[R-SIG-Mac] missing module when compiling R pkg:rms or external package SYMPHONY (in support of Bioc pkg symphony)
Frank Harrell
f.harrell at vanderbilt.edu
Fri May 5 16:46:40 CEST 2017
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 <bhh at xs4all.nl> wrote:
>
> > On 5 May 2017, at 03:12, David Winsemius <dwinsemius at 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 at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>
>
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