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Last login: Fri Mar 1 05:10:05 on console (base) Alis-iMac:~ [user]$ conda update --all Collecting package metadata: done Solving environment: \ Warning: 2 possible package resolutions (only showing differing packages): - defaults::nbconvert-5.3.1-py37_0, defaults::pandoc-2.2.3.2-0 - defaults::nbconvert-5.4.1-py37_0, defaults::pandoc-1.19.2.1-ha5e8f32done ## Package Plan ## environment location: /Users/[user]/anaconda3 The following packages will be UPDATED: appscript 1.0.1-py37h1de35cc_1 --> 1.1.0-py37h1de35cc_0 astropy 3.1-py37h1de35cc_0 --> 3.1.2-py37h1de35cc_0 atomicwrites pkgs/main/osx-64::atomicwrites-1.2.1-~ --> pkgs/main/noarch::atomicwrites-1.3.0-py_0 beautifulsoup4 4.6.3-py37_0 --> 4.7.1-py37_1 bleach 3.0.2-py37_0 --> 3.1.0-py37_0 blosc 1.14.4-hd9629dc_0 --> 1.15.0-hd9629dc_0 bokeh 1.0.2-py37_0 --> 1.0.4-py37_0 cffi 1.11.5-py37h6174b99_1 --> 1.12.1-py37hb5b8e2f_0 cloudpickle 0.6.1-py37_0 --> 0.8.0-py37_0 cryptography 2.4.2-py37ha12b0ac_0 --> 2.5-py37ha12b0ac_0 cython 0.29.2-py37h0a44026_0 --> 0.29.5-py37h0a44026_0 dask 1.0.0-py37_0 --> 1.1.2-py37_0 dask-core pkgs/main/osx-64::dask-core-1.0.0-py3~ --> pkgs/main/noarch::dask-core-1.1.2-py_0 dbus 1.13.2-h760590f_1 --> 1.13.6-h90a0687_0 decorator 4.3.0-py37_0 --> 4.3.2-py37_0 distributed 1.25.1-py37_0 --> 1.26.0-py37_0 entrypoints 0.2.3-py37_2 --> 0.3-py37_0 gevent 1.3.7-py37h1de35cc_1 --> 1.4.0-py37h1de35cc_0 h5py 2.8.0-py37h878fce3_3 --> 2.9.0-py37h3134771_0 hdf5 1.10.2-hfa1e0ec_1 --> 1.10.4-hfa1e0ec_0 imageio 2.4.1-py37_0 --> 2.5.0-py37_0 importlib_metadata 0.6-py37_0 --> 0.7-py37_0 ipython 7.2.0-py37h39e3cac_0 --> 7.3.0-py37h39e3cac_0 isort 4.3.4-py37_0 --> 4.3.8-py37_0 jedi 0.13.2-py37_0 --> 0.13.3-py37_0 keyring 17.0.0-py37_0 --> 18.0.0-py37_0 libedit 3.1.20170329-hb402a30_2 --> 3.1.20181209-hb402a30_0 liblief 0.9.0-h2a1bed3_0 --> 0.9.0-h2a1bed3_2 libpng 1.6.35-ha441bb4_0 --> 1.6.36-ha441bb4_0 libtiff 4.0.9-hcb84e12_2 --> 4.0.10-hcb84e12_2 libxml2 2.9.8-hab757c2_1 --> 2.9.9-hab757c2_0 libxslt 1.1.32-hb819dd2_0 --> 1.1.33-h33a18ac_0 llvmlite 0.26.0-py37h8c7ce04_0 --> 0.27.0-py37h8c7ce04_0 lxml 4.2.5-py37hef8c89e_0 --> 4.3.1-py37hef8c89e_0 markupsafe 1.1.0-py37h1de35cc_0 --> 1.1.1-py37h1de35cc_0 mkl_fft 1.0.6-py37h27c97d8_0 --> 1.0.10-py37h5e564d8_0 more-itertools 4.3.0-py37_0 --> 5.0.0-py37_0 msgpack-python 0.5.6-py37h04f5b5a_1 --> 0.6.1-py37h04f5b5a_1 numba 0.41.0-py37h6440ff4_0 --> 0.42.0-py37h6440ff4_0 numexpr 2.6.8-py37h7413580_0 --> 2.6.9-py37h7413580_0 openpyxl 2.5.12-py37_0 --> 2.6.0-py37_0 packaging 18.0-py37_0 --> 19.0-py37_0 pandas 0.23.4-py37h6440ff4_0 --> 0.24.1-py37h0a44026_0 pandoc 1.19.2.1-ha5e8f32_1 --> 2.2.3.2-0 parso 0.3.1-py37_0 --> 0.3.4-py37_0 pillow 5.3.0-py37hb68e598_0 --> 5.4.1-py37hb68e598_0 pip 18.1-py37_0 --> 19.0.3-py37_0 pkginfo 1.4.2-py37_1 --> 1.5.0.1-py37_0 pluggy 0.8.0-py37_0 --> 0.9.0-py37_0 prometheus_client 0.5.0-py37_0 --> 0.6.0-py37_0 prompt_toolkit 2.0.7-py37_0 --> 2.0.9-py37_0 psutil 5.4.8-py37h1de35cc_0 --> 5.5.0-py37h1de35cc_0 py 1.7.0-py37_0 --> 1.8.0-py37_0 py-lief 0.9.0-py37hd4eaf27_0 --> 0.9.0-py37h1413db1_2 pycodestyle 2.4.0-py37_0 --> 2.5.0-py37_0 pyflakes 2.0.0-py37_0 --> 2.1.0-py37_0 pyodbc 4.0.25-py37h0a44026_0 --> 4.0.26-py37h0a44026_0 pyopenssl 18.0.0-py37_0 --> 19.0.0-py37_0 pyparsing 2.3.0-py37_0 --> 2.3.1-py37_0 pytest 4.0.2-py37_0 --> 4.3.0-py37_0 pytest-openfiles 0.3.1-py37_0 --> 0.3.2-py37_0 python 3.7.1-haf84260_7 --> 3.7.2-haf84260_0 python-dateutil 2.7.5-py37_0 --> 2.8.0-py37_0 pytz 2018.7-py37_0 --> 2018.9-py37_0 pyzmq 