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

[Lucas Nell]

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 <hpages using 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]]
> >
> > _______________________________________________
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> >
> 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: hpages using fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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