[Bioc-devel] Rhtslib-linked package not compiling on Windows

[Lucas Nell]

Hello,

I'm having trouble linking to Rhtslib on Windows, specifically with finding
some of the required linked libraries (libcurl, among others). I made a
simple R package with only one function that compresses a file using BGZF
(link here <https://github.com/lucasnell/RhtslibTest>). After reading
through the Rhtslib instructions again, I tried building the package on
Windows 10 and got the output below. The directory C:/extsoft does not
exist, so I feel like there's something else I need to install.

Thanks for your help! (And thank you to the Rhtslib creators for a super
useful package!)

Cheers,
Lucas


==> Rcpp::compileAttributes()

* Updated R/RcppExports.R

==> Rcmd.exe INSTALL --preclean --no-multiarch --with-keep.source
RhtslibTest

* installing to library 'C:/Users/acuit/Documents/R/win-library/3.6'
* installing *source* package 'RhtslibTest' ...
** using staged installation
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/PROGRA~1/R/R-36~1.2/include"
-DNDEBUG -D_FILE_OFFSET_BITS=64
-I"C:/Users/acuit/Documents/R/win-library/3.6/Rcpp/include"
-I"C:/Users/acuit/Documents/R/win-library/3.6/Rhtslib/include"
-I"C:/Users/acuit/Documents/R/win-library/3.6/zlibbioc/include"        -O2
-Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/PROGRA~1/R/R-36~1.2/include"
-DNDEBUG -D_FILE_OFFSET_BITS=64
-I"C:/Users/acuit/Documents/R/win-library/3.6/Rcpp/include"
-I"C:/Users/acuit/Documents/R/win-library/3.6/Rhtslib/include"
-I"C:/Users/acuit/Documents/R/win-library/3.6/zlibbioc/include"        -O2
-Wall  -mtune=generic -c write_bgzf.cpp -o write_bgzf.o
write_bgzf.cpp: In function 'int compress_file(const string&, const int&)':
write_bgzf.cpp:54:9: warning: variable 'in_code' set but not used
[-Wunused-but-set-variable]
     int in_code;
         ^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o
RhtslibTest.dll tmp.def RcppExports.o write_bgzf.o
C:/Users/acuit/Documents/R/win-library/3.6/Rhtslib/usrlib/x64/libhts.a
-LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz
-lws2_32 -lwldap32 -lwinmm -LC:/PROGRA~1/R/R-36~1.2/bin/x64 -lR
C:/Rtools/mingw_64/bin/../lib/gcc/x86_64-w64-mingw32/4.9.3/../../../../x86_64-w64-mingw32/bin/ld.exe:
cannot find -lcurl
C:/Rtools/mingw_64/bin/../lib/gcc/x86_64-w64-mingw32/4.9.3/../../../../x86_64-w64-mingw32/bin/ld.exe:
cannot find -lrtmp
C:/Rtools/mingw_64/bin/../lib/gcc/x86_64-w64-mingw32/4.9.3/../../../../x86_64-w64-mingw32/bin/ld.exe:
cannot find -lssl
C:/Rtools/mingw_64/bin/../lib/gcc/x86_64-w64-mingw32/4.9.3/../../../../x86_64-w64-mingw32/bin/ld.exe:
cannot find -lssh2
C:/Rtools/mingw_64/bin/../lib/gcc/x86_64-w64-mingw32/4.9.3/../../../../x86_64-w64-mingw32/bin/ld.exe:
cannot find -lcrypto
collect2.exe: error: ld returned 1 exit status
no DLL was created
ERROR: compilation failed for package 'RhtslibTest'
* removing 'C:/Users/acuit/Documents/R/win-library/3.6/RhtslibTest'

Exited with status 1.

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