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MacOS 10.13 R cannot install some library with C compiler #9872

Closed ALLCCN closed 6 years ago

ALLCCN commented 6 years ago

Actual Behavior

Recently I update my mac from 10.12 to 10.13, and find out some libraries in R can not be used. Then I try to re-build the R env, but it shows that some library can not be install in R, like:

* installing *source* package ‘dbarts’ ...
** package ‘dbarts’ successfully unpacked and MD5 sums checked
checking for gcc... x86_64-apple-darwin13.4.0-clang
checking whether the C compiler works... no
configure: error: in `/private/var/folders/xl/lps1y28d097bgxv7krghnhz40000gn/T/RtmpnljNvA/R.INSTALLd04588f126f/dbarts':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘dbarts'

I'm sure I have install Xcode command line, and clang -v in conda r env:

clang version 4.0.1 (tags/RELEASE_401/final)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
InstalledDir: /Users/*/anaconda3/envs/ukR/bin

In the system env:

Apple LLVM version 9.1.0 (clang-902.0.39.2)
Target: x86_64-apple-darwin17.7.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

I also try #7068 with conda install clangxx_osx-64 and conda install gfortran_osx-64, but they have already been here.

Steps to Reproduce

Anaconda or Miniconda version: 1.8.7
Operating System: MacOs 10.13.6
conda info
     active environment : ukR
    active env location : /Users/*/anaconda3/envs/ukR
            shell level : 2
       user config file : /Users/*/.condarc
 populated config files : /Users/*/.condarc
          conda version : 4.5.9
    conda-build version : 3.12.0
         python version : 3.6.6.final.0
       base environment : /Users/*/anaconda3  (writable)
           channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/osx-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/osx-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /Users/*/anaconda3/pkgs
                          /Users/*/.conda/pkgs
       envs directories : /Users/*/anaconda3/envs
                          /Users/8/.conda/envs
               platform : osx-64
             user-agent : conda/4.5.9 requests/2.19.1 CPython/3.6.6 Darwin/17.7.0 OSX/10.13.6
                UID:GID : 501:20
             netrc file : None
           offline mode : False
conda list --show-channel-urls
# packages in environment at /Users/*/anaconda3/envs/ukR:
#
# Name                    Version                   Build  Channel
_r-mutex                  1.0.0               anacondar_1    defaults
appdirs                   1.4.3            py37h28b3542_0    defaults
appnope                   0.1.0                    py37_0    defaults
asn1crypto                0.24.0                   py37_0    defaults
attrs                     18.1.0                   py37_0    defaults
automat                   0.7.0                    py37_0    defaults
backcall                  0.1.0                    py37_0    defaults
blas                      1.0                    openblas    defaults
bleach                    2.1.3                    py37_0    defaults
bwidget                   1.9.11                        0    defaults
bzip2                     1.0.6                h1de35cc_5    defaults
ca-certificates           2018.03.07                    0    defaults
cairo                     1.14.12              hc4e6be7_4    defaults
cctools                   895                  h7512d6f_0    defaults
certifi                   2018.4.16                py37_0    defaults
cffi                      1.11.5           py37h342bebf_0    defaults
clang                     4.0.1                h662ec87_0    defaults
clang_osx-64              4.0.1               h1ce6c1d_11    defaults
clangxx                   4.0.1                hc9b4283_0    defaults
clangxx_osx-64            4.0.1               h22b1bf0_11    defaults
compiler-rt               4.0.1                h5487866_0    defaults
constantly                15.1.0           py37h28b3542_0    defaults
cryptography              2.2.2            py37h1de35cc_0    defaults
curl                      7.61.0               ha441bb4_0    defaults
decorator                 4.3.0                    py37_0    defaults
entrypoints               0.2.3                    py37_2    defaults
fontconfig                2.13.0               h5d5b041_1    defaults
freetype                  2.9.1                hb4e5f40_0    defaults
fribidi                   1.0.4                h1de35cc_0    defaults
gettext                   0.19.8.1             h15daf44_3    defaults
gfortran_osx-64           4.8.5                h22b1bf0_3    defaults
glib                      2.56.1               h35bc53a_0    defaults
graphite2                 1.3.11               h2098e52_2    defaults
gsl                       2.4                  h1de35cc_4    defaults
harfbuzz                  1.8.4                hb8d4a28_0    defaults
html5lib                  1.0.1                    py37_0    defaults
hyperlink                 18.0.0                   py37_0    defaults
icu                       58.2                 h4b95b61_1    defaults
idna                      2.7                      py37_0    defaults
incremental               17.5.0                   py37_0    defaults
ipykernel                 4.8.2                    py37_0    defaults
ipython                   6.5.0                    py37_0    defaults
ipython_genutils          0.2.0                    py37_0    defaults
jedi                      0.12.1                   py37_0    defaults
jinja2                    2.10                     py37_0    defaults
jpeg                      9b                   he5867d9_2    defaults
jsonschema                2.6.0                    py37_0    defaults
jupyter_client            5.2.3                    py37_0    defaults
jupyter_core              4.4.0                    py37_0    defaults
krb5                      1.16.1               h24a3359_6    defaults
ld64                      274.2                h7c2db76_0    defaults
libcurl                   7.61.0               hf30b1f0_0    defaults
libcxx                    4.0.1                h579ed51_0    defaults
libcxxabi                 4.0.1                hebd6815_0    defaults
libedit                   3.1.20170329         hb402a30_2    defaults
libffi                    3.2.1                h475c297_4    defaults
libgfortran               3.0.1                h93005f0_2    defaults
libiconv                  1.15                 hdd342a3_7    defaults
libopenblas               0.2.20               hdc02c5d_7    defaults
libpng                    1.6.34               he12f830_0    defaults
libsodium                 1.0.16               h3efe00b_0    defaults
libssh2                   1.8.0                h322a93b_4    defaults
libtiff                   4.0.9                hcb84e12_1    defaults
libxml2                   2.9.8                hab757c2_1    defaults
llvm                      4.0.1                hc748206_0    defaults
llvm-lto-tapi             4.0.1                h6701bc3_0    defaults
llvm-openmp               4.0.1                hda82c8b_0    defaults
make                      4.2.1                h3efe00b_1    defaults
markupsafe                1.0              py37h1de35cc_1    defaults
mistune                   0.8.3            py37h1de35cc_1    defaults
nbconvert                 5.3.1                    py37_0    defaults
nbformat                  4.4.0                    py37_0    defaults
ncurses                   6.1                  h0a44026_0    defaults
notebook                  5.6.0                    py37_0    defaults
openssl                   1.0.2o               h1de35cc_1    defaults
pandoc                    2.2.1                h1a437c5_0    defaults
pandocfilters             1.4.2                    py37_1    defaults
pango                     1.42.2               h060686c_0    defaults
parso                     0.3.1                    py37_0    defaults
pcre                      8.42                 h378b8a2_0    defaults
pexpect                   4.6.0                    py37_0    defaults
pickleshare               0.7.4                    py37_0    defaults
pip                       10.0.1                   py37_0    defaults
pixman                    0.34.0               hca0a616_3    defaults
prometheus_client         0.3.1                    py37_0    defaults
prompt_toolkit            1.0.15                   py37_0    defaults
ptyprocess                0.6.0                    py37_0    defaults
pyasn1                    0.4.4                    py37_0    defaults
pyasn1-modules            0.2.2                    py37_0    defaults
pycparser                 2.18                     py37_1    defaults
pygments                  2.2.0                    py37_0    defaults
pyopenssl                 18.0.0                   py37_0    defaults
python                    3.7.0                hc167b69_0    defaults
python-dateutil           2.7.3                    py37_0    defaults
pyzmq                     17.0.0           py37h1de35cc_3    defaults
r-abind                   1.4_5            r350h912f1d8_0    defaults
r-assertthat              0.2.0            r350h912f1d8_0    defaults
r-backports               1.1.2            r350h459e2dc_0    defaults
r-base                    3.5.0                hf781afb_1    defaults
r-base64enc               0.1_3            r350h459e2dc_4    defaults
r-bh                      1.66.0_1         r350h912f1d8_0    defaults
r-bindr                   0.1.1            r350h912f1d8_0    defaults
r-bindrcpp                0.2.2            r350h1104f25_0    defaults
r-boot                    1.3_20           r350h912f1d8_0    defaults
r-broom                   0.4.4            r350h912f1d8_0    defaults
r-callr                   2.0.3            r350h1104f25_0    defaults
r-caret                   6.0_79           r350h459e2dc_0    defaults
r-cellranger              1.1.0            r350h912f1d8_0    defaults
r-class                   7.3_14           r350h459e2dc_4    defaults
r-cli                     1.0.0            r350h912f1d8_0    defaults
r-cluster                 2.0.7_1          r350h9092e51_0    defaults
r-codetools               0.2_15           r350h912f1d8_0    defaults
r-colorspace              1.3_2            r350h459e2dc_0    defaults
