[R-pkg-devel] CRAN cannot find libraries on Windows
Lucas Nell
|uc@@ @end|ng |rom |uc@@ne||@com
Mon Feb 10 18:31:23 CET 2020
Hello Hervé,
Thanks for confirming what I was thinking. Does anyone know how long it
should take for win-builder to use the updated Rhtslib version? I just
tried it again today, and it's still using the older version.
Cheers,
Lucas
On Sun, Feb 2, 2020 at 11:34 PM Hervé Pagès <hpages using fredhutch.org> wrote:
> To me it looks like the situation on AppVeyor and on win-builder is not
> quite the same:
>
> - On AppVeyor the compiler and linker are expecting the "external
> software" to be in C:/projects/BUILD/R-source-win32/extsoft/ and no
> longer in C:/extsoft/lib/i386. This indicates that AppVeyor is using the
> latest Rhtslib (1.91.1). However the linker still cannot find libraries
> -lcurl, -lrtmp, -lssl, etc... Not sure why. Are curl.a, rtmp.a, ssl.a,
> really there? If not, this looks like a configuration issue with AppVeyor.
>
> - On win-builder the linker is still using -LC:/extsoft/lib/i386 which
> indicates that it's not using the latest Rhtslib.
>
> H.
>
>
> On 2/2/20 11:55, Lucas Nell wrote:
> >
> > Thanks everyone for your help. It's still giving me the same error on
> > the development win-builder and on AppVeyor. Truncated install logs for
> > both are below. I'm not sure that Rhtslib 1.91.1 (the one with the new
> > changes) is being used on win-builder, which is why I've included the
> > AppVeyor results—hopefully they're useful for what might happen on CRAN.
> >
> >
> > ## APPVEYOR
> >
> > * installing *source* package 'jackalope' ...
> > ** using staged installation
> > ** libs
> >
> > *** arch - i386
> > C:/Rtools/mingw_32/bin/g++ -std=gnu++11
> > -I"C:/RLibrary/zlibbioc/include" -I"c:/R/include" -DNDEBUG
> > -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'C:/RLibrary/Rcpp/include'
> > -I'C:/RLibrary/RcppArmadillo/include'
> > -I'C:/RLibrary/RcppProgress/include' -I'C:/RLibrary/Rhtslib/include'
> > -I'C:/RLibrary/zlibbioc/include'
> > -I"C:/projects/BUILD/R-source-win32/extsoft/include" -O2 -Wall
> > -mfpmath=sse -msse2 -c RcppExports.cpp -o RcppExports.o
> > C:/Rtools/mingw_32/bin/g++ -std=gnu++11
> > -I"C:/RLibrary/zlibbioc/include" -I"c:/R/include" -DNDEBUG
> > -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'C:/RLibrary/Rcpp/include'
> > -I'C:/RLibrary/RcppArmadillo/include'
> > -I'C:/RLibrary/RcppProgress/include' -I'C:/RLibrary/Rhtslib/include'
> > -I'C:/RLibrary/zlibbioc/include'
> > -I"C:/projects/BUILD/R-source-win32/extsoft/include" -O2 -Wall
> > -mfpmath=sse -msse2 -c alter_reference.cpp -o alter_reference.o
> >
> > [...]
> >
> > C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o jackalope.dll
> > tmp.def RcppExports.o alter_reference.o create_sequences.o
> > hts_illumina.o hts_pacbio.o io_fasta.o io_ms.o io_vcf.o mutator.o
> > mutator_indels.o mutator_subs.o phylogenomics.o ref_var_access.o
> > sub_models.o util.o var_classes.o vars_ssites.o -lws2_32 -Lc:/R/bin/i386
> > -lRlapack -Lc:/R/bin/i386 -lRblas -lgfortran -lm -lquadmath
> > C:/RLibrary/Rhtslib/usrlib/i386/libhts.a
> > -LC:/projects/BUILD/R-source-win32/extsoft/lib/i386 -lcurl -lrtmp -lssl
> > -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn
> > -LC:/RLibrary/zlibbioc/libs/i386 -lzlib1bioc
> > -LC:/projects/BUILD/R-source-win32/extsoft/lib/i386
> > -LC:/projects/BUILD/R-source-win32/extsoft/lib -Lc:/R/bin/i386 -lR
> >
> C:/Rtools/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
>
> > cannot find -lcurl
> >
> C:/Rtools/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
>
> > cannot find -lrtmp
> >
> C:/Rtools/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
>
> > cannot find -lssl
> >
> C:/Rtools/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
>
> > cannot find -lssh2
> >
> C:/Rtools/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
>
> > cannot find -lcrypto
> >
> C:/Rtools/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
>
> > cannot find -lidn
> > collect2.exe: error: ld returned 1 exit status
> > no DLL was created
> > ERROR: compilation failed for package 'jackalope'
> > * removing 'C:/projects/jackalope/jackalope.Rcheck/jackalope'
> >
> >
> > ## WIN-BUILDER
> > * installing *source* package 'jackalope' ...
