17 or -std=gnu++17 } else if constexpr (std::is_same_v<T, std::string>) { ^~~~~ /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:147:31: error: ‘is_same_v’ is not a member of ‘std’ } else if constexpr (std::is_same_v<T, std::string>) { ^~~~~ /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:147:31: note: suggested alternative: ‘is_same’ } else if constexpr (std::is_same_v<T, std::string>) { ^~~~~ is_same /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:147:42: error: expected primary-expression before ‘,’ token } else if constexpr (std::is_same_v<T, std::string>) { ^ /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:147:55: error: expected primary-expression before ‘>’ token } else if constexpr (std::is_same_v<T, std::string>) { ^ /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:147:56: error: expected primary-expression before ‘)’ token } else if constexpr (std::is_same_v<T, std::string>) { ^ /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:154:15: warning: ‘if constexpr’ only available with -std=c++17 or -std=gnu++17 } else if constexpr (std::is_class_v) { ^~~~~ /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:154:31: error: ‘is_class_v’ is not a member of ‘std’ } else if constexpr (std::is_class_v) { ^~~~~~ /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:154:31: note: suggested alternative: ‘is_class’ } else if constexpr (std::is_class_v) { ^~~~~~ is_class /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:154:43: error: expected primary-expression before ‘>’ token } else if constexpr (std::is_class_v) { ^ /usr/local/biotools/bsi/ver2/include/tesseract/serialis.h:154:44: error: expected primary-expression before ‘)’ token } else if constexpr (std::is_class_v) { ^ tesseract.cpp: In function ‘tesseract::TessBaseAPI make_analyze_api()’: tesseract.cpp:18:10: error: use of deleted function ‘tesseract::TessBaseAPI::TessBaseAPI(const tesseract::TessBaseAPI&)’ return api; ^~~ In file included from tesseract_types.h:1, from tesseract.cpp:1: /usr/local/biotools/bsi/ver2/include/tesseract/baseapi.h:82:3: note: declared here TessBaseAPI(TessBaseAPI const &) = delete; ^~~ tesseract.cpp: In function ‘Rcpp::List tesseract_config()’: tesseract.cpp:23:49: error: use of deleted function ‘tesseract::TessBaseAPI::TessBaseAPI(const tesseract::TessBaseAPI&)’ tesseract::TessBaseAPI api = make_analyze_api(); ^ In file included from tesseract_types.h:1, from tesseract.cpp:1: /usr/local/biotools/bsi/ver2/include/tesseract/baseapi.h:82:3: note: declared here TessBaseAPI(TessBaseAPI const &) = delete; ^~~ tesseract.cpp: In function ‘TessPtr tesseract_engine_internal(Rcpp::CharacterVector, Rcpp::CharacterVector, Rcpp::CharacterVector, Rcpp::CharacterVector, Rcpp::CharacterVector)’: tesseract.cpp:33:3: error: ‘GenericVector’ was not declared in this scope GenericVector params, values; ^~~~~ tesseract.cpp:33:3: note: suggested alternatives: In file included from tesseract.cpp:2: /usr/local/biotools/bsi/ver2/include/tesseract/genericvector.h:39:7: note: ‘tesseract::GenericVector’ class GenericVector { ^~~~~ In file included from /home/biotools/rpackages/R-4.0.3-2020-12-15/Rcpp/include/Rcpp/Vector.h:62, from /home/biotools/rpackages/R-4.0.3-2020-12-15/Rcpp/include/Rcpp.h:40, from tesseract_types.h:7, from tesseract.cpp:1: /home/biotools/rpackages/R-4.0.3-2020-12-15/Rcpp/include/Rcpp/vector/instantiation.h:36:28: note: ‘Rcpp::GenericVector’ typedef Vector GenericVector ; ^~~~~ tesseract.cpp:33:17: error: ‘STRING’ was not declared in this scope GenericVector params, values; ^~ tesseract.cpp:33:17: