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

[Uwe Ligges]

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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