> > ** using staged installation
> > ** libs
> >
> > *** arch - i386
> > d:/Compiler/gcc-4.9.3/mingw_32/bin/g++ -std=gnu++11
> > -I"D:/RCompile/CRANpkg/lib/4.0/zlibbioc/include"
> > -I"D:/RCompile/recent/R/include" -DNDEBUG -I../inst/include/
> > -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.0/Rcpp/include'
> > -I'D:/RCompile/CRANpkg/lib/4.0/RcppArmadillo/include'
> > -I'D:/RCompile/CRANpkg/lib/4.0/RcppProgress/include'
> > -I'D:/RCompile/CRANpkg/lib/4.0/Rhtslib/include'
> > -I'D:/RCompile/CRANpkg/lib/4.0/zlibbioc/include'
> > -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2
> > -c RcppExports.cpp -o RcppExports.o
> > d:/Compiler/gcc-4.9.3/mingw_32/bin/g++ -std=gnu++11
> > -I"D:/RCompile/CRANpkg/lib/4.0/zlibbioc/include"
> > -I"D:/RCompile/recent/R/include" -DNDEBUG -I../inst/include/
> > -D_FILE_OFFSET_BITS=64 -I'D:/RCompile/CRANpkg/lib/4.0/Rcpp/include'
> > -I'D:/RCompile/CRANpkg/lib/4.0/RcppArmadillo/include'
> > -I'D:/RCompile/CRANpkg/lib/4.0/RcppProgress/include'
> > -I'D:/RCompile/CRANpkg/lib/4.0/Rhtslib/include'
> > -I'D:/RCompile/CRANpkg/lib/4.0/zlibbioc/include'
> > -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall -mtune=core2
> > -c alter_reference.cpp -o alter_reference.o
> >
> > [...]
> >
> > d:/Compiler/gcc-4.9.3/mingw_32/bin/g++ -shared -s -static-libgcc -o
> > jackalope.dll tmp.def RcppExports.o alter_reference.o create_sequences.o
> > hts_illumina.o hts_pacbio.o io_fasta.o io_ms.o io_vcf.o mutator.o
> > mutator_indels.o mutator_subs.o phylogenomics.o ref_var_access.o
> > sub_models.o util.o var_classes.o vars_ssites.o -lws2_32
> > -LD:/RCompile/recent/R/bin/i386 -lRlapack
> > -LD:/RCompile/recent/R/bin/i386 -lRblas -lgfortran -lm -lquadmath
> > D:/RCompile/CRANpkg/lib/4.0/Rhtslib/usrlib/i386/libhts.a
> > -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz
> > -lws2_32 -lwldap32 -lwinmm -lidn
> > -LD:/RCompile/CRANpkg/lib/4.0/zlibbioc/libs/i386 -lzlib1bioc
> > -Ld:/Compiler/gcc-4.9.3/local330/lib/i386
> > -Ld:/Compiler/gcc-4.9.3/local330/lib -LD:/RCompile/recent/R/bin/i386 -lR
> >
> D:/Compiler/gcc-4.9.3/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
>
> > cannot find -lcurl
> >
> D:/Compiler/gcc-4.9.3/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
>
> > cannot find -lrtmp
> >
> D:/Compiler/gcc-4.9.3/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
>
> > cannot find -lssl
> >
> D:/Compiler/gcc-4.9.3/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
>
> > cannot find -lssh2
> >
> D:/Compiler/gcc-4.9.3/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
>
> > cannot find -lcrypto
> >
> D:/Compiler/gcc-4.9.3/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
>
> > cannot find -lidn
> > collect2.exe: error: ld returned 1 exit status
> > no DLL was created
> > ERROR: compilation failed for package 'jackalope'
> > * removing 'd:/RCompile/CRANguest/R-devel/lib/jackalope'
> >
> >
> >
> >
> >
> >
> > On Mon, Jan 27, 2020 at 5:45 PM Pages, Herve <hpages using fredhutch.org
> > <mailto:hpages using fredhutch.org>> wrote:
> >
> > OK thanks. I'm using LOCAL_SOFT now in Rhtslib instead of hardcoded
> > C:/extsoft:
> >
> >
> >
> https://github.com/Bioconductor/Rhtslib/commit/1052c4c2e467fa8e3db613a70af2f77448956d38
> > <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Rhtslib_commit_1052c4c2e467fa8e3db613a70af2f77448956d38&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=xiTfiuG9CwLnlGAyvQGivg_JKm3MmKwMoMzTqTFCuSk&s=PvRg3n4qfjPrOSZuov1NuLFPXB8Wi8hLDHEK7V4q2ZE&e=
> >
> >
> > H.
