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

[Lucas Nell]

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'

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