[R-pkg-devel] CRAN cannot find libraries on Windows

[Lucas Nell]

Hello all,

My package (source here ) 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
. 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'

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Re: [R-pkg-devel] CRAN cannot find libraries on Windows

[Lucas Nell]

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  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"
> >>  >> lig...@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
> >>  >
> >>  >
> >>  >
> >>  > * installi

Re: [R-pkg-devel] CRAN cannot find libraries on Windows

[Lucas Nell]

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  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*