> >
> > On 1/27/20 15:15, Duncan Murdoch wrote:
> > > On 27/01/2020 5:48 p.m., Martin Morgan wrote:
> > >> what are the correct paths?
> > >
> > > The src/gnuwin32/MkRules.dist file gives the patterns. They are
> > based
> > > on environment variables LOCAL_SOFT, R_HOME, etc. Most people
> > should
> > > modify that file to MkRules.local when building R; the variables
> > defined
> > > there get re-used when building packages. I forget what gets
> > baked into
> > > the Windows binary distributions.
> > >
> > > Duncan Murdoch
> > >
> > >>
> > >> On 1/27/20, 3:32 PM, "R-package-devel on behalf of Uwe Ligges"
> > >> <r-package-devel-bounces using r-project.org
> > <mailto:r-package-devel-bounces using r-project.org> on behalf of
> > >> ligges using statistik.tu-dortmund.de
> > <mailto:ligges using statistik.tu-dortmund.de>> wrote:
> > >>
> > >> Thanks, one suspicious part from the log below is
> > >> -LC:/extsoft/lib/i386
> > >> which is clearly not in any variable we define on CRAN.
> > >> Looking close shows that
> > >> > Rhtslib::pkgconfig("PKG_LIBS")
> > >> gives
> > >> 'D:/RCompile/CRANpkg/lib/4.0/Rhtslib/usrlib/x64/libhts.a'
> > >> -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto
> > -lgdi32 -lz
> > >> -lws2_32 -lwldap32 -lwinmm
> > >> and that is wrong as -LC:/extsoft/lib/i386 or
> > C:/extsoft/lib/x64
> > >> are not
> > >> directories where the software is installed on winbuilder.
> > >> Pls use the directories the other packages are using, too.
> > >> Best,
> > >> Uwe Ligges
> > >> On 26.01.2020 22:40, Lucas Nell wrote:
> > >> > Hello all,
> > >> >
> > >> > My package (source here
> > >>
> > <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_lucasnell_jackalope&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=rbTXQQLd6r1RKFIeCzZLf3oG7wNkyQ7ajc_OWw6ptl8&s=pTaNljvQ8YT-dMzHgasiRYlhEdPYJq5pmcDu44IrFAk&e=
> >
> > >> >) no longer
> > >> > compiles on a standard Windows installation (see truncated
> > >> install log
> > >> > below). The problem seems to be the libraries required by
> > the
> > >> Bioconductor
> > >> > package Rhtslib
> > >> >
> > >>
> > <
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_packages_release_bioc_html_Rhtslib.html&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=rbTXQQLd6r1RKFIeCzZLf3oG7wNkyQ7ajc_OWw6ptl8&s=oV05PFPLvWBLVj_pX9VeJX8fT565yXNxji0sihhuXGU&e=
> >
> > >> >. My
> > >> > package compiles fine when using GCC 8 via Rtools 40 (and
> > when
> > >> built using
> > >> > "r-devel-windows-ix86+x86_64-gcc8" on CRAN), but when
> > trying to
> > >> submit a
> > >> > new version to CRAN, it fails its automatic tests without
> > >> working using GCC
> > >> > 4 on Windows. Does anyone have ideas on how to fix this?
> > Thank
> > >> you!
> > >> >
> > >> > Cheers,
> > >> > Lucas
> > >> >
> > >> >
> > >> >
> > >> > * installing *source* package 'jackalope' ...
> > >> > ** using staged installation
> > >> > ** libs
> > >> >
> > >> > *** arch - i386
> > >> > d:/Compiler/gcc-4.9.3/mingw_32/bin/g++ -std=gnu++11
> > >> > -I"D:/RCompile/CRANpkg/lib/4.0/zlibbioc/include"
> > >> > -I"D:/RCompile/recent/R/include" -DNDEBUG
> -I../inst/include/
> > >> > -D_FILE_OFFSET_BITS=64
> > >> -I'D:/RCompile/CRANpkg/lib/4.0/Rcpp/include'
> > >> >
> > -I'D:/RCompile/CRANincoming/R-devel/lib/RcppArmadillo/include'
> > >> > -I'D:/RCompile/CRANpkg/lib/4.0/RcppProgress/include'
> > >> > -I'D:/RCompile/CRANpkg/lib/4.0/Rhtslib/include'
> > >> > -I'D:/RCompile/CRANpkg/lib/4.0/zlibbioc/include'
> > >> > -I"d:/Compiler/gcc-4.9.3/local330/include" -O2 -Wall
> > >> -mtune=core2 -c
> > >> > RcppExports.cpp -o RcppExports.o
> > >> >
> > >> > [...]