r-crayon                  1.3.4            r350h912f1d8_0    defaults
r-curl                    3.2              r350h459e2dc_0    defaults
r-cvst                    0.2_1            r350h912f1d8_0    defaults
r-data.table              1.10.4_3         r350h459e2dc_0    defaults
r-dbi                     0.8              r350h912f1d8_0    defaults
r-dbplyr                  1.2.1            r350h912f1d8_0    defaults
r-ddalpha                 1.3.2            r350h82edaba_0    defaults
r-debugme                 1.1.0            r350h912f1d8_0    defaults
r-deoptimr                1.0_8            r350h912f1d8_0    defaults
r-devtools                1.13.5           r350h1104f25_0    defaults
r-dichromat               2.0_0            r350h912f1d8_4    defaults
r-digest                  0.6.15           r350h459e2dc_0    defaults
r-dimred                  0.1.0            r350h912f1d8_0    defaults
r-dplyr                   0.7.4            r350h1104f25_0    defaults
r-drr                     0.0.3            r350h912f1d8_0    defaults
r-essentials              3.5.0                    r350_0    defaults
r-evaluate                0.10.1           r350h912f1d8_0    defaults
r-forcats                 0.3.0            r350h912f1d8_0    defaults
r-foreach                 1.4.4            r350h912f1d8_0    defaults
r-foreign                 0.8_70           r350h459e2dc_0    defaults
r-formatr                 1.5              r350h912f1d8_0    defaults
r-geometry                0.3_6            r350h459e2dc_0    defaults
r-ggplot2                 2.2.1            r350h912f1d8_0    defaults
r-git2r                   0.21.0           r350h459e2dc_0    defaults
r-glmnet                  2.0_16           r350h9092e51_0    defaults
r-glue                    1.2.0            r350h459e2dc_0    defaults
r-gower                   0.1.2            r350h459e2dc_0    defaults
r-gtable                  0.2.0            r350h912f1d8_0    defaults
r-haven                   1.1.1            r350h1104f25_0    defaults
r-hexbin                  1.27.2           r350h9092e51_0    defaults
r-highr                   0.6              r350h912f1d8_0    defaults
r-hms                     0.4.2            r350h912f1d8_0    defaults
r-htmltools               0.3.6            r350h1104f25_0    defaults
r-htmlwidgets             1.2              r350h912f1d8_0    defaults
r-httpuv                  1.4.1            r350h1104f25_0    defaults
r-httr                    1.3.1            r350h912f1d8_0    defaults
r-ipred                   0.9_6            r350h459e2dc_0    defaults
r-irdisplay               0.4.4            r350h912f1d8_0    defaults
r-irkernel                0.8.11                   r350_0    defaults
r-iterators               1.0.9            r350h912f1d8_0    defaults
r-jsonlite                1.5              r350h459e2dc_0    defaults
r-kernlab                 0.9_25           r350h82edaba_0    defaults
r-kernsmooth              2.23_15          r350h9092e51_4    defaults
r-knitr                   1.20             r350h912f1d8_0    defaults
r-labeling                0.3              r350h912f1d8_4    defaults
r-later                   0.7.1            r350h1104f25_0    defaults
r-lattice                 0.20_35          r350h459e2dc_0    defaults
r-lava                    1.6.1            r350h912f1d8_0    defaults
r-lazyeval                0.2.1            r350h459e2dc_0    defaults
r-lubridate               1.7.4            r350h1104f25_0    defaults
r-magic                   1.5_8            r350h912f1d8_0    defaults
r-magrittr                1.5              r350h912f1d8_4    defaults
r-maps                    3.3.0            r350h459e2dc_0    defaults
r-markdown                0.8              r350h459e2dc_0    defaults
r-mass                    7.3_49           r350h459e2dc_0    defaults
r-matrix                  1.2_14           r350h459e2dc_0    defaults
r-memoise                 1.1.0            r350h912f1d8_0    defaults
r-mgcv                    1.8_23           r350h459e2dc_0    defaults
r-mime                    0.5              r350h459e2dc_0    defaults
r-mnormt                  1.5_5            r350h9092e51_0    defaults
r-modelmetrics            1.1.0            r350h1104f25_0    defaults
r-modelr                  0.1.1            r350h912f1d8_0    defaults
r-munsell                 0.4.3            r350h912f1d8_0    defaults
r-nlme                    3.1_137          r350h9092e51_0    defaults
r-nnet                    7.3_12           r350h459e2dc_0    defaults
r-numderiv                2016.8_1         r350h912f1d8_0    defaults
r-openssl                 1.0.1            r350h459e2dc_0    defaults
r-pbdzmq                  0.3_2            r350h1104f25_0    defaults
r-pillar                  1.2.1            r350h912f1d8_0    defaults
r-pkgconfig               2.0.1            r350h912f1d8_0    defaults
r-plogr                   0.2.0            r350h912f1d8_0    defaults
r-plyr                    1.8.4            r350h1104f25_0    defaults
r-praise                  1.0.0            r350h912f1d8_4    defaults
r-prodlim                 2018.04.18       r350h1104f25_0    defaults
r-promises                1.0.1            r350h1104f25_0    defaults
r-psych                   1.8.3.3          r350h912f1d8_0    defaults
r-purrr                   0.2.4            r350h459e2dc_0    defaults
r-quantmod                0.4_13           r350h912f1d8_0    defaults
r-r6                      2.2.2            r350h912f1d8_0    defaults
r-randomforest            4.6_14           r350h9092e51_0    defaults
r-rbokeh                  0.6.3                    r350_0    defaults
r-rcolorbrewer            1.1_2            r350h912f1d8_0    defaults
r-rcpp                    0.12.16          r350h1104f25_0    defaults
r-rcpproll                0.2.2            r350h1104f25_0    defaults
r-readr                   1.1.1            r350h1104f25_0    defaults
r-readxl                  1.1.0            r350h1104f25_0    defaults
r-recipes                 0.1.2            r350h912f1d8_0    defaults
r-recommended             3.5.0                    r350_0    defaults
r-rematch                 1.0.1            r350h912f1d8_0    defaults
r-repr                    0.13             r350h912f1d8_0    defaults
r-reprex                  0.1.2            r350h912f1d8_0    defaults
r-reshape2                1.4.3            r350h1104f25_0    defaults
r-rlang                   0.2.0            r350h459e2dc_0    defaults
r-rmarkdown               1.9              r350h912f1d8_0    defaults
r-robustbase              0.92_8           r350h9092e51_0    defaults
r-rpart                   4.1_13           r350h459e2dc_0    defaults
r-rprojroot               1.3_2            r350h912f1d8_0    defaults
r-rstudioapi              0.7              r350h912f1d8_0    defaults
r-rvest                   0.3.2            r350h912f1d8_0    defaults
r-scales                  0.5.0            r350h1104f25_0    defaults
r-selectr                 0.4_1            r350h912f1d8_0    defaults
r-sfsmisc                 1.1_2            r350h912f1d8_0    defaults
r-shiny                   1.0.5            r350h912f1d8_0    defaults
r-sourcetools             0.1.6            r350h1104f25_0    defaults
r-spatial                 7.3_11           r350h459e2dc_4    defaults
r-squarem                 2017.10_1        r350h912f1d8_0    defaults
r-stringi                 1.1.7            r350h1104f25_0    defaults
r-stringr                 1.3.0            r350h912f1d8_0    defaults
r-survival                2.42_3           r350h459e2dc_0    defaults
r-testthat                2.0.0            r350h1104f25_0    defaults
r-tibble                  1.4.2            r350h459e2dc_0    defaults
r-tidyr                   0.8.0            r350h1104f25_0    defaults
r-tidyselect              0.2.4            r350h1104f25_0    defaults
r-tidyverse               1.2.1            r350h912f1d8_0    defaults
r-timedate                3043.102         r350h912f1d8_0    defaults
r-ttr                     0.23_3           r350h9092e51_0    defaults
r-utf8                    1.1.3            r350h459e2dc_0    defaults
r-uuid                    0.1_2            r350h459e2dc_4    defaults
r-viridislite             0.3.0            r350h912f1d8_0    defaults
r-whisker                 0.3_2            r350h912f1d8_4    defaults
r-withr                   2.1.2            r350h912f1d8_0    defaults
r-xml2                    1.2.0            r350h1104f25_0    defaults
r-xtable                  1.8_2            r350h912f1d8_0    defaults
r-xts                     0.10_2           r350h9092e51_0    defaults
r-yaml                    2.1.18           r350h459e2dc_0    defaults
r-zoo                     1.8_1            r350h459e2dc_0    defaults
readline                  7.0                  hc1231fa_4    defaults
send2trash                1.5.0                    py37_0    defaults
service_identity          17.0.0           py37h28b3542_0    defaults
setuptools                39.2.0                   py37_0    defaults
simplegeneric             0.8.1                    py37_2    defaults
six                       1.11.0                   py37_1    defaults
sqlite                    3.24.0               ha441bb4_0    defaults
terminado                 0.8.1                    py37_1    defaults
testpath                  0.3.1                    py37_0    defaults
tk                        8.6.7                h35a86e2_3    defaults
tktable                   2.10                 h1de35cc_0    defaults
tornado                   5.0.2            py37h1de35cc_0    defaults
traitlets                 4.3.2                    py37_0    defaults
twisted                   18.4.0           py37h1de35cc_0    defaults
wcwidth                   0.1.7                    py37_0    defaults
webencodings              0.5.1                    py37_1    defaults
wheel                     0.31.1                   py37_0    defaults
xz                        5.2.4                h1de35cc_4    defaults
zeromq                    4.2.5                h0a44026_0    defaults
zlib                      1.2.11               hf3cbc9b_2    defaults
zope                      1.0                      py37_0    defaults
zope.interface            4.5.0            py37h1de35cc_0    defaults
mingwandroid commented 6 years ago

