Hello, this is my second day of learning R. All has been well until an hour ago when I could not install tidyverse package. I am coding in R Studio which is running from anacoda. The package seem to show that it is installing and then deleted. The main error I am getting is installation of package ‘tidyverse’ had non-zero exit status
My apologies for pasting a damn long error (below). But I hope it's important for helping you understanding the error. I have looked and all responses related to this question but they have not worked for me. Assistance will be highly appreciated. Thank you.
The detail error is below.
trying URL 'https://cran.rstudio.com/src/contrib/pkgbuild_1.0.8.tar.gz'
Content type 'application/x-gzip' length 29485 bytes (28 KB)
==================================================
downloaded 28 KB
trying URL 'https://cran.rstudio.com/src/contrib/pkgload_1.1.0.tar.gz'
Content type 'application/x-gzip' length 58046 bytes (56 KB)
==================================================
downloaded 56 KB
trying URL 'https://cran.rstudio.com/src/contrib/ps_1.3.3.tar.gz'
Content type 'application/x-gzip' length 98973 bytes (96 KB)
==================================================
downloaded 96 KB
trying URL 'https://cran.rstudio.com/src/contrib/testthat_2.3.2.tar.gz'
Content type 'application/x-gzip' length 249661 bytes (243 KB)
==================================================
downloaded 243 KB
trying URL 'https://cran.rstudio.com/src/contrib/processx_3.4.3.tar.gz'
Content type 'application/x-gzip' length 132841 bytes (129 KB)
==================================================
downloaded 129 KB
trying URL 'https://cran.rstudio.com/src/contrib/isoband_0.2.2.tar.gz'
Content type 'application/x-gzip' length 2295931 bytes (2.2 MB)
==================================================
downloaded 2.2 MB
trying URL 'https://cran.rstudio.com/src/contrib/callr_3.4.3.tar.gz'
Content type 'application/x-gzip' length 85802 bytes (83 KB)
==================================================
downloaded 83 KB
trying URL 'https://cran.rstudio.com/src/contrib/fs_1.4.2.tar.gz'
Content type 'application/x-gzip' length 819583 bytes (800 KB)
==================================================
downloaded 800 KB
trying URL 'https://cran.rstudio.com/src/contrib/ggplot2_3.3.2.tar.gz'
Content type 'application/x-gzip' length 3054431 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
trying URL 'https://cran.rstudio.com/src/contrib/reprex_0.3.0.tar.gz'
Content type 'application/x-gzip' length 1052597 bytes (1.0 MB)
==================================================
downloaded 1.0 MB
trying URL 'https://cran.rstudio.com/src/contrib/tidyverse_1.3.0.tar.gz'
Content type 'application/x-gzip' length 712837 bytes (696 KB)
==================================================
downloaded 696 KB
* installing *source* package ‘ps’ ...
** package ‘ps’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/john/opt/anaconda3/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/john/opt/anaconda3=/usr/local/src/conda-prefix -Wall px.c -o px
ld: warning: ignoring file /Library/Developer/CommandLineTools/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): /Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd
Undefined symbols for architecture x86_64:
"___error", referenced from:
_echo_from_fd in px-27602b.o
"___stack_chk_fail", referenced from:
_cat2 in px-27602b.o
_cat in px-27602b.o
_echo_from_fd in px-27602b.o
_main in px-27602b.o
"___stack_chk_guard", referenced from:
_cat2 in px-27602b.o
_cat in px-27602b.o
_echo_from_fd in px-27602b.o
_main in px-27602b.o
"___stderrp", referenced from:
_usage in px-27602b.o
_cat2 in px-27602b.o
_cat in px-27602b.o
_write_to_fd in px-27602b.o
_echo_from_fd in px-27602b.o
_main in px-27602b.o
"___stdoutp", referenced from:
_echo_from_fd in px-27602b.o
_main in px-27602b.o
"_close", referenced from:
_cat in px-27602b.o
"_exit", referenced from:
_cat2 in px-27602b.o
_cat in px-27602b.o
"_fflush", referenced from:
_echo_from_fd in px-27602b.o
_main in px-27602b.o
"_fprintf", referenced from:
_cat2 in px-27602b.o
_cat in px-27602b.o
_write_to_fd in px-27602b.o
_echo_from_fd in px-27602b.o
_main in px-27602b.o
"_fputs", referenced from:
_main in px-27602b.o
"_fwrite", referenced from:
_usage in px-27602b.o
_main in px-27602b.o
"_getenv", referenced from:
_main in px-27602b.o
"_open", referenced from:
_cat in px-27602b.o
"_printf", referenced from:
_main in px-27602b.o
"_puts", referenced from:
_main in px-27602b.o
"_read", referenced from:
_cat2 in px-27602b.o
_cat in px-27602b.o
_echo_from_fd in px-27602b.o
"_sleep", referenced from:
_main in px-27602b.o
"_sscanf", referenced from:
_main in px-27602b.o
"_strcmp", referenced from:
_main in px-27602b.o
"_strerror", referenced from:
_echo_from_fd in px-27602b.o
"_strlen", referenced from:
_write_to_fd in px-27602b.o
_echo_from_fd in px-27602b.o
_main in px-27602b.o
"_usleep", referenced from:
_main in px-27602b.o
"_write", referenced from:
_cat2 in px-27602b.o
_cat in px-27602b.o
_write_to_fd in px-27602b.o
_echo_from_fd in px-27602b.o
_main in px-27602b.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/john/opt/anaconda3/lib/R/library/ps’
Warning in install.packages :
installation of package ‘ps’ had non-zero exit status
* installing *source* package ‘fs’ ...
