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

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"
<r-package-devel-bounces at r-project.org on behalf of
ligges at 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
     >
     >
     >
     > * 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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--
Herv? Pag?s

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