Hello Herve, Thank you so much for your help! The package I'm developing is actually on CRAN, but using the new Rtools40 with gcc 8.0 seems to work. For a testing environment on Windows, win-builder <https://win-builder.r-project.org/upload.aspx> has a version that uses Rtools40.
Cheers, Lucas On Tue, Jan 21, 2020 at 12:16 PM Pages, Herve <hpa...@fredhutch.org> wrote: > Hi Lucas, > > In order to compile an Rhtslib client package on Windows you need a > setup that mimics closely what we have on our Windows builders. In > particular you need to install a bunch of external libraries in > C:\extsoft and edit R\etc\i386\Makeconf and R\etc\x64\Makeconf to let R > know about these external libraries. The exact setup is documented here: > > > > https://github.com/Bioconductor/BBS/blob/master/Doc/Prepare-Windows-Server-2012-HOWTO.md > > End users don't need any of this because they typically install the > Windows package binaries which are statically linked. > > Unfortunately, if Windows is the platform where you intend to develop > your package, you'll have to go thru the complicated setup described > above. Alternatively, if that's an option for you, you could develop > your package on Linux. Installing the external libraries there is very > easy so the development process will be a lot easier. Then, when you > summit your package to Bioconductor, we'll start building the Windows > and Mac binaries for you so you'll get build reports for these > platforms. Also, once the package is accepted, we'll distribute the > Windows and Mac binaries so on these platforms your users won't need any > of the external dependencies. > > Hope this helps, > > H. > > On 1/20/20 14:09, Lucas Nell wrote: > > 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://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_lucasnell_RhtslibTest&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=M_5C6uruEPQfiEzLNV1mTopiZUJFpvKl7CLciyW9Dy8&s=CgHR-N9UB_5VJQ26fH3tIjkgqoljnilxhldpBmbxRaE&e= > >). 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. > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=M_5C6uruEPQfiEzLNV1mTopiZUJFpvKl7CLciyW9Dy8&s=fXiXCaC0HTtpKTHt3AVTisnRXYGRpWBwdkcwiU5FBSs&e= > > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
