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

[Martin Morgan]

what are the correct paths?

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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