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-boun...@r-project.org on behalf of 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://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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