> On May 4, 2017, at 6:12 PM, 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):
Also tried to see which gfortran was retruned along hte R search path:
> system("gfortran -v")
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/gfortran/libexec/gcc/x86_64-apple-darwin15/6.1.0/lto-wrapper
Target: x86_64-apple-darwin15
Configured with: ../gcc-6.1.0/configure --prefix=/usr/local/gfortran
--with-gmp=/Users/fx/devel/gcc/deps-static/x86_64
--enable-languages=c,c++,fortran,objc,obj-c++ --build=x86_64-apple-darwin15
Thread model: posix
gcc version 6.1.0 (GCC)
>
> 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?
>
> --
>
> 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
>
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David Winsemius
Alameda, CA, USA
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