Hello Hervé, Thanks for confirming what I was thinking. Does anyone know how long it should take for win-builder to use the updated Rhtslib version? I just tried it again today, and it's still using the older version.
Cheers, Lucas On Sun, Feb 2, 2020 at 11:34 PM Hervé Pagès <hpa...@fredhutch.org> wrote: > To me it looks like the situation on AppVeyor and on win-builder is not > quite the same: > > - On AppVeyor the compiler and linker are expecting the "external > software" to be in C:/projects/BUILD/R-source-win32/extsoft/ and no > longer in C:/extsoft/lib/i386. This indicates that AppVeyor is using the > latest Rhtslib (1.91.1). However the linker still cannot find libraries > -lcurl, -lrtmp, -lssl, etc... Not sure why. Are curl.a, rtmp.a, ssl.a, > really there? If not, this looks like a configuration issue with AppVeyor. > > - On win-builder the linker is still using -LC:/extsoft/lib/i386 which > indicates that it's not using the latest Rhtslib. > > H. > > > On 2/2/20 11:55, Lucas Nell wrote: > > > > 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 > > <mailto: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 > > < > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Rhtslib_commit_1052c4c2e467fa8e3db613a70af2f77448956d38&d=DwMFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=xiTfiuG9CwLnlGAyvQGivg_JKm3MmKwMoMzTqTFCuSk&s=PvRg3n4qfjPrOSZuov1NuLFPXB8Wi8hLDHEK7V4q2ZE&e= > > > > > > 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 > > <mailto:r-package-devel-boun...@r-project.org> on behalf of > > >> lig...@statistik.tu-dortmund.de > > <mailto: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 > > <mailto: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 > > <mailto: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 > > <mailto: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 <mailto:hpa...@fredhutch.org> > > Phone: (206) 667-5791 > > Fax: (206) 667-1319 > > > > -- > 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
