No longer failing in efforts to compile rms 5.1-1 from source. Probably related to the change in Makvears that Berend suggested. Appears the CRAN machine is now also distributing that versions in binary.
Thanks, Berend. David. > On May 5, 2017, at 7:46 AM, Frank Harrell <f.harr...@vanderbilt.edu> wrote: > > Please remove me from the emails and substitute Cole Beck > Frank > > > Frank E Harrell Jr Professor and Chairman School of > Medicine > > Department of Biostatistics Vanderbilt University > > On Fri, May 5, 2017 at 2:13 AM, Berend Hasselman <b...@xs4all.nl> wrote: > > > On 5 May 2017, at 03:12, David Winsemius <dwinsem...@comcast.net> wrote: > > > > Failing to get current rms package to compile (and appears that the CRAN > > build machine fails as well). The penultimate version of rms succeeds. > > > > Both from console and cmd-line I get this response in R 3.4.0 (just > > installed today) running El Cap 10.11.6 with Xcode Version 8.2.1 (8C1002): > > > > trying URL 'https://cran.cnr.berkeley.edu/src/contrib/rms_5.1-1.tar.gz' > > Content type 'application/x-gzip' length 521311 bytes (509 KB) > > ================================================== > > downloaded 509 KB > > > > Loading required package: lattice > > Loading required package: sos > > Loading required package: brew > > Loading required package: rms > > Loading required package: Hmisc > > Loading required package: survival > > Loading required package: Formula > > Loading required package: stats > > Loading required package: ggplot2 > > > > Attaching package: ‘Hmisc’ > > > > The following objects are masked from ‘package:base’: > > > > format.pval, round.POSIXt, trunc.POSIXt, units > > > > Loading required package: SparseM > > > > Attaching package: ‘SparseM’ > > > > The following object is masked from ‘package:base’: > > > > backsolve > > > > ##------ 2017-05-04 ------## > > Loading required package: graphics > > > > Attaching package: ‘graphics’ > > > > The following object is masked from ‘package:SparseM’: > > > > image > > > > * installing *source* package ‘rms’ ... > > ** package ‘rms’ successfully unpacked and MD5 sums checked > > ** libs > > clang -I/Library/Frameworks/R.framework/Resources/include > > -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o > > gfortran -fPIC -g -O2 -c lrmfit.f -o lrmfit.o > > gfortran -fPIC -g -O2 -c mlmats.f -o mlmats.o > > gfortran -fPIC -g -O2 -c ormuv.f -o ormuv.o > > gfortran -fPIC -g -O2 -c robcovf.f -o robcovf.o > > clang -dynamiclib -Wl,-headerpad_max_install_names -undefined > > dynamic_lookup -single_module -multiply_defined suppress > > -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o rms.so > > init.o lrmfit.o mlmats.o ormuv.o robcovf.o > > -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 > > -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm > > -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework > > -Wl,CoreFoundation > > installing to > > /Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs > > ** R > > ** demo > > ** inst > > ** preparing package for lazy loading > > ** help > > *** installing help indices > > ** building package indices > > ** testing if installed package can be loaded > > Loading required package: lattice > > Loading required package: sos > > Loading required package: brew > > Loading required package: rms > > Loading required package: Hmisc > > Loading required package: survival > > Loading required package: Formula > > Loading required package: stats > > Loading required package: ggplot2 > > > > Attaching package: ‘Hmisc’ > > > > The following objects are masked from ‘package:base’: > > > > format.pval, round.POSIXt, trunc.POSIXt, units > > > > Loading required package: SparseM > > > > Attaching package: ‘SparseM’ > > > > The following object is masked from ‘package:base’: > > > > backsolve > > > > Error: package or namespace load failed for ‘rms’ in dyn.load(file, DLLpath > > = DLLpath, ...): > > unable to load shared object > > '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so': > > dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so, > > 6): Symbol not found: ___addtf3 > > Referenced from: /usr/local/lib/libquadmath.0.dylib > > Expected