17.1.2-py37h1de35cc_0 --> 18.0.0-py37h0a44026_0 qtawesome pkgs/main/osx-64::qtawesome-0.5.3-py3~ --> pkgs/main/noarch::qtawesome-0.5.6-py_0 qtpy pkgs/main/osx-64::qtpy-1.5.2-py37_0 --> pkgs/main/noarch::qtpy-1.6.0-py_0 rope 0.11.0-py37_0 --> 0.12.0-py37_0 scikit-learn 0.20.1-py37h27c97d8_0 --> 0.20.2-py37h27c97d8_0 scipy 1.1.0-py37h1410ff5_2 --> 1.2.1-py37h1410ff5_0 setuptools 40.6.3-py37_0 --> 40.8.0-py37_0 sortedcollections 1.0.1-py37_0 --> 1.1.2-py37_0 sphinx 1.8.2-py37_0 --> 1.8.4-py37_0 spyder 3.3.2-py37_0 --> 3.3.3-py37_0 spyder-kernels 0.3.0-py37_0 --> 0.4.2-py37_0 sqlalchemy 1.2.15-py37h1de35cc_0 --> 1.2.18-py37h1de35cc_0 tqdm pkgs/main/osx-64::tqdm-4.28.1-py37h28~ --> pkgs/main/noarch::tqdm-4.31.1-py_0 wheel 0.32.3-py37_0 --> 0.33.1-py37_0 wrapt 1.10.11-py37h1de35cc_2 --> 1.11.1-py37h1de35cc_0 xlsxwriter 1.1.2-py37_0 --> 1.1.5-py37_0 xlwings 0.15.1-py37_0 --> 0.15.3-py37_0 zeromq 4.2.5-h0a44026_1 --> 4.3.1-h0a44026_3 The following packages will be DOWNGRADED: nbconvert 5.4.0-py37_1 --> 5.3.1-py37_0 pytables 3.4.4-py37h13cba08_0 --> 3.4.4-py37h5bccee9_0 Proceed ([y]/n)? y Preparing transaction: done Verifying transaction: done Executing transaction: done (base) Alis-iMac:~ [user]$ R R version 3.5.1 (2018-07-02) -- "Feather Spray" 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("ps") --- 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 (Hong Kong) [https] 17: China (Guangzhou) [https] 18: China (Lanzhou) [https] 19: China (Shanghai 1) [https] 20: China (Shanghai 2) [https] 21: Colombia (Cali) [https] 22: Czech Republic [https] 23: Denmark [https] 24: East Asia [https] 25: Ecuador (Cuenca) [https] 26: Ecuador (Quito) [https] 27: Estonia [https] 28: France (Lyon 1) [https] 29: France (Lyon 2) [https] 30: France (Marseille) [https] 31: France (Montpellier) [https] 32: France (Paris 2) [https] 33: Germany (Erlangen) [https] 34: Germany (Göttingen) [https] 35: Germany (Münster) [https] 36: Greece [https] 37: Iceland [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 (Gyeongsan-si) [https] 45: Korea (Seoul 1) [https] 46: Korea (Ulsan) [https] 47: Malaysia [https] 48: Mexico (Mexico City) [https] 49: Norway [https] 50: Philippines [https] 51: Serbia [https] 52: Spain (A Coruña) [https] 53: Spain (Madrid) [https] 54: Sweden [https] 55: Switzerland [https] 56: Turkey (Denizli) [https] 57: Turkey (Mersin) [https] 58: UK (Bristol) [https] 59: UK (London 1) [https] 60: USA (CA 1) [https] 61: USA (IA) [https] 62: USA (KS) [https] 63: USA (MI 1) [https] 64: USA (OR) [https] 65: USA (TN) [https] 66: USA (TX 1) [https] 67: Uruguay [https] 68: (other mirrors) Selection: 60 trying URL 'https://cran.cnr.berkeley.edu/src/contrib/ps_1.3.0.tar.gz' Content type 'application/x-gzip' length 261887 bytes (255 KB) ================================================== downloaded 255 KB * installing *source* package ‘ps’ ... ** package ‘ps’ successfully unpacked and MD5 sums checked ** libs x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/[user]/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -Wall px.c -o px ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd Undefined symbols for architecture x86_64: "___error", referenced from: _echo_from_fd in px-24adb6.o "___stack_chk_fail", referenced from: _cat2 in px-24adb6.o _cat in px-24adb6.o _echo_from_fd in px-24adb6.o _main in px-24adb6.o "___stack_chk_guard", referenced from: _cat2 in px-24adb6.o _cat in px-24adb6.o _echo_from_fd in px-24adb6.o _main in px-24adb6.o "___stderrp", referenced from: _usage in px-24adb6.o _cat2 in px-24adb6.o _cat in