** package ‘fs’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/john/opt/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/john/opt/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/john/opt/anaconda3/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/john/opt/anaconda3=/usr/local/src/conda-prefix -c error.cc -o error.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/john/opt/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/john/opt/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/john/opt/anaconda3/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/john/opt/anaconda3=/usr/local/src/conda-prefix -c getmode.cc -o getmode.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/john/opt/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/john/opt/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/john/opt/anaconda3/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/john/opt/anaconda3=/usr/local/src/conda-prefix -c dir.cc -o dir.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/john/opt/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/john/opt/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/john/opt/anaconda3/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/john/opt/anaconda3=/usr/local/src/conda-prefix -c utils.cc -o utils.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/john/opt/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/john/opt/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/john/opt/anaconda3/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/john/opt/anaconda3=/usr/local/src/conda-prefix -c link.cc -o link.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/john/opt/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/john/opt/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/john/opt/anaconda3/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/john/opt/anaconda3=/usr/local/src/conda-prefix -c path.cc -o path.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/john/opt/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/john/opt/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/john/opt/anaconda3/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/john/opt/anaconda3=/usr/local/src/conda-prefix -c file.cc -o file.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/john/opt/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/john/opt/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/john/opt/anaconda3/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/john/opt/anaconda3=/usr/local/src/conda-prefix -c id.cc -o id.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/john/opt/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/john/opt/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/john/opt/anaconda3/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/john/opt/anaconda3=/usr/local/src/conda-prefix -c fs.cc -o fs.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/john/opt/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/john/opt/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/john/opt/anaconda3/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/john/opt/anaconda3=/usr/local/src/conda-prefix -c init.cc -o init.o
x86_64-apple-darwin13.4.0-clang++ -std=gnu++11 -I"/Users/john/opt/anaconda3/lib/R/include" -DNDEBUG -I./libuv/include -I. -pthread -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/john/opt/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/john/opt/anaconda3/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/john/opt/anaconda3=/usr/local/src/conda-prefix -c unix/getmode.cc -o unix/getmode.o
(cd libuv \
&& 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/john/opt/anaconda3/include -fdebug-prefix-map=/opt/concourse/worker/volumes/live/59b7f007-fada-42cf-7435-5bbd0518eaa4/volume/r-base_1570124919999/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/Users/john/opt/anaconda3=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/john/opt/anaconda3/include -fPIC " AR="x86_64-apple-darwin13.4.0-ar" RANLIB="x86_64-apple-darwin13.4.0-ranlib" LDFLAGS="-Wl,-dead_strip_dylibs -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/john/opt/anaconda3/lib -L/Users/john/opt/anaconda3/lib" ./configure --quiet)
configure: error: in `/private/var/folders/rm/wkbrctj527x2jcs8_3zs8xk00000gn/T/Rtmpeew481/R.INSTALL15a393b251cf1/fs/src/libuv':
configure: error: C compiler cannot create executables
See `config.log' for more details
make: *** [Makevars:29: libuv/Makefile] Error 77
ERROR: compilation failed for package ‘fs’
* removing ‘/Users/john/opt/anaconda3/lib/R/library/fs’
Warning in install.packages :
installation of package ‘fs’ had non-zero exit status
ERROR: dependency ‘ps’ is not available for package ‘processx’
* removing ‘/Users/john/opt/anaconda3/lib/R/library/processx’
Warning in install.packages :
installation of package ‘processx’ had non-zero exit status
ERROR: dependency ‘processx’ is not available for package ‘callr’
* removing ‘/Users/john/opt/anaconda3/lib/R/library/callr’
Warning in install.packages :
installation of package ‘callr’ had non-zero exit status
ERROR: dependency ‘callr’ is not available for package ‘pkgbuild’
* removing ‘/Users/john/opt/anaconda3/lib/R/library/pkgbuild’
Warning in install.packages :
installation of package ‘pkgbuild’ had non-zero exit status
ERROR: dependencies ‘callr’, ‘fs’ are not available for package ‘reprex’
* removing ‘/Users/john/opt/anaconda3/lib/R/library/reprex’
Warning in install.packages :
installation of package ‘reprex’ had non-zero exit status
ERROR: dependency ‘pkgbuild’ is not available for package ‘pkgload’
* removing ‘/Users/john/opt/anaconda3/lib/R/library/pkgload’
Warning in install.packages :
installation of package ‘pkgload’ had non-zero exit status
ERROR: dependency ‘pkgload’ is not available for package ‘testthat’
* removing ‘/Users/john/opt/anaconda3/lib/R/library/testthat’
Warning in install.packages :
installation of package ‘testthat’ had non-zero exit status
ERROR: dependency ‘testthat’ is not available for package ‘isoband’
* removing ‘/Users/john/opt/anaconda3/lib/R/library/isoband’
Warning in install.packages :
installation of package ‘isoband’ had non-zero exit status
ERROR: dependency ‘isoband’ is not available for package ‘ggplot2’
* removing ‘/Users/john/opt/anaconda3/lib/R/library/ggplot2’
Warning in install.packages :
installation of package ‘ggplot2’ had non-zero exit status
ERROR: dependencies ‘ggplot2’, ‘reprex’ are not available for package ‘tidyverse’
* removing ‘/Users/john/opt/anaconda3/lib/R/library/tidyverse’
Warning in install.packages :
installation of package ‘tidyverse’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/rm/wkbrctj527x2jcs8_3zs8xk00000gn/T/Rtmpg0rK1C/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done```