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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