px-24adb6.o _write_to_fd in px-24adb6.o _echo_from_fd in px-24adb6.o _main in px-24adb6.o "___stdoutp", referenced from: _echo_from_fd in px-24adb6.o _main in px-24adb6.o "_close", referenced from: _cat in px-24adb6.o "_exit", referenced from: _cat2 in px-24adb6.o _cat in px-24adb6.o "_fflush", referenced from: _echo_from_fd in px-24adb6.o _main in px-24adb6.o "_fprintf", referenced from: _cat2 in px-24adb6.o _cat in px-24adb6.o _write_to_fd in px-24adb6.o _echo_from_fd in px-24adb6.o _main in px-24adb6.o "_fputs", referenced from: _main in px-24adb6.o "_fwrite", referenced from: _usage in px-24adb6.o _main in px-24adb6.o "_getenv", referenced from: _main in px-24adb6.o "_open", referenced from: _cat in px-24adb6.o "_printf", referenced from: _main in px-24adb6.o "_puts", referenced from: _main in px-24adb6.o "_read", referenced from: _cat2 in px-24adb6.o _cat in px-24adb6.o _echo_from_fd in px-24adb6.o "_sleep", referenced from: _main in px-24adb6.o "_sscanf", referenced from: _main in px-24adb6.o "_strcmp", referenced from: _main in px-24adb6.o "_strerror", referenced from: _echo_from_fd in px-24adb6.o "_strlen", referenced from: _write_to_fd in px-24adb6.o _echo_from_fd in px-24adb6.o _main in px-24adb6.o "_usleep", referenced from: _main in px-24adb6.o "_write", referenced from: _cat2 in px-24adb6.o _cat in px-24adb6.o _write_to_fd in px-24adb6.o _echo_from_fd in px-24adb6.o _main in px-24adb6.o (maybe you meant: _write_to_fd) ld: symbol(s) not found for architecture x86_64 clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [Makevars:11: px] Error 1 ERROR: compilation failed for package ‘ps’ * removing ‘/Users/[user]/anaconda3/lib/R/library/ps’ The downloaded source packages are in ‘/private/var/folders/y6/ntnz7dyd2w3f5qvlrpxvpw6m0000gn/T/RtmpkN4iJB/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning message: In install.packages("ps") : installation of package ‘ps’ had non-zero exit status > install.packages("devtools") also installing the dependencies ‘ps’, ‘ini’, ‘processx’, ‘desc’, ‘xopen’, ‘clipr’, ‘clisymbols’, ‘fs’, ‘gh’, ‘whisker’, ‘callr’, ‘git2r’, ‘memoise’, ‘pkgbuild’, ‘pkgload’, ‘rcmdcheck’, ‘remotes’, ‘sessioninfo’, ‘usethis’ trying URL 'https://cran.cnr.berkeley.edu/src/contrib/ps_1.3.0.tar.gz' Content type 'application/x-gzip' length 261887 bytes (255 KB) ================================================== downloaded 255 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/ini_0.3.1.tar.gz' Content type 'application/x-gzip' length 3488 bytes ================================================== downloaded 3488 bytes trying URL 'https://cran.cnr.berkeley.edu/src/contrib/processx_3.2.1.tar.gz' Content type 'application/x-gzip' length 101057 bytes (98 KB) ================================================== downloaded 98 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/desc_1.2.0.tar.gz' Content type 'application/x-gzip' length 65612 bytes (64 KB) ================================================== downloaded 64 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/xopen_1.0.0.tar.gz' Content type 'application/x-gzip' length 11221 bytes (10 KB) ================================================== downloaded 10 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/clipr_0.5.0.tar.gz' Content type 'application/x-gzip' length 13731 bytes (13 KB) ================================================== downloaded 13 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/clisymbols_1.2.0.tar.gz' Content type 'application/x-gzip' length 9666 bytes ================================================== downloaded 