note: suggested alternative: ‘SING’ GenericVector params, values; ^~ SING tesseract.cpp:33:25: error: ‘params’ was not declared in this scope GenericVector params, values; ^~ tesseract.cpp:33:33: error: ‘values’ was not declared in this scope GenericVector params, values; ^~ tesseract.cpp:33:33: note: suggested alternative: ‘valloc’ GenericVector params, values; ^~ valloc tesseract.cpp: In function ‘Rcpp::LogicalVector validate_params(Rcpp::CharacterVector)’: tesseract.cpp:79:3: error: ‘STRING’ was not declared in this scope STRING str; ^~ tesseract.cpp:79:3: note: suggested alternative: ‘SING’ STRING str; ^~ SING tesseract.cpp:80:49: error: use of deleted function ‘tesseract::TessBaseAPI::TessBaseAPI(const tesseract::TessBaseAPI&)’ tesseract::TessBaseAPI api = make_analyze_api(); ^ In file included from tesseract_types.h:1, from tesseract.cpp:1: /usr/local/biotools/bsi/ver2/include/tesseract/baseapi.h:82:3: note: declared here TessBaseAPI(TessBaseAPI const &) = delete; ^~~ tesseract.cpp:83:53: error: ‘str’ was not declared in this scope out[i] = api.GetVariableAsString(params.at(i), &str); ^~~ tesseract.cpp:83:53: note: suggested alternative: ‘std’ out[i] = api.GetVariableAsString(params.at(i), &str); ^~~ std tesseract.cpp: In function ‘Rcpp::List engine_info_internal(TessPtr)’: tesseract.cpp:90:3: error: ‘GenericVector’ was not declared in this scope GenericVector langs; ^~~~~ tesseract.cpp:90:3: note: suggested alternatives: In file included from tesseract.cpp:2: /usr/local/biotools/bsi/ver2/include/tesseract/genericvector.h:39:7: note: ‘tesseract::GenericVector’ class GenericVector { ^~~~~ In file included from /home/biotools/rpackages/R-4.0.3-2020-12-15/Rcpp/include/Rcpp/Vector.h:62, from /home/biotools/rpackages/R-4.0.3-2020-12-15/Rcpp/include/Rcpp.h:40, from tesseract_types.h:7, from tesseract.cpp:1: /home/biotools/rpackages/R-4.0.3-2020-12-15/Rcpp/include/Rcpp/vector/instantiation.h:36:28: note: ‘Rcpp::GenericVector’ typedef Vector GenericVector ; ^~~~~ tesseract.cpp:90:17: error: ‘STRING’ was not declared in this scope GenericVector langs; ^~ tesseract.cpp:90:17: note: suggested alternative: ‘SING’ GenericVector langs; ^~ SING tesseract.cpp:90:25: error: ‘langs’ was not declared in this scope GenericVector langs; ^~~~~ tesseract.cpp:90:25: note: suggested alternative: ‘labs’ GenericVector langs; ^~~~~ labs tesseract.cpp: In function ‘Rcpp::String print_params(std::string)’: tesseract.cpp:109:49: error: use of deleted function ‘tesseract::TessBaseAPI::TessBaseAPI(const tesseract::TessBaseAPI&)’ tesseract::TessBaseAPI api = make_analyze_api(); ^ In file included from tesseract_types.h:1, from tesseract.cpp:1: /usr/local/biotools/bsi/ver2/include/tesseract/baseapi.h:82:3: note: declared here TessBaseAPI(TessBaseAPI const &) = delete; ^~~ tesseract.cpp: In function ‘Rcpp::CharacterVector get_param_values(TessPtr, Rcpp::CharacterVector)’: tesseract.cpp:118:3: error: ‘STRING’ was not declared in this scope STRING str; ^~ tesseract.cpp:118:3: note: suggested alternative: ‘SING’ STRING str; ^~ SING tesseract.cpp:122:54: error: ‘str’ was not declared in this scope out[i] = api->GetVariableAsString(params.at(i), &str) ? Rcpp::String(str.c_str()) : NA_STRING; ^~~ tesseract.cpp:122:54: note: suggested alternative: ‘ptr’ out[i] = api->GetVariableAsString(params.at(i), &str) ? Rcpp::String(str.c_str()) : NA_STRING; ^~~ ptr make: *** [/home/biotools/r/R-4.0.3/lib64/R/etc/Makeconf:181: tesseract.o] Error 1 ERROR: compilation failed for package ‘tesseract’
• removing ‘/home/biotools/rpackages/R-4.0.3-2020-12-15/tesseract’