You are meant to use Anacondas compilers.

On Sat, Aug 4, 2018, 4:30 PM AL notifications@github.com wrote:

Actual Behavior

Recently I update my mac from 10.12 to 10.13, and find out some libraries in R can not be used. Then I try to re-build the R env, but it shows that some library can not be install in R, like:

  • installing source package ‘dbarts’ ... ** package ‘dbarts’ successfully unpacked and MD5 sums checked checking for gcc... x86_64-apple-darwin13.4.0-clang checking whether the C compiler works... no configure: error: in /private/var/folders/xl/lps1y28d097bgxv7krghnhz40000gn/T/RtmpnljNvA/R.INSTALLd04588f126f/dbarts': configure: error: C compiler cannot create executables Seeconfig.log' for more details ERROR: configuration failed for package ‘dbarts'

I'm sure I have install Xcode command line, and clang -v in conda r env:

clang version 4.0.1 (tags/RELEASE_401/final) Target: x86_64-apple-darwin17.7.0 Thread model: posix InstalledDir: /Users/*/anaconda3/envs/ukR/bin

In the system env:

Apple LLVM version 9.1.0 (clang-902.0.39.2) Target: x86_64-apple-darwin17.7.0 Thread model: posix InstalledDir: /Library/Developer/CommandLineTools/usr/bin

Steps to Reproduce

  • conda create -n ukR r-essentials
  • open R in terminal
  • install.packages('rbarts')

Anaconda or Miniconda version: 1.8.7 Operating System: MacOs 10.13.6 conda info

 active environment : ukR
active env location : /Users/*/anaconda3/envs/ukR
        shell level : 2
   user config file : /Users/*/.condarc

populated config files : /Users//.condarc conda version : 4.5.9 conda-build version : 3.12.0 python version : 3.6.6.final.0 base environment : /Users//anaconda3 (writable) channel URLs : https://repo.anaconda.com/pkgs/main/osx-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/osx-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/osx-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/pro/osx-64 https://repo.anaconda.com/pkgs/pro/noarch package cache : /Users//anaconda3/pkgs /Users//.conda/pkgs envs directories : /Users/*/anaconda3/envs /Users/8/.conda/envs platform : osx-64 user-agent : conda/4.5.9 requests/2.19.1 CPython/3.6.6 Darwin/17.7.0 OSX/10.13.6 UID:GID : 501:20 netrc file : None offline mode : False

conda list --show-channel-urls

packages in environment at /Users/*/anaconda3/envs/ukR:

#

Name Version Build Channel

_r-mutex 1.0.0 anacondar_1 defaults appdirs 1.4.3 py37h28b3542_0 defaults appnope 0.1.0 py37_0 defaults asn1crypto 0.24.0 py37_0 defaults attrs 18.1.0 py37_0 defaults automat 0.7.0 py37_0 defaults backcall 0.1.0 py37_0 defaults blas 1.0 openblas defaults bleach 2.1.3 py37_0 defaults bwidget 1.9.11 0 defaults bzip2 1.0.6 h1de35cc_5 defaults ca-certificates 2018.03.07 0 defaults cairo 1.14.12 hc4e6be7_4 defaults cctools 895 h7512d6f_0 defaults certifi 2018.4.16 py37_0 defaults cffi 1.11.5 py37h342bebf_0 defaults clang 4.0.1 h662ec87_0 defaults clang_osx-64 4.0.1 h1ce6c1d_11 defaults clangxx 4.0.1 hc9b4283_0 defaults clangxx_osx-64 4.0.1 h22b1bf0_11 defaults compiler-rt 4.0.1 h5487866_0 defaults constantly 15.1.0 py37h28b3542_0 defaults cryptography 2.2.2 py37h1de35cc_0 defaults curl 7.61.0 ha441bb4_0 defaults decorator 4.3.0 py37_0 defaults entrypoints 0.2.3 py37_2 defaults fontconfig 2.13.0 h5d5b041_1 defaults freetype 2.9.1 hb4e5f40_0 defaults fribidi 1.0.4 h1de35cc_0 defaults gettext 0.19.8.1 h15daf44_3 defaults gfortran_osx-64 4.8.5 h22b1bf0_3 defaults glib 2.56.1 h35bc53a_0 defaults graphite2 1.3.11 h2098e52_2 defaults gsl 2.4 h1de35cc_4 defaults harfbuzz 1.8.4 hb8d4a28_0 defaults html5lib 1.0.1 py37_0 defaults hyperlink 18.0.0 py37_0 defaults icu 58.2 h4b95b61_1 defaults idna 2.7 py37_0 defaults incremental 17.5.0 py37_0 defaults ipykernel 4.8.2 py37_0 defaults ipython 6.5.0 py37_0 defaults ipython_genutils 0.2.0 py37_0 defaults jedi 0.12.1 py37_0 defaults jinja2 2.10 py37_0 defaults jpeg 9b he5867d9_2 defaults jsonschema 2.6.0 py37_0 defaults jupyter_client 5.2.3 py37_0 defaults jupyter_core 4.4.0 py37_0 defaults krb5 1.16.1 h24a3359_6 defaults ld64 274.2 h7c2db76_0 defaults libcurl 7.61.0 hf30b1f0_0 defaults libcxx 4.0.1 h579ed51_0 defaults libcxxabi 4.0.1 hebd6815_0 defaults libedit 3.1.20170329 hb402a30_2 defaults libffi 3.2.1 h475c297_4 defaults libgfortran 3.0.1 h93005f0_2 defaults libiconv 1.15 hdd342a3_7 defaults libopenblas 0.2.20 hdc02c5d_7 defaults libpng 1.6.34 he12f830_0 defaults libsodium 1.0.16 h3efe00b_0 defaults libssh2 1.8.0 h322a93b_4 defaults libtiff 4.0.9 hcb84e12_1 defaults libxml2 2.9.8 hab757c2_1 defaults llvm 4.0.1 hc748206_0 defaults llvm-lto-tapi 4.0.1 h6701bc3_0 defaults llvm-openmp 4.0.1 hda82c8b_0 defaults make 4.2.1 h3efe00b_1 defaults markupsafe 1.0 py37h1de35cc_1 defaults mistune 0.8.3 py37h1de35cc_1 defaults nbconvert 5.3.1 py37_0 defaults nbformat 4.4.0 py37_0 defaults ncurses 6.1 h0a44026_0 defaults notebook 5.6.0 py37_0 defaults openssl 1.0.2o h1de35cc_1 defaults pandoc 2.2.1 h1a437c5_0 defaults pandocfilters 1.4.2 py37_1 defaults pango 1.42.2 h060686c_0 defaults parso 0.3.1 py37_0 defaults pcre 8.42 h378b8a2_0 defaults pexpect 4.6.0 py37_0 defaults pickleshare 0.7.4 py37_0 defaults pip 10.0.1 py37_0 defaults pixman 0.34.0 hca0a616_3 defaults prometheus_client 0.3.1 py37_0 defaults prompt_toolkit 1.0.15 py37_0 defaults ptyprocess 0.6.0 py37_0 defaults pyasn1 0.4.4 py37_0 defaults pyasn1-modules 0.2.2 py37_0 defaults pycparser 2.18 py37_1 defaults pygments 2.2.0 py37_0 defaults pyopenssl 18.0.0 py37_0 defaults python 3.7.0 hc167b69_0 defaults python-dateutil 2.7.3 py37_0 defaults pyzmq 17.0.0 py37h1de35cc_3 defaults r-abind 1.4_5 r350h912f1d8_0 defaults r-assertthat 0.2.0 r350h912f1d8_0 defaults r-backports 1.1.2 r350h459e2dc_0 defaults r-base 3.5.0 hf781afb_1 defaults r-base64enc 0.1_3 r350h459e2dc_4 defaults r-bh 1.66.0_1 r350h912f1d8_0 defaults r-bindr 0.1.1 r350h912f1d8_0 defaults r-bindrcpp 0.2.2 r350h1104f25_0 defaults r-boot 1.3_20 r350h912f1d8_0 defaults r-broom 0.4.4 r350h912f1d8_0 defaults r-callr 2.0.3 r350h1104f25_0 defaults r-caret 6.0_79 r350h459e2dc_0 defaults r-cellranger 1.1.0 r350h912f1d8_0 defaults r-class 7.3_14 r350h459e2dc_4 defaults r-cli 1.0.0 r350h912f1d8_0 defaults r-cluster 2.0.7_1 r350h9092e51_0 defaults r-codetools 0.2_15 r350h912f1d8_0 defaults r-colorspace 1.3_2 r350h459e2dc_0 defaults r-crayon 1.3.4 r350h912f1d8_0 defaults r-curl 3.2 r350h459e2dc_0 defaults r-cvst 0.2_1 r350h912f1d8_0 defaults r-data.table 1.10.4_3 r350h459e2dc_0 defaults r-dbi 0.8 r350h912f1d8_0 defaults r-dbplyr 1.2.1 r350h912f1d8_0 defaults r-ddalpha 1.3.2 r350h82edaba_0 defaults r-debugme 1.1.0 r350h912f1d8_0 defaults r-deoptimr 1.0_8 r350h912f1d8_0 defaults r-devtools 1.13.5 r350h1104f25_0 defaults r-dichromat 2.0_0 r350h912f1d8_4 defaults r-digest 0.6.15 r350h459e2dc_0 defaults r-dimred 0.1.0 r350h912f1d8_0 defaults r-dplyr 0.7.4 r350h1104f25_0 defaults r-drr 0.0.3 r350h912f1d8_0 defaults r-essentials 3.5.0 r350_0 defaults r-evaluate 0.10.1 r350h912f1d8_0 defaults r-forcats 0.3.0 r350h912f1d8_0 defaults r-foreach 1.4.4 r350h912f1d8_0 defaults r-foreign 0.8_70 r350h459e2dc_0 defaults r-formatr 1.5 r350h912f1d8_0 defaults r-geometry 0.3_6 r350h459e2dc_0 defaults r-ggplot2 2.2.1 r350h912f1d8_0 defaults r-git2r 0.21.0 r350h459e2dc_0 defaults r-glmnet 2.0_16 r350h9092e51_0 defaults r-glue 1.2.0 r350h459e2dc_0 defaults r-gower 0.1.2 r350h459e2dc_0 defaults r-gtable 0.2.0 r350h912f1d8_0 defaults r-haven 1.1.1 r350h1104f25_0 defaults r-hexbin 1.27.2 r350h9092e51_0 defaults r-highr 0.6 r350h912f1d8_0 defaults r-hms 0.4.2 r350h912f1d8_0 defaults r-htmltools 0.3.6 r350h1104f25_0 defaults r-htmlwidgets 1.2 r350h912f1d8_0 defaults r-httpuv 1.4.1 r350h1104f25_0 defaults r-httr 1.3.1 r350h912f1d8_0 defaults r-ipred 0.9_6 r350h459e2dc_0 defaults r-irdisplay 0.4.4 r350h912f1d8_0 defaults r-irkernel 0.8.11 r350_0 defaults r-iterators 1.0.9 r350h912f1d8_0 defaults r-jsonlite 1.5 r350h459e2dc_0 defaults r-kernlab 0.9_25 r350h82edaba_0 defaults r-kernsmooth 2.23_15 r350h9092e51_4 defaults r-knitr 1.20 r350h912f1d8_0 defaults r-labeling 0.3 r350h912f1d8_4 defaults r-later 0.7.1 r350h1104f25_0 defaults r-lattice 0.20_35 r350h459e2dc_0 defaults r-lava 1.6.1 r350h912f1d8_0 defaults r-lazyeval 0.2.1 r350h459e2dc_0 defaults r-lubridate 1.7.4 r350h1104f25_0 defaults r-magic 1.5_8 r350h912f1d8_0 defaults r-magrittr 1.5 r350h912f1d8_4 defaults r-maps 3.3.0 r350h459e2dc_0 defaults r-markdown 0.8 r350h459e2dc_0 defaults r-mass 7.3_49 r350h459e2dc_0 defaults r-matrix 1.2_14 r350h459e2dc_0 defaults r-memoise 1.1.0 r350h912f1d8_0 defaults r-mgcv 1.8_23 r350h459e2dc_0 defaults r-mime 0.5 r350h459e2dc_0 defaults r-mnormt 1.5_5 r350h9092e51_0 defaults r-modelmetrics 1.1.0 r350h1104f25_0 defaults r-modelr 0.1.1 r350h912f1d8_0 defaults r-munsell 0.4.3 r350h912f1d8_0 defaults r-nlme 3.1_137 r350h9092e51_0 defaults r-nnet 7.3_12 r350h459e2dc_0 defaults r-numderiv 2016.8_1 r350h912f1d8_0 defaults r-openssl 1.0.1 r350h459e2dc_0 defaults r-pbdzmq 0.3_2 r350h1104f25_0 defaults r-pillar 1.2.1 r350h912f1d8_0 defaults r-pkgconfig 2.0.1 r350h912f1d8_0 defaults r-plogr 0.2.0 r350h912f1d8_0 defaults r-plyr 1.8.4 r350h1104f25_0 defaults r-praise 1.0.0 r350h912f1d8_4 defaults r-prodlim 2018.04.18 r350h1104f25_0 defaults r-promises 1.0.1 r350h1104f25_0 defaults r-psych 1.8.3.3 r350h912f1d8_0 defaults r-purrr 0.2.4 r350h459e2dc_0 defaults r-quantmod 0.4_13 r350h912f1d8_0 defaults r-r6 2.2.2 r350h912f1d8_0 defaults r-randomforest 4.6_14 r350h9092e51_0 defaults r-rbokeh 0.6.3 r350_0 defaults r-rcolorbrewer 1.1_2 r350h912f1d8_0 defaults r-rcpp 0.12.16 r350h1104f25_0 defaults r-rcpproll 0.2.2 r350h1104f25_0 defaults r-readr 1.1.1 r350h1104f25_0 defaults r-readxl 1.1.0 r350h1104f25_0 defaults r-recipes 0.1.2 r350h912f1d8_0 defaults r-recommended 3.5.0 r350_0 defaults r-rematch 1.0.1 r350h912f1d8_0 defaults r-repr 0.13 r350h912f1d8_0 defaults r-reprex 0.1.2 r350h912f1d8_0 defaults r-reshape2 1.4.3 r350h1104f25_0 defaults r-rlang 0.2.0 r350h459e2dc_0 defaults r-rmarkdown 1.9 r350h912f1d8_0 defaults r-robustbase 0.92_8 r350h9092e51_0 defaults r-rpart 4.1_13 r350h459e2dc_0 defaults r-rprojroot 1.3_2 r350h912f1d8_0 defaults r-rstudioapi 0.7 r350h912f1d8_0 defaults r-rvest 0.3.2 r350h912f1d8_0 defaults r-scales 0.5.0 r350h1104f25_0 defaults r-selectr 0.4_1 r350h912f1d8_0 defaults r-sfsmisc 1.1_2 r350h912f1d8_0 defaults r-shiny 1.0.5 r350h912f1d8_0 defaults r-sourcetools 0.1.6 r350h1104f25_0 defaults r-spatial 7.3_11 r350h459e2dc_4 defaults r-squarem 2017.10_1 r350h912f1d8_0 defaults r-stringi 1.1.7 r350h1104f25_0 defaults r-stringr 1.3.0 r350h912f1d8_0 defaults r-survival 2.42_3 r350h459e2dc_0 defaults r-testthat 2.0.0 r350h1104f25_0 defaults r-tibble 1.4.2 r350h459e2dc_0 defaults r-tidyr 0.8.0 r350h1104f25_0 defaults r-tidyselect 0.2.4 r350h1104f25_0 defaults r-tidyverse 1.2.1 r350h912f1d8_0 defaults r-timedate 3043.102 r350h912f1d8_0 defaults r-ttr 0.23_3 r350h9092e51_0 defaults r-utf8 1.1.3 r350h459e2dc_0 defaults r-uuid 0.1_2 r350h459e2dc_4 defaults r-viridislite 0.3.0 r350h912f1d8_0 defaults r-whisker 0.3_2 r350h912f1d8_4 defaults r-withr 2.1.2 r350h912f1d8_0 defaults r-xml2 1.2.0 r350h1104f25_0 defaults r-xtable 1.8_2 r350h912f1d8_0 defaults r-xts 0.10_2 r350h9092e51_0 defaults r-yaml 2.1.18 r350h459e2dc_0 defaults r-zoo 1.8_1 r350h459e2dc_0 defaults readline 7.0 hc1231fa_4 defaults send2trash 1.5.0 py37_0 defaults service_identity 17.0.0 py37h28b3542_0 defaults setuptools 39.2.0 py37_0 defaults simplegeneric 0.8.1 py37_2 defaults six 1.11.0 py37_1 defaults sqlite 3.24.0 ha441bb4_0 defaults terminado 0.8.1 py37_1 defaults testpath 0.3.1 py37_0 defaults tk 8.6.7 h35a86e2_3 defaults tktable 2.10 h1de35cc_0 defaults tornado 5.0.2 py37h1de35cc_0 defaults traitlets 4.3.2 py37_0 defaults twisted 18.4.0 py37h1de35cc_0 defaults wcwidth 0.1.7 py37_0 defaults webencodings 0.5.1 py37_1 defaults wheel 0.31.1 py37_0 defaults xz 5.2.4 h1de35cc_4 defaults zeromq 4.2.5 h0a44026_0 defaults zlib 1.2.11 hf3cbc9b_2 defaults zope 1.0 py37_0 defaults zope.interface 4.5.0 py37h1de35cc_0 defaults