9666 bytes trying URL 'https://cran.cnr.berkeley.edu/src/contrib/fs_1.2.6.tar.gz' Content type 'application/x-gzip' length 799325 bytes (780 KB) ================================================== downloaded 780 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/gh_1.0.1.tar.gz' Content type 'application/x-gzip' length 15513 bytes (15 KB) ================================================== downloaded 15 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/whisker_0.3-2.tar.gz' Content type 'application/x-gzip' length 27707 bytes (27 KB) ================================================== downloaded 27 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/callr_3.1.1.tar.gz' Content type 'application/x-gzip' length 41273 bytes (40 KB) ================================================== downloaded 40 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/git2r_0.24.0.tar.gz' Content type 'application/x-gzip' length 1151420 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/memoise_1.1.0.tar.gz' Content type 'application/x-gzip' length 11025 bytes (10 KB) ================================================== downloaded 10 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/pkgbuild_1.0.2.tar.gz' Content type 'application/x-gzip' length 25264 bytes (24 KB) ================================================== downloaded 24 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/pkgload_1.0.2.tar.gz' Content type 'application/x-gzip' length 55605 bytes (54 KB) ================================================== downloaded 54 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/rcmdcheck_1.3.2.tar.gz' Content type 'application/x-gzip' length 1408582 bytes (1.3 MB) ================================================== downloaded 1.3 MB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/remotes_2.0.2.tar.gz' Content type 'application/x-gzip' length 79682 bytes (77 KB) ================================================== downloaded 77 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/sessioninfo_1.1.1.tar.gz' Content type 'application/x-gzip' length 46027 bytes (44 KB) ================================================== downloaded 44 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/usethis_1.4.0.tar.gz' Content type 'application/x-gzip' length 325703 bytes (318 KB) ================================================== downloaded 318 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/devtools_2.0.1.tar.gz' Content type 'application/x-gzip' length 388953 bytes (379 KB) ================================================== downloaded 379 KB * installing *source* package ‘ps’ ... ** package ‘ps’ successfully unpacked and MD5 sums checked ** libs x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/[user]/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -Wall px.c -o px ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd Undefined symbols for architecture x86_64: "___error", referenced from: _echo_from_fd in px-7d1ac9.o "___stack_chk_fail", referenced from: _cat2 in px-7d1ac9.o _cat in px-7d1ac9.o _echo_from_fd in px-7d1ac9.o _main in px-7d1ac9.o "___stack_chk_guard", referenced from: _cat2 in px-7d1ac9.o _cat in px-7d1ac9.o _echo_from_fd in px-7d1ac9.o _main in px-7d1ac9.o "___stderrp", referenced from: _usage in px-7d1ac9.o _cat2 in px-7d1ac9.o _cat in px-7d1ac9.o _write_to_fd in px-7d1ac9.o _echo_from_fd in px-7d1ac9.o _main in px-7d1ac9.o "___stdoutp", referenced from: _echo_from_fd in px-7d1ac9.o _main in px-7d1ac9.o "_close", referenced from: _cat in px-7d1ac9.o "_exit", referenced