in: /usr/local/lib/libgcc_s.1.dylib > > in /usr/local/lib/libquadmath.0.dylib > > ##------ 2017-05-04 ------## > > Loading required package: graphics > > > > Attaching package: ‘graphics’ > > > > The following object is masked from ‘package:SparseM’: > > > > image > > > > Error: package or namespace load failed for ‘rms’ in dyn.load(file, DLLpath > > = DLLpath, ...): > > unable to load shared object > > '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so': > > dlopen(/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms/libs/rms.so, > > 6): Symbol not found: ___addtf3 > > Referenced from: /usr/local/lib/libquadmath.0.dylib > > Expected in: /usr/local/lib/libgcc_s.1.dylib > > in /usr/local/lib/libquadmath.0.dylib > > Error: loading failed > > Execution halted > > > > The downloaded source packages are in > > > > ‘/private/var/folders/yq/m3j1jqtj6hq6s5mq_v0jn3s80000gn/T/Rtmpplg8Th/downloaded_packages’ > > > > (WARNING: partial output only, ask package author to use Rprintf instead!) > > ERROR: loading failed > > * removing > > ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms’ > > * restoring previous > > ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/rms’ > > > > I get the same result with this (minus the request "to use Rprinf instead!" > > > > $ R CMD INSTALL /Users/davidwinsemius/Downloads/rms_5.1-1.tar.gz > > > > Reported to Frank but he has seen no problems in his Linux builds. > > > > This page: > > > > https://github.com/JuliaLang/julia/issues/636 > > > > ... has a posting that says: > > > > "I found the solution: putting /usr/local/gfortran/lib at the beginning of > > DYLD_LIBRARY_PATH solved the problem. Previously I had .../gfortran/lib at > > the end of DYLD_LIBRARY_PATH." > > > > What more do I need to supply? > > > > A binary version of rms_5.1-1 is available on CRAN (now). > > I downloaded the rms source (manually) and ran R CMD check on the source with > this: > > _R_CHECK_FORCE_SUGGESTS_=0 R CMD check rms > > and have not encountered any problems. > > From the output you provided you appear to be using Apple's clang and not > clang4. > > I'm using clang4 as indicated on https://cran.r-project.org/bin/macosx/tools/ > and have this in my private Makevars: > > CC=/usr/local/clang4/bin/clang > CXX=/usr/local/clang4/bin/clang++ > LDFLAGS =-L/usr/local/clang4/lib > > I also have gfortran 6.1 for El Capitan (same as you). > Maybe not using clang4 is the source of the problem. > > Berend Hasselman > > -- > > > > David Winsemius > > Alameda, CA, USA > > > > > >> sessionInfo() > > R version 3.4.0 (2017-04-21) > > Platform: x86_64-apple-darwin15.6.0 (64-bit) > > Running under: OS X El Capitan 10.11.6 > > > > Matrix products: default > > BLAS: > > /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib > > LAPACK: > > /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib > > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] grDevices utils datasets graphics stats methods base > > > > other attached packages: > > [1] rms_5.1-1 SparseM_1.77 Hmisc_4.0-3 ggplot2_2.2.1 > > [5] Formula_1.2-1 survival_2.41-3 sos_1.4-1 brew_1.0-6 > > [9] lattice_0.20-35 > > > > loaded via a namespace (and not attached): > > [1] Rcpp_0.12.10 compiler_3.4.0 RColorBrewer_1.1-2 > > [4] plyr_1.8.4 base64enc_0.1-3 tools_3.4.0 > > [7] rpart_4.1-11 digest_0.6.12 tibble_1.3.0 > > [10] polspline_1.1.12 gtable_0.2.0 checkmate_1.8.2 > > [13] htmlTable_1.9 nlme_3.1-131 Matrix_1.2-10 > > [16] mvtnorm_1.0-6 gridExtra_2.2.1 stringr_1.2.0 > > [19] cluster_2.0.6 knitr_1.15.1 htmlwidgets_0.8 > > [22] MatrixModels_0.4-1 grid_3.4.0 nnet_7.3-12 > > [25] data.table_1.10.4 foreign_0.8-68 multcomp_1.4-6 > > [28] TH.data_1.0-8 latticeExtra_0.6-28 magrittr_1.5 > > [31] codetools_0.2-15 MASS_7.3-47 backports_1.0.5 > > [34] scales_0.4.1 htmltools_0.3.6 splines_3.4.0 > > [37] colorspace_1.3-2 quantreg_5.33 sandwich_2.3-4 > > [40] stringi_1.1.5 acepack_1.4.1 lazyeval_0.2.0 > > [43] munsell_0.4.3 zoo_1.8-0 > > > > _______________________________________________ > > R-SIG-Mac mailing list > > R-SIG-Mac@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac > > David Winsemius Alameda, CA, USA _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