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mingwandroid commented 6 years ago

Cannot reproduce, did you activate your environment?

Here's my full session log:

conda create -n ukR r-essentials
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 4.5.8
  latest version: 4.5.9

Please update conda by running

    $ conda update -n base -c defaults conda

## Package Plan ##

  environment location: /opt/conda/envs/ukR

  added / updated specs:
    - r-essentials

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    r-pbdzmq-0.3_2             |   r350h1104f25_0         387 KB  defaults
    r-caret-6.0_79             |   r350h459e2dc_0         5.9 MB  defaults
    r-whisker-0.3_2            |   r350h912f1d8_4          66 KB  defaults
    r-magic-1.5_8              |   r350h912f1d8_0         579 KB  defaults
    ipython-6.5.0              |           py37_0         1.0 MB  defaults
    r-modelmetrics-1.1.0       |   r350h1104f25_0          93 KB  defaults
    r-irdisplay-0.4.4          |   r350h912f1d8_0          33 KB  defaults
    r-recipes-0.1.2            |   r350h912f1d8_0         1.2 MB  defaults
    r-deoptimr-1.0_8           |   r350h912f1d8_0          45 KB  defaults
    r-numderiv-2016.8_1        |   r350h912f1d8_0         117 KB  defaults
    r-repr-0.13                |   r350h912f1d8_0         104 KB  defaults
    r-randomforest-4.6_14      |   r350h9092e51_0         223 KB  defaults
    r-cvst-0.2_1               |   r350h912f1d8_0          85 KB  defaults
    r-dimred-0.1.0             |   r350h912f1d8_0         612 KB  defaults
    r-ggplot2-2.2.1            |   r350h912f1d8_0         3.1 MB  defaults
    r-essentials-3.5.0         |           r350_0           5 KB  defaults
    r-drr-0.0.3                |   r350h912f1d8_0         166 KB  defaults
    r-viridislite-0.3.0        |   r350h912f1d8_0          63 KB  defaults
    r-irkernel-0.8.11          |           r350_0         199 KB  defaults
    r-glmnet-2.0_16            |   r350h9092e51_0         1.4 MB  defaults
    r-ttr-0.23_3               |   r350h9092e51_0         506 KB  defaults
    r-kernlab-0.9_25           |   r350h82edaba_0         2.1 MB  defaults
    r-maps-3.3.0               |   r350h459e2dc_0         3.5 MB  defaults
    r-hexbin-1.27.2            |   r350h9092e51_0         860 KB  defaults
    r-sfsmisc-1.1_2            |   r350h912f1d8_0         605 KB  defaults
    r-timedate-3043.102        |   r350h912f1d8_0         1.5 MB  defaults
    r-lubridate-1.7.4          |   r350h1104f25_0         1.0 MB  defaults
    r-xts-0.10_2               |   r350h9092e51_0         892 KB  defaults
    r-modelr-0.1.1             |   r350h912f1d8_0         160 KB  defaults
    r-reprex-0.1.2             |   r350h912f1d8_0          54 KB  defaults
    r-selectr-0.4_1            |   r350h912f1d8_0         368 KB  defaults
    pyasn1-0.4.4               |           py37_0         101 KB  defaults
    r-formatr-1.5              |   r350h912f1d8_0         150 KB  defaults
    r-colorspace-1.3_2         |   r350h459e2dc_0         512 KB  defaults
    parso-0.3.1                |           py37_0         114 KB  defaults
    r-munsell-0.4.3            |   r350h912f1d8_0         158 KB  defaults
    r-gtable-0.2.0             |   r350h912f1d8_0          88 KB  defaults
    jedi-0.12.1                |           py37_0         225 KB  defaults
    r-rbokeh-0.6.3             |           r350_0         4.1 MB  defaults
    r-iterators-1.0.9          |   r350h912f1d8_0         334 KB  defaults
    r-lava-1.6.1               |   r350h912f1d8_0         2.2 MB  defaults
    r-robustbase-0.92_8        |   r350h9092e51_0         3.2 MB  defaults
    r-gower-0.1.2              |   r350h459e2dc_0          38 KB  defaults
    r-rcpproll-0.2.2           |   r350h1104f25_0         132 KB  defaults
    r-squarem-2017.10_1        |   r350h912f1d8_0         289 KB  defaults
    r-zoo-1.8_1                |   r350h459e2dc_0         1.0 MB  defaults
    r-geometry-0.3_6           |   r350h459e2dc_0         421 KB  defaults
    r-scales-0.5.0             |   r350h1104f25_0         300 KB  defaults
    r-quantmod-0.4_13          |   r350h912f1d8_0         952 KB  defaults
    r-dichromat-2.0_0          |   r350h912f1d8_4         151 KB  defaults
    r-testthat-2.0.0           |   r350h1104f25_0         962 KB  defaults
    r-rcolorbrewer-1.1_2       |   r350h912f1d8_0          58 KB  defaults
    r-tidyverse-1.2.1          |   r350h912f1d8_0          92 KB  defaults
    r-labeling-0.3             |   r350h912f1d8_4          64 KB  defaults
    r-callr-2.0.3              |   r350h1104f25_0         430 KB  defaults
    r-ddalpha-1.3.2            |   r350h82edaba_0         1.8 MB  defaults
    r-data.table-1.10.4_3      |   r350h459e2dc_0         1.2 MB  defaults
    prometheus_client-0.3.1    |           py37_0          51 KB  defaults
    r-debugme-1.1.0            |   r350h912f1d8_0        1005 KB  defaults
    _r-mutex-1.0.0             |      anacondar_1           2 KB  defaults
    r-rvest-0.3.2              |   r350h912f1d8_0         871 KB  defaults
    r-praise-1.0.0             |   r350h912f1d8_4          21 KB  defaults
    r-uuid-0.1_2               |   r350h459e2dc_4          19 KB  defaults
    r-abind-1.4_5              |   r350h912f1d8_0          66 KB  defaults
    r-prodlim-2018.04.18       |   r350h1104f25_0         396 KB  defaults
    r-ipred-0.9_6              |   r350h459e2dc_0         383 KB  defaults
    r-foreach-1.4.4            |   r350h912f1d8_0         403 KB  defaults
    ------------------------------------------------------------
                                           Total:        48.8 MB