from: _cat2 in px-7d1ac9.o _cat in px-7d1ac9.o "_fflush", referenced from: _echo_from_fd in px-7d1ac9.o _main in px-7d1ac9.o "_fprintf", referenced from: _cat2 in px-7d1ac9.o _cat in px-7d1ac9.o _write_to_fd in px-7d1ac9.o _echo_from_fd in px-7d1ac9.o _main in px-7d1ac9.o "_fputs", referenced from: _main in px-7d1ac9.o "_fwrite", referenced from: _usage in px-7d1ac9.o _main in px-7d1ac9.o "_getenv", referenced from: _main in px-7d1ac9.o "_open", referenced from: _cat in px-7d1ac9.o "_printf", referenced from: _main in px-7d1ac9.o "_puts", referenced from: _main in px-7d1ac9.o "_read", referenced from: _cat2 in px-7d1ac9.o _cat in px-7d1ac9.o _echo_from_fd in px-7d1ac9.o "_sleep", referenced from: _main in px-7d1ac9.o "_sscanf", referenced from: _main in px-7d1ac9.o "_strcmp", referenced from: _main in px-7d1ac9.o "_strerror", referenced from: _echo_from_fd in px-7d1ac9.o "_strlen", referenced from: _write_to_fd in px-7d1ac9.o _echo_from_fd in px-7d1ac9.o _main in px-7d1ac9.o "_usleep", referenced from: _main in px-7d1ac9.o "_write", referenced from: _cat2 in px-7d1ac9.o _cat in px-7d1ac9.o _write_to_fd in px-7d1ac9.o _echo_from_fd in px-7d1ac9.o _main in px-7d1ac9.o (maybe you meant: _write_to_fd) ld: symbol(s) not found for architecture x86_64 clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [Makevars:11: px] Error 1 ERROR: compilation failed for package ‘ps’ * removing ‘/Users/[user]/anaconda3/lib/R/library/ps’ * installing *source* package ‘ini’ ... ** package ‘ini’ successfully unpacked and MD5 sums checked ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (ini) * installing *source* package ‘desc’ ... ** package ‘desc’ successfully unpacked and MD5 sums checked ** 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 (desc) * installing *source* package ‘clipr’ ... ** package ‘clipr’ successfully unpacked and MD5 sums checked ** 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 (clipr) * installing *source* package ‘clisymbols’ ... ** package ‘clisymbols’ successfully unpacked and MD5 sums checked ** 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 (clisymbols) * installing *source* package ‘fs’ ... ** package ‘fs’ successfully unpacked and MD5 sums checked ** libs x86_64-apple-darwin13.4.0-clang++ -I"/Users/[user]/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/Users/[user]/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/[user]/anaconda3/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/Users/[user]/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c error.cc -o error.o x86_64-apple-darwin13.4.0-clang++ -I"/Users/[user]/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/Users/[user]/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/[user]/anaconda3/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/Users/[user]/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c dir.cc -o dir.o x86_64-apple-darwin13.4.0-clang++ -I"/Users/[user]/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/Users/[user]/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/[user]/anaconda3/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/Users/[user]/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c utils.cc -o utils.o x86_64-apple-darwin13.4.0-clang++ -I"/Users/[user]/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/Users/[user]/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/[user]/anaconda3/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/Users/[user]/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c link.cc -o link.o