[R-SIG-Mac] missing module when compiling R pkg:rms or external package SYMPHONY (in support of Bioc pkg symphony)

Fri May 5 03:12:34 CEST 2017

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?

-- 

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   