The following NEW packages will be INSTALLED:

    _r-mutex:          1.0.0-anacondar_1         defaults
    appdirs:           1.4.3-py37h28b3542_0      defaults
    appnope:           0.1.0-py37_0              defaults
    asn1crypto:        0.24.0-py37_0             defaults
    attrs:             18.1.0-py37_0             defaults
    automat:           0.7.0-py37_0              defaults
    backcall:          0.1.0-py37_0              defaults
    blas:              1.0-openblas              defaults
    bleach:            2.1.3-py37_0              defaults
    bwidget:           1.9.11-0                  defaults
    bzip2:             1.0.6-h1de35cc_5          defaults
    ca-certificates:   2018.03.07-0              defaults
    cairo:             1.14.12-hc4e6be7_4        defaults
    cctools:           895-h7512d6f_0            defaults
    certifi:           2018.4.16-py37_0          defaults
    cffi:              1.11.5-py37h342bebf_0     defaults
    clang:             4.0.1-h662ec87_0          defaults
    clang_osx-64:      4.0.1-h1ce6c1d_11         defaults
    clangxx:           4.0.1-hc9b4283_0          defaults
    clangxx_osx-64:    4.0.1-h22b1bf0_11         defaults
    compiler-rt:       4.0.1-h5487866_0          defaults
    constantly:        15.1.0-py37h28b3542_0     defaults
    cryptography:      2.2.2-py37h1de35cc_0      defaults
    curl:              7.61.0-ha441bb4_0         defaults
    decorator:         4.3.0-py37_0              defaults
    entrypoints:       0.2.3-py37_2              defaults
    fontconfig:        2.13.0-h5d5b041_1         defaults
    freetype:          2.9.1-hb4e5f40_0          defaults
    fribidi:           1.0.4-h1de35cc_0          defaults
    gettext:           0.19.8.1-h15daf44_3       defaults
    gfortran_osx-64:   4.8.5-h22b1bf0_3          defaults
    glib:              2.56.1-h35bc53a_0         defaults
    graphite2:         1.3.11-h2098e52_2         defaults
    gsl:               2.4-h1de35cc_4            defaults
    harfbuzz:          1.8.4-hb8d4a28_0          defaults
    html5lib:          1.0.1-py37_0              defaults
    hyperlink:         18.0.0-py37_0             defaults
    icu:               58.2-h4b95b61_1           defaults
    idna:              2.7-py37_0                defaults
    incremental:       17.5.0-py37_0             defaults
    ipykernel:         4.8.2-py37_0              defaults
    ipython:           6.5.0-py37_0              defaults
    ipython_genutils:  0.2.0-py37_0              defaults
    jedi:              0.12.1-py37_0             defaults
    jinja2:            2.10-py37_0               defaults
    jpeg:              9b-he5867d9_2             defaults
    jsonschema:        2.6.0-py37_0              defaults
    jupyter_client:    5.2.3-py37_0              defaults
    jupyter_core:      4.4.0-py37_0              defaults
    krb5:              1.16.1-h24a3359_6         defaults
    ld64:              274.2-h7c2db76_0          defaults
    libcurl:           7.61.0-hf30b1f0_0         defaults
    libcxx:            4.0.1-h579ed51_0          defaults
    libcxxabi:         4.0.1-hebd6815_0          defaults
    libedit:           3.1.20170329-hb402a30_2   defaults
    libffi:            3.2.1-h475c297_4          defaults
    libgfortran:       3.0.1-h93005f0_2          defaults
    libiconv:          1.15-hdd342a3_7           defaults
    libopenblas:       0.2.20-hdc02c5d_7         defaults
    libpng:            1.6.34-he12f830_0         defaults
    libsodium:         1.0.16-h3efe00b_0         defaults
    libssh2:           1.8.0-h322a93b_4          defaults
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    pycparser:         2.18-py37_1               defaults
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    python:            3.7.0-hc167b69_0          defaults
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    setuptools:        39.2.0-py37_0             defaults
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    sqlite:            3.24.0-ha441bb4_0         defaults
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    zlib:              1.2.11-hf3cbc9b_2         defaults
    zope:              1.0-py37_0                defaults
    zope.interface:    4.5.0-py37h1de35cc_0      defaults

Proceed ([y]/n)? y

Downloading and Extracting Packages
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r-whisker-0.3_2      |   66 KB | ####################################################################################################################################################################################################################################### | 100%
r-magic-1.5_8        |  579 KB | ####################################################################################################################################################################################################################################### | 100%
ipython-6.5.0        |  1.0 MB | ####################################################################################################################################################################################################################################### | 100%
r-modelmetrics-1.1.0 |   93 KB | ####################################################################################################################################################################################################################################### | 100%
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r-essentials-3.5.0   |    5 KB | ####################################################################################################################################################################################################################################### | 100%
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Preparing transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate ukR
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(base) 0313-rdonnelly:~ rdonnelly$ conda activate ukR
INFO: activate-gfortran_osx-64.sh made the following environmental changes:
+DEBUG_FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments
+F95=/opt/conda/envs/ukR/bin/x86_64-apple-darwin13.4.0-gfortran
+FC=/opt/conda/envs/ukR/bin/x86_64-apple-darwin13.4.0-gfortran
+FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe
+FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe
+GFORTRAN=/opt/conda/envs/ukR/bin/x86_64-apple-darwin13.4.0-gfortran
R(ukR) 0313-rdonnelly:~ rdonnelly$ R

R version 3.5.0 (2018-04-23) -- "Joy in Playing"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> install.packages('rbarts')
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors

 1: 0-Cloud [https]                   2: Algeria [https]
 3: Australia (Canberra) [https]      4: Australia (Melbourne 1) [https]
 5: Australia (Melbourne 2) [https]   6: Australia (Perth) [https]
 7: Austria [https]                   8: Belgium (Ghent) [https]
 9: Brazil (PR) [https]              10: Brazil (RJ) [https]
11: Brazil (SP 1) [https]            12: Brazil (SP 2) [https]
13: Bulgaria [https]                 14: Chile 1 [https]
15: Chile 2 [https]                  16: China (Guangzhou) [https]
17: China (Lanzhou) [https]          18: China (Shanghai 1) [https]
19: China (Shanghai 2) [https]       20: Colombia (Cali) [https]
21: Czech Republic [https]           22: Denmark [https]
23: East Asia [https]                24: Ecuador (Cuenca) [https]
25: Ecuador (Quito) [https]          26: Estonia [https]
27: France (Lyon 1) [https]          28: France (Lyon 2) [https]
29: France (Marseille) [https]       30: France (Montpellier) [https]
31: France (Paris 2) [https]         32: Germany (Erlangen) [https]
33: Germany (Göttingen) [https]      34: Germany (Münster) [https]
35: Greece [https]                   36: Iceland [https]
37: India [https]                    38: Indonesia (Jakarta) [https]
39: Ireland [https]                  40: Italy (Padua) [https]
41: Japan (Tokyo) [https]            42: Japan (Yonezawa) [https]
43: Korea (Busan) [https]            44: Korea (Seoul 1) [https]
45: Korea (Ulsan) [https]            46: Malaysia [https]
47: Mexico (Mexico City) [https]     48: Norway [https]
49: Philippines [https]              50: Serbia [https]
51: Spain (A Coruña) [https]         52: Spain (Madrid) [https]
53: Sweden [https]                   54: Switzerland [https]
55: Turkey (Denizli) [https]         56: Turkey (Mersin) [https]
57: UK (Bristol) [https]             58: UK (London 1) [https]
59: USA (CA 1) [https]               60: USA (IA) [https]
61: USA (KS) [https]                 62: USA (MI 1) [https]
63: USA (NY) [https]                 64: USA (OR) [https]
65: USA (TN) [https]                 66: USA (TX 1) [https]
67: Vietnam [https]                  68: (other mirrors)