x86_64-apple-darwin13.4.0-clang++ -I"/Users/[user]/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/Users/[user]/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/[user]/anaconda3/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/Users/[user]/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c path.cc -o path.o x86_64-apple-darwin13.4.0-clang++ -I"/Users/[user]/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/Users/[user]/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/[user]/anaconda3/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/Users/[user]/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c file.cc -o file.o x86_64-apple-darwin13.4.0-clang++ -I"/Users/[user]/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/Users/[user]/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/[user]/anaconda3/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/Users/[user]/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c fs.cc -o fs.o x86_64-apple-darwin13.4.0-clang++ -I"/Users/[user]/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/Users/[user]/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/[user]/anaconda3/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/Users/[user]/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c id.cc -o id.o x86_64-apple-darwin13.4.0-clang++ -I"/Users/[user]/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/Users/[user]/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/[user]/anaconda3/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/Users/[user]/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c unix/getmode.cc -o unix/getmode.o x86_64-apple-darwin13.4.0-clang++ -I"/Users/[user]/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -I"/Users/[user]/anaconda3/lib/R/library/Rcpp/include" -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/[user]/anaconda3/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/Users/[user]/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o cp -p -f libuv/m4/lt_obsolete.m4 libuv/m4/lt~obsolete.m4 (cd libuv \ && touch aclocal.m4 \ && touch -r aclocal.m4 configure Makefile.in \ && CC="x86_64-apple-darwin13.4.0-clang" CFLAGS="-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/[user]/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -fPIC " AR="x86_64-apple-darwin13.4.0-ar" RANLIB="x86_64-apple-darwin13.4.0-ranlib" LDFLAGS="-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/[user]/anaconda3/lib -L/Users/[user]/anaconda3/lib" ./configure --quiet) configure: error: in `/private/var/folders/y6/ntnz7dyd2w3f5qvlrpxvpw6m0000gn/T/RtmpvzRhzC/R.INSTALL83d75a99468/fs/src/libuv': configure: error: C compiler cannot create executables See `config.log' for more details make: *** [Makevars:32: libuv/Makefile] Error 77 ERROR: compilation failed for package ‘fs’ * removing ‘/Users/[user]/anaconda3/lib/R/library/fs’ * installing *source* package ‘whisker’ ... ** package ‘whisker’ successfully unpacked and MD5 sums checked ** 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 (whisker) * installing *source* package ‘git2r’ ... ** package ‘git2r’ successfully unpacked and MD5 sums checked checking build system type... x86_64-apple-darwin18.2.0 checking host system type... x86_64-apple-darwin18.2.0 checking for gcc... x86_64-apple-darwin13.4.0-clang checking whether the C compiler works... no configure: error: in `/private/var/folders/y6/ntnz7dyd2w3f5qvlrpxvpw6m0000gn/T/RtmpsM7bpR/R.INSTALL9545691fd31/git2r': configure: error: C compiler cannot create executables See `config.log' for more