Hi all,
I am using file-locking functions in C that can be found in the
<stdio.h> in Unix
extern void flockfile (FILE *__stream) __THROW;
extern int ftrylockfile (FILE *__stream) __THROW __wur;
extern void funlockfile (FILE *__stream) __THROW;
When submitting to CRAN I have troubles with the win-builder.
<stdio.h> in windows does not contain those functions. But I found them
in the <pthread_unistd.h>.
But even when including all possible header files for pthread like:*
*
*#include <windows.h>**#include <sys/locking.h>*
*#include <pthread_unistd.h>****#include <pthread.h>****#include
<pthread_compat.h>****#include <pthread_signal.h>****#include <pthread_time.h>*
I am aways getting the same error from win-builder:
bed2vector.cpp:2667:19: error: 'flockfile' was not declared in this scope
flockfile(stream);
^
bed2vector.cpp:2670:46: error: 'getc_unlocked' was not declared in this scope
for (int ch = 0; (ch = getc_unlocked(stream)) != EOF;) {
^
bed2vector.cpp:2678:27: error: 'funlockfile' was not declared in this scope
funlockfile(stream);
^
bed2vector.cpp:2694:21: error: 'funlockfile' was not declared in this scope
funlockfile(stream);
^
So the header files are there, but the functions are not defined. I am
not an expert in C, but
have to submit a package that uses C-code. Does someone have more
experience with this?
Thanks,
Carmen
On 19/02/2018 15:22, Mauro Donadello wrote:
> Prova ad aggiungere
>
> #include <windows.h>
> #include <sys/locking.h>
>
>
>> On 19 Feb 2018, at 15:07, Carmen M. Livi<carmen.l...@ifom.eu> wrote:
>>
>> Ciao Mauro,
>> Posso disturbarti un secondo di pomeriggio e scendere un attimo? Ho un
>> problema con C... cioe' io e linux no, ma Windows.
>> Sulle nostre macchine compila senza problemi ma su Windows mi da un errore.
>>
>> Lancio il seguente commando:
>> g++ -m64 -std=gnu++11 -I"/lustre/home/clivi/programs/R-devel/include"
>> -DNDEBUG -I"/lustre/home/clivi/programs/R-devel/library/Rcpp/include/"
>> -I"/lustre/home/clivi/programs/R-devel/library/BH/include/"
>> -I"/usr/lib/gcc/x86_64-redhat-linux/4.8.5/include" -I./ -D_FASTMAP
>> -DMAQ_LONGREADS -lbz2 -O2 -Wall -mtune=core2 -c bed2vector.cpp -o
>> bed2vector.o
>> Allegato il codice da eseguire.
>>
>> l messaggio di errore:
>> * installing *source* package 'spp' ...
>> ** libs
>> Warning: this package has a non-empty 'configure.win' file,
>> so building only the main architecture
>>
>> d:/Compiler/gcc-4.9.3/mingw_64/bin/g++ -m64 -std=gnu++11
>> -I"D:/RCompile/recent/R-3.4.3/include" -DNDEBUG
>> -I"d:/RCompile/CRANpkg/lib/3.4/Rcpp/include"
>> -I"d:/RCompile/CRANpkg/lib/3.4/BH/include"
>> -I"d:/Compiler/gcc-4.9.3/local330/include" -I./ -D_FASTMAP -DMAQ_LONGREADS
>> -lbz2 -O2 -Wall -mtune=core2 -c bed2vector.cpp -o bed2vector.o
>> In file included from D:/RCompile/recent/R-3.4.3/include/Rdefines.h:37:0,
>> from bed2vector.cpp:22:
>> D:/RCompile/recent/R-3.4.3/include/R_ext/RS.h:55:0: warning: "ERROR"
>> redefined
>> #define ERROR ),error(R_problem_buf);}
>> ^
>> In file included from
>> D:/Compiler/gcc-4.9.3/mingw_64/x86_64-w64-mingw32/include/windows.h:71:0,
>> from d:/Compiler/gcc-4.9.3/local330/include/bzlib.h:79,
>> from bed2vector.cpp:15:
>> D:/Compiler/gcc-4.9.3/mingw_64/x86_64-w64-mingw32/include/wingdi.h:75:0:
>> note: this is the location of the previous definition
>> #define ERROR 0
>> ^
>> bed2vector.cpp: In function 'int get_bzline(BZFILE*, std::string&)':
>> bed2vector.cpp:48:11: warning: variable 'nBuf' set but not used
>> [-Wunused-but-set-variable]
>> int nBuf;
>> ^
>> bed2vector.cpp: In function 'SEXPREC* read_eland_mismatches(SEXP)':
>> bed2vector.cpp:654:11: warning: variable 'nm' set but not used
>> [-Wunused-but-set-variable]
>> int nm=0;
>> ^
>> bed2vector.cpp: In function 'SEXPREC* read_eland_extended(SEXP, SEXP, SEXP)':
>> bed2vector.cpp:1074:20: warning: comparison between signed and unsigned
>> integer expressions [-Wsign-compare]
>> for(int i=0;i<str_nm.size();i++) {
>> ^
>> bed2vector.cpp: In function 'ssize_t getline_local(char**, size_t*, FILE*)':
>> bed2vector.cpp:2659:19:
>> error
>> : 'flockfile' was not declared in this scope
>> flockfile(stream);
>> ^
>> bed2vector.cpp:2662:46:
>> error
>> : 'getc_unlocked' was not declared in this scope
>> for (int ch = 0; (ch = getc_unlocked(stream)) != EOF;) {
>> ^
>> bed2vector.cpp:2670:27:
>> error
>> : 'funlockfile' was not declared in this scope
>> funlockfile(stream);
>> ^
>> bed2vector.cpp:2686:21:
>> error:
>> 'funlockfile' was not declared in this scope
>> funlockfile(stream);
>> ^
>> make: *** [bed2vector.o] Error 1
>> Warning: running command 'make -f "Makevars.win" -f
>> "D:/RCompile/recent/R-3.4.3/etc/x64/Makeconf" -f
>> "D:/RCompile/recent/R-3.4.3/etc/x64/Makevars.site" -f
>> "D:/RCompile/recent/R-3.4.3/share/make/winshlib.mk" CXX='$(CXX11)
>> $(CXX11STD)' CXXFLAGS='$(CXX11FLAGS)' CXXPICFLAGS='$(CXX11PICFLAGS)'
>> SHLIB_LDFLAGS='$(SHLIB_CXX11LDFLAGS)' SHLIB_LD='$(SHLIB_CXX11LD)'
>> SHLIB="spp.dll" WIN=64 TCLBIN=64 OBJECTS="bed2vector.o cdensum.o maqmap.o
>> maqread.o peaks.o spp_init.o wdl.o"' had status 2
>> ERROR: compilation failed for package 'spp'
>> * removing 'd:/RCompile/CRANguest/R-release/lib/spp'
>> In R CMD INSTALL
>>
>> <bed2vector.cpp>
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