On May 5, 2017, at 7:46 AM, Frank Harrell <f.harrell at 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 <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
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