details ERROR: configuration failed for package ‘git2r’ * removing ‘/Users/[user]/anaconda3/lib/R/library/git2r’ * installing *source* package ‘memoise’ ... ** package ‘memoise’ successfully unpacked and MD5 sums checked ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (memoise) * installing *source* package ‘remotes’ ... ** package ‘remotes’ successfully unpacked and MD5 sums checked ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (remotes) * installing *source* package ‘sessioninfo’ ... ** package ‘sessioninfo’ successfully unpacked and MD5 sums checked ** 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 (sessioninfo) ERROR: dependency ‘ps’ is not available for package ‘processx’ * removing ‘/Users/[user]/anaconda3/lib/R/library/processx’ * installing *source* package ‘gh’ ... ** package ‘gh’ successfully unpacked and MD5 sums checked ** 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 (gh) ERROR: dependency ‘processx’ is not available for package ‘xopen’ * removing ‘/Users/[user]/anaconda3/lib/R/library/xopen’ ERROR: dependency ‘processx’ is not available for package ‘callr’ * removing ‘/Users/[user]/anaconda3/lib/R/library/callr’ ERROR: dependencies ‘fs’, ‘git2r’ are not available for package ‘usethis’ * removing ‘/Users/[user]/anaconda3/lib/R/library/usethis’ ERROR: dependency ‘callr’ is not available for package ‘pkgbuild’ * removing ‘/Users/[user]/anaconda3/lib/R/library/pkgbuild’ ERROR: dependency ‘pkgbuild’ is not available for package ‘pkgload’ * removing ‘/Users/[user]/anaconda3/lib/R/library/pkgload’ ERROR: dependencies ‘callr’, ‘pkgbuild’, ‘xopen’ are not available for package ‘rcmdcheck’ * removing ‘/Users/[user]/anaconda3/lib/R/library/rcmdcheck’ ERROR: dependencies ‘callr’, ‘git2r’, ‘pkgbuild’, ‘pkgload’, ‘rcmdcheck’, ‘usethis’ are not available for package ‘devtools’ * removing ‘/Users/[user]/anaconda3/lib/R/library/devtools’ The downloaded source packages are in ‘/private/var/folders/y6/ntnz7dyd2w3f5qvlrpxvpw6m0000gn/T/RtmpkN4iJB/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done There were 11 warnings (use warnings() to see them) > warnings() Warning messages: 1: In install.packages("devtools") : installation of package ‘ps’ had non-zero exit status 2: In install.packages("devtools") : installation of package ‘fs’ had non-zero exit status 3: In install.packages("devtools") : installation of package ‘git2r’ had non-zero exit status 4: In install.packages("devtools") : installation of package ‘processx’ had non-zero exit status 5: In install.packages("devtools") : installation of package ‘xopen’ had non-zero exit status 6: In install.packages("devtools") : installation of package ‘callr’ had non-zero exit status 7: In install.packages("devtools") : installation of package ‘usethis’ had non-zero exit status 8: In install.packages("devtools") : installation of package ‘pkgbuild’ had non-zero exit status 9: In install.packages("devtools") : installation of package ‘pkgload’ had non-zero exit status 10: In install.packages("devtools") : installation of package ‘rcmdcheck’ had non-zero exit status 11: In install.packages("devtools") : installation of package ‘devtools’ had non-zero exit status > install.packages(callr) Error in install.packages(callr) : object 'callr' not found > install.packages("callr") also installing the dependencies ‘ps’, ‘processx’ trying URL 'https://cran.cnr.berkeley.edu/src/contrib/ps_1.3.0.tar.gz' Content type 'application/x-gzip' length 261887 bytes (255 KB) ================================================== downloaded 255 