[R-pkg-devel] CRAN cannot find libraries on Windows
Lucas Nell
|uc@@ @end|ng |rom |uc@@ne||@com
Sun Feb 2 20:55:58 CET 2020
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> wrote:
> OK thanks. I'm using LOCAL_SOFT now in Rhtslib instead of hardcoded
> C:/extsoft:
>
>
>
> https://github.com/Bioconductor/Rhtslib/commit/1052c4c2e467fa8e3db613a70af2f77448956d38
>
> 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 on behalf of
> >> 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 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 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 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
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
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