Selection: 60
Warning message:
package ‘rbarts’ is not available (for R version 3.5.0)
> install.packages('rbarts', source=True)
Warning message:
package ‘rbarts’ is not available (for R version 3.5.0)
> install.packages('dbarts', source=True)
trying URL 'https://mirror.las.iastate.edu/CRAN/src/contrib/dbarts_0.9-5.tar.gz'
Content type 'application/x-gzip' length 293683 bytes (286 KB)
==================================================
downloaded 286 KB

* installing *source* package ‘dbarts’ ...
** package ‘dbarts’ successfully unpacked and MD5 sums checked
checking for gcc... x86_64-apple-darwin13.4.0-clang
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether x86_64-apple-darwin13.4.0-clang accepts -g... yes
checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C89... none needed
checking for x86_64-apple-darwin13.4.0-clang option to accept ISO C99... none needed
checking how to run the C preprocessor... x86_64-apple-darwin13.4.0-clang -E
checking whether we are using the GNU C++ compiler... yes
checking whether x86_64-apple-darwin13.4.0-clang++ accepts -g... yes
checking how to run the C++ preprocessor... x86_64-apple-darwin13.4.0-clang++ -E
checking for C/C++ restrict keyword... __restrict
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking whether byte ordering is bigendian... no
checking build system type... x86_64-apple-darwin17.6.0
checking host system type... x86_64-apple-darwin17.6.0
checking for x86 cpuid  output... unknown
checking for x86-AVX xgetbv  output... unknown
checking for x86 cpuid 0x00000001 output... 40661:6100800:7ffafbff:bfebfbff
checking whether mmx is supported... yes
checking whether sse is supported... yes
checking whether sse2 is supported... yes
checking whether sse3 is supported... yes
checking whether ssse3 is supported... yes
checking whether sse4.1 is supported... yes
checking whether sse4.2 is supported... yes
checking whether avx is supported by processor... yes
checking for x86-AVX xgetbv 0x00000000 output... 7:0
checking whether avx is supported by operating system... yes
checking whether C compiler accepts -mmmx... yes
checking whether C compiler accepts -msse... yes
checking whether C compiler accepts -msse2... yes
checking whether C compiler accepts -msse3... yes
checking whether C compiler accepts -mssse3... yes
checking whether C compiler accepts -msse4.1... yes
checking whether C compiler accepts -msse4.2... yes
checking whether C compiler accepts -mavx... yes
checking for a sed that does not truncate output... /usr/bin/sed
checking whether x86_64-apple-darwin13.4.0-clang is Clang... yes
checking whether Clang needs flag to prevent "argument unused" warning when linking with -pthread... -Qunused-arguments
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking cstdint usability... yes
checking cstdint presence... yes
checking for cstdint... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking malloc.h usability... no
checking malloc.h presence... no
checking for malloc.h... no
checking for int64_t... yes
checking for uint64_t... yes
checking size of size_t... 8
checking alignment of void*... 8
checking for gettimeofday... yes
checking for clock_gettime... no
checking for ffs... yes
checking for size_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for working posix_memalign... yes
checking for snprintf... yes
checking if g++ supports namespace std... yes
checking whether snprintf is in std::... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.hpp
config.status: creating src/dbarts/config.hpp
config.status: creating src/external/config.h
** libs
x86_64-apple-darwin13.4.0-clang++  -I"/opt/conda/envs/ukR/lib/R/include" -DNDEBUG -I../inst/include -Iinclude -Qunused-arguments -pthread   -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include   -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c R_C_interface.cpp -o R_C_interface.o
x86_64-apple-darwin13.4.0-clang++  -I"/opt/conda/envs/ukR/lib/R/include" -DNDEBUG -I../inst/include -Iinclude -Qunused-arguments -pthread   -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include   -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c R_interface.cpp -o R_interface.o
x86_64-apple-darwin13.4.0-clang++  -I"/opt/conda/envs/ukR/lib/R/include" -DNDEBUG -I../inst/include -Iinclude -Qunused-arguments -pthread   -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include   -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c R_interface_common.cpp -o R_interface_common.o
x86_64-apple-darwin13.4.0-clang++  -I"/opt/conda/envs/ukR/lib/R/include" -DNDEBUG -I../inst/include -Iinclude -Qunused-arguments -pthread   -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include   -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c R_interface_crossvalidate.cpp -o R_interface_crossvalidate.o
x86_64-apple-darwin13.4.0-clang++  -I"/opt/conda/envs/ukR/lib/R/include" -DNDEBUG -I../inst/include -Iinclude -Qunused-arguments -pthread   -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include   -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c R_interface_sampler.cpp -o R_interface_sampler.o
x86_64-apple-darwin13.4.0-clang++  -I"/opt/conda/envs/ukR/lib/R/include" -DNDEBUG -I../inst/include -Iinclude -Qunused-arguments -pthread   -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include   -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c crossvalidate.cpp -o crossvalidate.o
x86_64-apple-darwin13.4.0-clang++  -I"/opt/conda/envs/ukR/lib/R/include" -DNDEBUG -I../inst/include -Iinclude -Qunused-arguments -pthread   -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include   -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c guessNumCores.cpp -o guessNumCores.o
x86_64-apple-darwin13.4.0-clang -I"/opt/conda/envs/ukR/lib/R/include" -DNDEBUG -I../inst/include -Iinclude -Qunused-arguments -pthread   -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include   -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c makeModelMatrixFromDataFrame.c -o makeModelMatrixFromDataFrame.o
make[1]: Entering directory '/private/var/folders/sn/44hk_kjx1px9d73t7yyj3g000000gn/T/RtmpNIpwDt/R.INSTALL113204185fa4b/dbarts/src/dbarts'
x86_64-apple-darwin13.4.0-clang++  -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../../inst/include -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include  -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c bartFit.cpp -o bartFit.o
x86_64-apple-darwin13.4.0-clang++  -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../../inst/include -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include  -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c binaryIO.cpp -o binaryIO.o
x86_64-apple-darwin13.4.0-clang++  -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../../inst/include -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include  -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c birthDeathRule.cpp -o birthDeathRule.o
x86_64-apple-darwin13.4.0-clang++  -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../../inst/include -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include  -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c changeRule.cpp -o changeRule.o
x86_64-apple-darwin13.4.0-clang++  -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../../inst/include -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include  -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c functions.cpp -o functions.o
x86_64-apple-darwin13.4.0-clang++  -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../../inst/include -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include  -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c likelihood.cpp -o likelihood.o
x86_64-apple-darwin13.4.0-clang++  -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../../inst/include -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include  -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c node.cpp -o node.o
x86_64-apple-darwin13.4.0-clang++  -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../../inst/include -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include  -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c parameterPrior.cpp -o parameterPrior.o
x86_64-apple-darwin13.4.0-clang++  -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../../inst/include -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include  -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c state.cpp -o state.o
x86_64-apple-darwin13.4.0-clang++  -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../../inst/include -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include  -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c swapRule.cpp -o swapRule.o
x86_64-apple-darwin13.4.0-clang++  -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../../inst/include -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include  -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c tree.cpp -o tree.o
x86_64-apple-darwin13.4.0-clang++  -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../../inst/include -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include  -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c treePrior.cpp -o treePrior.o
x86_64-apple-darwin13.4.0-ar rv libdbarts.a bartFit.o binaryIO.o birthDeathRule.o changeRule.o functions.o likelihood.o node.o parameterPrior.o state.o swapRule.o tree.o treePrior.o
x86_64-apple-darwin13.4.0-ar: creating archive libdbarts.a
a - bartFit.o
a - binaryIO.o
a - birthDeathRule.o
a - changeRule.o
a - functions.o
a - likelihood.o
a - node.o
a - parameterPrior.o
a - state.o
a - swapRule.o
a - tree.o
a - treePrior.o
make[1]: Leaving directory '/private/var/folders/sn/44hk_kjx1px9d73t7yyj3g000000gn/T/RtmpNIpwDt/R.INSTALL113204185fa4b/dbarts/src/dbarts'
make[1]: Entering directory '/private/var/folders/sn/44hk_kjx1px9d73t7yyj3g000000gn/T/RtmpNIpwDt/R.INSTALL113204185fa4b/dbarts/src/external'
x86_64-apple-darwin13.4.0-clang -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c adaptiveRadixTree.c -o adaptiveRadixTree.o
x86_64-apple-darwin13.4.0-clang -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c binaryIO.c -o binaryIO.o
x86_64-apple-darwin13.4.0-clang -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c blockingThreadManager.c -o blockingThreadManager.o
x86_64-apple-darwin13.4.0-clang -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c io.c -o io.o
x86_64-apple-darwin13.4.0-clang -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c hierarchicalThreadManager.c -o hierarchicalThreadManager.o
x86_64-apple-darwin13.4.0-clang -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c linearAlgebra.c -o linearAlgebra.o
x86_64-apple-darwin13.4.0-clang -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c moments.c -o moments.o
x86_64-apple-darwin13.4.0-clang -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c randomBase.c -o randomBase.o
x86_64-apple-darwin13.4.0-clang -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c randomNorm.c -o randomNorm.o
x86_64-apple-darwin13.4.0-clang -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c random.c -o random.o
x86_64-apple-darwin13.4.0-clang -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c string.c -o string.o
x86_64-apple-darwin13.4.0-clang -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../include -Qunused-arguments -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c thread.c -o thread.o
x86_64-apple-darwin13.4.0-ar rv libexternal.a adaptiveRadixTree.o binaryIO.o blockingThreadManager.o io.o hierarchicalThreadManager.o linearAlgebra.o moments.o randomBase.o randomNorm.o random.o string.o thread.o
x86_64-apple-darwin13.4.0-ar: creating archive libexternal.a
a - adaptiveRadixTree.o
a - binaryIO.o
a - blockingThreadManager.o
a - io.o
a - hierarchicalThreadManager.o
a - linearAlgebra.o
a - moments.o
a - randomBase.o
a - randomNorm.o
a - random.o
a - string.o
a - thread.o
make[1]: Leaving directory '/private/var/folders/sn/44hk_kjx1px9d73t7yyj3g000000gn/T/RtmpNIpwDt/R.INSTALL113204185fa4b/dbarts/src/external'
make[1]: Entering directory '/private/var/folders/sn/44hk_kjx1px9d73t7yyj3g000000gn/T/RtmpNIpwDt/R.INSTALL113204185fa4b/dbarts/src/rc'
x86_64-apple-darwin13.4.0-clang -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c bounds.c -o bounds.o
x86_64-apple-darwin13.4.0-clang -I/opt/conda/envs/ukR/lib/R/include -DNDEBUG -I../include -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/opt/conda/envs/ukR/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/opt/conda/envs/ukR/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c util.c -o util.o
x86_64-apple-darwin13.4.0-ar rv librc.a bounds.o util.o
x86_64-apple-darwin13.4.0-ar: creating archive librc.a
a - bounds.o
a - util.o
make[1]: Leaving directory '/private/var/folders/sn/44hk_kjx1px9d73t7yyj3g000000gn/T/RtmpNIpwDt/R.INSTALL113204185fa4b/dbarts/src/rc'
x86_64-apple-darwin13.4.0-clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/conda/envs/ukR/lib/R/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/opt/conda/envs/ukR/lib -L/opt/conda/envs/ukR/lib -o dbarts.so R_C_interface.o R_interface.o R_interface_common.o R_interface_crossvalidate.o R_interface_sampler.o crossvalidate.o guessNumCores.o makeModelMatrixFromDataFrame.o dbarts/libdbarts.a external/libexternal.a rc/librc.a -L/opt/conda/envs/ukR/lib/R/lib -lRlapack -L/opt/conda/envs/ukR/lib/R/lib -lRblas -L/opt/conda/conda-bld/r-base_1532450192736/_build_env/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5 -L/opt/conda/conda-bld/r-base_1532450192736/_build_env/lib/gcc -L/opt/conda/conda-bld/r-base_1532450192736/_build_env/lib -lgfortran -lquadmath -lm -L/opt/conda/envs/ukR/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/opt/conda/conda-bld/r-base_1532450192736/_build_env/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5'
ld: warning: directory not found for option '-L/opt/conda/conda-bld/r-base_1532450192736/_build_env/lib/gcc'
ld: warning: directory not found for option '-L/opt/conda/conda-bld/r-base_1532450192736/_build_env/lib'
ld: warning: -pie being ignored. It is only used when linking a main executable
installing to /opt/conda/envs/ukR/lib/R/library/dbarts/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (dbarts)