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/processx_3.2.1.tar.gz' Content type 'application/x-gzip' length 101057 bytes (98 KB) ================================================== downloaded 98 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/callr_3.1.1.tar.gz' Content type 'application/x-gzip' length 41273 bytes (40 KB) ================================================== downloaded 40 KB * installing *source* package ‘ps’ ... ** package ‘ps’ successfully unpacked and MD5 sums checked ** libs x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/[user]/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -Wall px.c -o px ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd Undefined symbols for architecture x86_64: "___error", referenced from: _echo_from_fd in px-fac98a.o "___stack_chk_fail", referenced from: _cat2 in px-fac98a.o _cat in px-fac98a.o _echo_from_fd in px-fac98a.o _main in px-fac98a.o "___stack_chk_guard", referenced from: _cat2 in px-fac98a.o _cat in px-fac98a.o _echo_from_fd in px-fac98a.o _main in px-fac98a.o "___stderrp", referenced from: _usage in px-fac98a.o _cat2 in px-fac98a.o _cat in px-fac98a.o _write_to_fd in px-fac98a.o _echo_from_fd in px-fac98a.o _main in px-fac98a.o "___stdoutp", referenced from: _echo_from_fd in px-fac98a.o _main in px-fac98a.o "_close", referenced from: _cat in px-fac98a.o "_exit", referenced from: _cat2 in px-fac98a.o _cat in px-fac98a.o "_fflush", referenced from: _echo_from_fd in px-fac98a.o _main in px-fac98a.o "_fprintf", referenced from: _cat2 in px-fac98a.o _cat in px-fac98a.o _write_to_fd in px-fac98a.o _echo_from_fd in px-fac98a.o _main in px-fac98a.o "_fputs", referenced from: _main in px-fac98a.o "_fwrite", referenced from: _usage in px-fac98a.o _main in px-fac98a.o "_getenv", referenced from: _main in px-fac98a.o "_open", referenced from: _cat in px-fac98a.o "_printf", referenced from: _main in px-fac98a.o "_puts", referenced from: _main in px-fac98a.o "_read", referenced from: _cat2 in px-fac98a.o _cat in px-fac98a.o _echo_from_fd in px-fac98a.o "_sleep", referenced from: _main in px-fac98a.o "_sscanf", referenced from: _main in px-fac98a.o "_strcmp", referenced from: _main in px-fac98a.o "_strerror", referenced from: _echo_from_fd in px-fac98a.o "_strlen", referenced from: _write_to_fd in px-fac98a.o _echo_from_fd in px-fac98a.o _main in px-fac98a.o "_usleep", referenced from: _main in px-fac98a.o "_write", referenced from: _cat2 in px-fac98a.o _cat in px-fac98a.o _write_to_fd in px-fac98a.o _echo_from_fd in px-fac98a.o _main in px-fac98a.o (maybe you meant: _write_to_fd) ld: symbol(s) not found for architecture x86_64 clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [Makevars:11: px] Error 1 ERROR: compilation failed for package ‘ps’ * removing ‘/Users/[user]/anaconda3/lib/R/library/ps’ ERROR: dependency ‘ps’ is not available for package ‘processx’ * removing ‘/Users/[user]/anaconda3/lib/R/library/processx’ ERROR: dependency ‘processx’ is not available for package ‘callr’ * removing ‘/Users/[user]/anaconda3/lib/R/library/callr’ The downloaded source packages are in ‘/private/var/folders/y6/ntnz7dyd2w3f5qvlrpxvpw6m0000gn/T/RtmpkN4iJB/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning messages: 1: In install.packages("callr") : installation of package ‘ps’ had non-zero exit status 2: In install.packages("callr") : installation of package ‘processx’ had non-zero exit status 3: In install.packages("callr") : installation of package ‘callr’ had non-zero exit status >
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