> > >> >
> > >> > d:/Compiler/gcc-4.9.3/mingw_32/bin/g++ -shared -s
> > >> -static-libgcc -o
> > >> > jackalope.dll tmp.def RcppExports.o alter_reference.o
> > >> create_sequences.o
> > >> > hts_illumina.o hts_pacbio.o io_fasta.o io_ms.o io_vcf.o
> > mutator.o
> > >> > mutator_indels.o mutator_subs.o phylogenomics.o
> > ref_var_access.o
> > >> > sub_models.o util.o var_classes.o vars_ssites.o -lws2_32
> > >> > -LD:/RCompile/recent/R/bin/i386 -lRlapack
> > >> -LD:/RCompile/recent/R/bin/i386
> > >> > -lRblas -lgfortran -lm -lquadmath
> > >> > D:/RCompile/CRANpkg/lib/4.0/Rhtslib/usrlib/i386/libhts.a
> > >> > -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto
> > >> -lgdi32 -lz
> > >> > -lws2_32 -lwldap32 -lwinmm -lidn
> > >> > -LD:/RCompile/CRANpkg/lib/4.0/zlibbioc/libs/i386
> -lzlib1bioc
> > >> > -Ld:/Compiler/gcc-4.9.3/local330/lib/i386
> > >> > -Ld:/Compiler/gcc-4.9.3/local330/lib
> > >> -LD:/RCompile/recent/R/bin/i386 -lR
> > >> >
> > >>
> >
> D:/Compiler/gcc-4.9.3/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
> >
> > >>
> > >> > cannot find -lcurl
> > >> >
> > >>
> >
> D:/Compiler/gcc-4.9.3/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
> >
> > >>
> > >> > cannot find -lrtmp
> > >> >
> > >>
> >
> D:/Compiler/gcc-4.9.3/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
> >
> > >>
> > >> > cannot find -lssl
> > >> >
> > >>
> >
> D:/Compiler/gcc-4.9.3/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
> >
> > >>
> > >> > cannot find -lssh2
> > >> >
> > >>
> >
> D:/Compiler/gcc-4.9.3/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
> >
> > >>
> > >> > cannot find -lcrypto
> > >> >
> > >>
> >
> D:/Compiler/gcc-4.9.3/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe:
> >
> > >>
> > >> > cannot find -lidn
> > >> > collect2.exe: error: ld returned 1 exit status
> > >> > no DLL was created
> > >> > ERROR: compilation failed for package 'jackalope'
> > >> > * removing
> 'd:/RCompile/CRANincoming/R-devel/lib/jackalope'
> > >> >
> > >> > [[alternative HTML version deleted]]
> > >> >
> > >> > ______________________________________________
> > >> > R-package-devel using r-project.org
> > <mailto:R-package-devel using r-project.org> mailing list
> > >> >
> > >>
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dpackage-2Ddevel&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=rbTXQQLd6r1RKFIeCzZLf3oG7wNkyQ7ajc_OWw6ptl8&s=cxFKMxmeHWC_Ha6Oad1iwH0ljS0Oqkusb8nkpHRp-LY&e=
> >
> > >> >
> > >> ______________________________________________
> > >> R-package-devel using r-project.org
> > <mailto:R-package-devel using r-project.org> mailing list
> > >>
> > >>
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dpackage-2Ddevel&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=rbTXQQLd6r1RKFIeCzZLf3oG7wNkyQ7ajc_OWw6ptl8&s=cxFKMxmeHWC_Ha6Oad1iwH0ljS0Oqkusb8nkpHRp-LY&e=
> >
> > >> ______________________________________________
> > >> R-package-devel using r-project.org
> > <mailto:R-package-devel using r-project.org> mailing list
> > >>
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dpackage-2Ddevel&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=rbTXQQLd6r1RKFIeCzZLf3oG7wNkyQ7ajc_OWw6ptl8&s=cxFKMxmeHWC_Ha6Oad1iwH0ljS0Oqkusb8nkpHRp-LY&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 <mailto:hpages using fredhutch.org>
> > Phone: (206) 667-5791
> > Fax: (206) 667-1319
> >
>
> --
> 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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