The downloaded source packages are in ‘/local1/tmp/RtmpBVBRk6/downloaded_packages’ Warning message: In install.packages("tesseract") : installation of package ‘tesseract’ had non-zero exit status

[jeroen]

I think there may be an issue with your installation of libtesseract in /usr/local/biotools/bsi/ver2. Which version is this?

[pvo93]

It's 5.0.0-alpha-2-2-1224. I had problems trying to compile 4.1.1.

[m015733@dudley]/usr/local/biotools/bsi/ver2/lib: ls -l libtesseract. -rw-r--r-- 1 wa03872 rcode 196086110 Mar 16 09:19 libtesseract.a -rwxr-xr-x 1 wa03872 rcode 1101 Mar 16 09:19 libtesseract.la lrwxrwxrwx 1 wa03872 rcode 21 Mar 16 09:19 libtesseract.so -> libtesseract.so.5.0.0 lrwxrwxrwx 1 wa03872 rcode 21 Mar 16 09:19 libtesseract.so.5 -> libtesseract.so.5.0.0 -rwxr-xr-x 1 wa03872 rcode 63307408 Mar 16 09:19 libtesseract.so.5.0.0*

[jeroen]

I haven't tested the R package with 5.x. What problems did you have with 4.1? Do you not have the option to install tesseract-devel from EPEL?

[pvo93]

I install and maintain our R packages, but I don't have root access so I typically compile from source. I was able to compile tesseract 4.1.1, but I get the following error when I try to install the R package. I verified the existence of the header file.

install.packages("tesseract") Installing package into ‘/home/m015733/R/x86_64-pc-linux-gnu-library/4.0’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/src/contrib/tesseract_4.1.tar.gz' Content type 'application/x-gzip' length 447439 bytes (436 KB)

downloaded 436 KB

• installing source package ‘tesseract’ ... package ‘tesseract’ successfully unpacked and MD5 sums checked using staged installation Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/local1/tmp/m015733/test/include -I/usr/local/biotools/bsi/ver2/include/leptonica
  Using PKG_LIBS=-L/local1/tmp/m015733/test/lib -ltesseract -lcurl
  Using CXX11CPP: g++ -E -std=gnu++11 ** libs rm -f tesseract.so RcppExports.o tesseract.o g++ -std=gnu++11 -I"/home/biotools/r/R-4.0.3/lib64/R/include" -DNDEBUG -I/local1/tmp/m015733/test/include -I/usr/local/biotools/bsi/ver2/include/leptonica -I'/home/biotools/rpackages/R-4.0.3-2020-12-15/Rcpp/include' -I/usr/local/include -fvisibility=hidden -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: tesseract_types.h:2:10: fatal error: leptonica/allheaders.h: No such file or directory

  include <leptonica/allheaders.h>

    ^~~~~~~~~~~~~~~~~~~~~~~~

  compilation terminated. make: *** [/home/biotools/r/R-4.0.3/lib64/R/etc/Makeconf:181: RcppExports.o] Error 1 ERROR: compilation failed for package ‘tesseract’

• removing ‘/home/m015733/R/x86_64-pc-linux-gnu-library/4.0/tesseract’

The downloaded source packages are in ‘/local1/tmp/Rtmp8QaFlz/downloaded_packages’ Warning message: In install.packages("tesseract") : installation of package ‘tesseract’ had non-zero exit status

system("ls -l /usr/local/biotools/bsi/ver2/include/leptonica") total 588 -rw-r--r-- 1 wa03872 rcode 259877 Mar 16 10:35 allheaders.h . . .

[jeroen]

Looks like you should be compiling with -I/usr/local/biotools/bsi/ver2/include ?