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

[Duncan Murdoch]

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://github.com/lucasnell/jackalope>) 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://bioconductor.org/packages/release/bioc/html/Rhtslib.html>. 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]]
>      >
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