Thanks everyone for your help. It's still giving me the same error on the development win-builder and on AppVeyor. Truncated install logs for both are below. I'm not sure that Rhtslib 1.91.1 (the one with the new changes) is being used on win-builder, which is why I've included the AppVeyor results—hopefully they're useful for what might happen on CRAN.
## APPVEYOR * installing *source* package 'jackalope' ... ** using staged installation ** libs *** arch - i386 C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/RLibrary/zlibbioc/include" -I"c:/R/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'C:/RLibrary/Rcpp/include' -I'C:/RLibrary/RcppArmadillo/include' -I'C:/RLibrary/RcppProgress/include' -I'C:/RLibrary/Rhtslib/include' -I'C:/RLibrary/zlibbioc/include' -I"C:/projects/BUILD/R-source-win32/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -c RcppExports.cpp -o RcppExports.o C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/RLibrary/zlibbioc/include" -I"c:/R/include" -DNDEBUG -I../inst/include/ -D_FILE_OFFSET_BITS=64 -I'C:/RLibrary/Rcpp/include' -I'C:/RLibrary/RcppArmadillo/include' -I'C:/RLibrary/RcppProgress/include' -I'C:/RLibrary/Rhtslib/include' -I'C:/RLibrary/zlibbioc/include' -I"C:/projects/BUILD/R-source-win32/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -c alter_reference.cpp -o alter_reference.o [...] C:/Rtools/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 -Lc:/R/bin/i386 -lRlapack -Lc:/R/bin/i386 -lRblas -lgfortran -lm -lquadmath C:/RLibrary/Rhtslib/usrlib/i386/libhts.a -LC:/projects/BUILD/R-source-win32/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/RLibrary/zlibbioc/libs/i386 -lzlib1bioc -LC:/projects/BUILD/R-source-win32/extsoft/lib/i386 -LC:/projects/BUILD/R-source-win32/extsoft/lib -Lc:/R/bin/i386 -lR C:/Rtools/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -lcurl C:/Rtools/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -lrtmp C:/Rtools/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -lssl C:/Rtools/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -lssh2 C:/Rtools/mingw_32/bin/../lib/gcc/i686-w64-mingw32/4.9.3/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -lcrypto C:/Rtools/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 'C:/projects/jackalope/jackalope.Rcheck/jackalope' ## WIN-BUILDER * 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/CRANpkg/lib/4.0/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++ -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/CRANpkg/lib/4.0/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 alter_reference.cpp -o alter_reference.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/CRANguest/R-devel/lib/jackalope' On Mon, Jan 27, 2020 at 5:45 PM Pages, Herve <hpa...@fredhutch.org> wrote: > 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-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://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]] > >> > > >> > ______________________________________________ > >> > R-package-devel@r-project.org mailing list > >> > > >> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dpackage-2Ddevel&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=rbTXQQLd6r1RKFIeCzZLf3oG7wNkyQ7ajc_OWw6ptl8&s=cxFKMxmeHWC_Ha6Oad1iwH0ljS0Oqkusb8nkpHRp-LY&e= > >> > > >> ______________________________________________ > >> R-package-devel@r-project.org mailing list > >> > >> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dpackage-2Ddevel&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=rbTXQQLd6r1RKFIeCzZLf3oG7wNkyQ7ajc_OWw6ptl8&s=cxFKMxmeHWC_Ha6Oad1iwH0ljS0Oqkusb8nkpHRp-LY&e= > >> ______________________________________________ > >> R-package-devel@r-project.org mailing list > >> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dpackage-2Ddevel&d=DwIDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=rbTXQQLd6r1RKFIeCzZLf3oG7wNkyQ7ajc_OWw6ptl8&s=cxFKMxmeHWC_Ha6Oad1iwH0ljS0Oqkusb8nkpHRp-LY&e= > >> > > > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpa...@fredhutch.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