The downloaded source packages are in
    ‘/private/var/folders/sn/44hk_kjx1px9d73t7yyj3g000000gn/T/RtmplNgMIx/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done

Regardless of not being able to reproduce this, you are best off (for reasons of performance consistency and compatibility) doing it this way:

export CONDA_R=3.5.0
conda activate base
conda install conda-build
conda skeleton cran dbarts
echo "CONDA_BUILD_SYSROOT:" > conda_build_config.yaml
echo "  - /opt/MacOSX10.9.sdk" >> conda_build_config.yaml
conda-build r-dbarts
conda activate ukR
conda install -c local r-dbarts
mingwandroid commented 6 years ago

You need to provide your own SDK here too. You can use the Xcode one but your software won't work on old versions of macOS.

ALLCCN commented 6 years ago

Install this library by conda-build seems work (I haven't try), but the C compiler can not work in the process of installation, then it may also not work when using this library. So I wanna know how to solve this issue by make some change to the C compiler.

When I activate this env, it shows:

INFO: activate-gfortran_osx-64.sh made the following environmental changes:
+DEBUG_FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments
+F95=/Users/*/anaconda3/envs/ukR/bin/x86_64-apple-darwin13.4.0-gfortran
+FC=/Users/*/anaconda3/envs/ukR/bin/x86_64-apple-darwin13.4.0-gfortran
+FFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe
+FORTRANFLAGS=-march=nocona -mtune=core2 -ftree-vectorize -fPIC -fstack-protector -O2 -pipe
+GFORTRAN=/Users/*/anaconda3/envs/ukR/bin/x86_64-apple-darwin13.4.0-gfortran
+HOST=x86_64-apple-darwin13.4.0

I use an older version of R with r-essentials==3.4.3:

R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

and install.packages("git2r")

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/git2r_0.23.0.tar.gz'
Content type 'application/x-gzip' length 1150314 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

* installing *source* package ‘git2r’ ...
** package ‘git2r’ successfully unpacked and MD5 sums checked
checking build system type... x86_64-apple-darwin17.7.0
checking host system type... x86_64-apple-darwin17.7.0
checking for gcc... x86_64-apple-darwin13.4.0-clang
checking whether the C compiler works... no
configure: error: in `/private/var/folders/xl/lps1y28d097bgxv7krghnhz40000gn/T/RtmpVrNvWo/R.INSTALL37dd203413e1/git2r':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘git2r’
* removing ‘/Users/*/anaconda3/envs/ukR/lib/R/library/git2r’

The downloaded source packages are in
    ‘/private/var/folders/xl/lps1y28d097bgxv7krghnhz40000gn/T/RtmpnBCLBv/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("git2r") :
  installation of package ‘git2r’ had non-zero exit status

btw, how can I check my own SDK?

mingwandroid commented 6 years ago

Google for it? You can also get then from old xcode versions. Why are you using old R?

ALLCCN commented 6 years ago

I try an old R for test, still no work.

I want to use the old xcode versions, and MacOSX10.9.sdk is in my compter, but I do not know did R use this version? I wanna try to degrade my OS to 10.12 to see can this work.

mingwandroid commented 6 years ago

There's no need to downgrade your os. If you use an old SDK and follow my instructions it should work fine.