[R-SIG-Mac] missing module when compiling R pkg:rms or external package SYMPHONY (in support of Bioc pkg symphony)
David Winsemius
dwinsemius at comcast.net
Fri May 5 09:44:59 CEST 2017
> On May 5, 2017, at 12:13 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.
Thank you, Berend, for pointing me to the fine manual. After making those changes to my Makevars file, installing clang4, compiling rms 5.1-1 from source, and rebooting R I'm getting no further errors.
--
>
> 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
>>
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>
David Winsemius
Alameda, CA, USA
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