Jocelyn Ireson-Paine
2017-Aug-17 09:26 UTC
[R] How to install Tidyverse on Ubuntu 17.04? Getting gcc errors for -fstack-protector-strong and -Wdate-time
I'm running Ubuntu 17.04 and R 3.4.1. I installed the latter yesterday, so
I presume it's the latest version. I want to install Tidyverse, which
I've
spent many happy hours with under Windows. But when I do
install.packages("tidyverse") , I get errors about unrecognized
command
line options to gcc. These start when the install hits the colorspace and
munsell packages. I'll show an example at the end of this post.
I've not found anyone else who had exactly that problem on Ubuntu 17.04.
But posts from people with similar problems suggest that my gcc might be a
version that's too old to recognise the options -fstack-protector-strong
and -Wdate-time.
Possible work-arounds that I've thought of:
1) Find an older version of Tidyverse that doesn't need those compiler
options.
2) Upgrade my Ubuntu's gcc so that whichever one Tidyverse needs becomes
the default. But I don't know whether that would nuke other software on my
machine that expects an older gcc. And I don't know exactly what software
the installer expects, so I'd have to keep installing different gccs until
I found one that worked.
(A suggestion: it would be excellent if the installer could detect such
errors, then fetch and install needed software for itself. If it can't do
that, couldn't it at least tell me which version it wants, instead of
making me deduce it from the compiler options it's using?)
3) Install a new gcc just for Tidyverse, and somehow play with paths to
fool the installer into calling it. Perhaps by following the advice in
https://askubuntu.com/questions/466651/how-do-i-use-the-latest-gcc-on-ubuntu
. But that sounds risky.
4) Change operating systems? I know Tidyverse works on Windows straight out
of the box. Maybe it's not designed to work on Ubuntu. Anyone know?
Here's an install that failed:
R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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("tidyverse")
Installing package into ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4?
(as ?lib? is unspecified)
also installing the dependencies ?colorspace?, ?munsell?, ?plyr?, ?psych?,
?reshape2?, ?bindrcpp?, ?Rcpp?, ?digest?, ?scales?, ?curl?, ?openssl?,
?cellranger?, ?stringi?, ?selectr?, ?tidyselect?, ?broom?, ?dplyr?,
?forcats?, ?ggplot2?, ?haven?, ?httr?, ?jsonlite?, ?lubridate?, ?modelr?,
?purrr?, ?readr?, ?readxl?, ?stringr?, ?tibble?, ?rvest?, ?tidyr?, ?xml2?
trying URL
'https://cran.rstudio.com/src/contrib/colorspace_1.3-2.tar.gz'
Content type 'application/x-gzip' length 293433 bytes (286 KB)
=================================================downloaded 286 KB
trying URL 'https://cran.rstudio.com/src/contrib/munsell_0.4.3.tar.gz'
Content type 'application/x-gzip' length 97244 bytes (94 KB)
=================================================downloaded 94 KB
trying URL 'https://cran.rstudio.com/src/contrib/plyr_1.8.4.tar.gz'
Content type 'application/x-gzip' length 392451 bytes (383 KB)
=================================================downloaded 383 KB
trying URL 'https://cran.rstudio.com/src/contrib/psych_1.7.5.tar.gz'
Content type 'application/x-gzip' length 3219737 bytes (3.1 MB)
=================================================downloaded 3.1 MB
trying URL 'https://cran.rstudio.com/src/contrib/reshape2_1.4.2.tar.gz'
Content type 'application/x-gzip' length 34688 bytes (33 KB)
=================================================downloaded 33 KB
trying URL 'https://cran.rstudio.com/src/contrib/bindrcpp_0.2.tar.gz'
Content type 'application/x-gzip' length 8089 bytes
=================================================downloaded 8089 bytes
trying URL 'https://cran.rstudio.com/src/contrib/Rcpp_0.12.12.tar.gz'
Content type 'application/x-gzip' length 2421289 bytes (2.3 MB)
=================================================downloaded 2.3 MB
trying URL 'https://cran.rstudio.com/src/contrib/digest_0.6.12.tar.gz'
Content type 'application/x-gzip' length 120337 bytes (117 KB)
=================================================downloaded 117 KB
trying URL 'https://cran.rstudio.com/src/contrib/scales_0.4.1.tar.gz'
Content type 'application/x-gzip' length 57703 bytes (56 KB)
=================================================downloaded 56 KB
trying URL 'https://cran.rstudio.com/src/contrib/curl_2.8.1.tar.gz'
Content type 'application/x-gzip' length 409743 bytes (400 KB)
=================================================downloaded 400 KB
trying URL 'https://cran.rstudio.com/src/contrib/openssl_0.9.6.tar.gz'
Content type 'application/x-gzip' length 1239339 bytes (1.2 MB)
=================================================downloaded 1.2 MB
trying URL
'https://cran.rstudio.com/src/contrib/cellranger_1.1.0.tar.gz'
Content type 'application/x-gzip' length 63857 bytes (62 KB)
=================================================downloaded 62 KB
trying URL 'https://cran.rstudio.com/src/contrib/stringi_1.1.5.tar.gz'
Content type 'application/x-gzip' length 3645872 bytes (3.5 MB)
=================================================downloaded 3.5 MB
trying URL 'https://cran.rstudio.com/src/contrib/selectr_0.3-1.tar.gz'
Content type 'application/x-gzip' length 42098 bytes (41 KB)
=================================================downloaded 41 KB
trying URL
'https://cran.rstudio.com/src/contrib/tidyselect_0.1.1.tar.gz'
Content type 'application/x-gzip' length 18670 bytes (18 KB)
=================================================downloaded 18 KB
trying URL 'https://cran.rstudio.com/src/contrib/broom_0.4.2.tar.gz'
Content type 'application/x-gzip' length 1388242 bytes (1.3 MB)
=================================================downloaded 1.3 MB
trying URL 'https://cran.rstudio.com/src/contrib/dplyr_0.7.2.tar.gz'
Content type 'application/x-gzip' length 692952 bytes (676 KB)
=================================================downloaded 676 KB
trying URL 'https://cran.rstudio.com/src/contrib/forcats_0.2.0.tar.gz'
Content type 'application/x-gzip' length 95288 bytes (93 KB)
=================================================downloaded 93 KB
trying URL 'https://cran.rstudio.com/src/contrib/ggplot2_2.2.1.tar.gz'
Content type 'application/x-gzip' length 2213308 bytes (2.1 MB)
=================================================downloaded 2.1 MB
trying URL 'https://cran.rstudio.com/src/contrib/haven_1.1.0.tar.gz'
Content type 'application/x-gzip' length 184056 bytes (179 KB)
=================================================downloaded 179 KB
trying URL 'https://cran.rstudio.com/src/contrib/httr_1.3.0.tar.gz'
Content type 'application/x-gzip' length 147567 bytes (144 KB)
=================================================downloaded 144 KB
trying URL 'https://cran.rstudio.com/src/contrib/jsonlite_1.5.tar.gz'
Content type 'application/x-gzip' length 1096810 bytes (1.0 MB)
=================================================downloaded 1.0 MB
trying URL 'https://cran.rstudio.com/src/contrib/lubridate_1.6.0.tar.gz'
Content type 'application/x-gzip' length 317672 bytes (310 KB)
=================================================downloaded 310 KB
trying URL 'https://cran.rstudio.com/src/contrib/modelr_0.1.1.tar.gz'
Content type 'application/x-gzip' length 83629 bytes (81 KB)
=================================================downloaded 81 KB
trying URL 'https://cran.rstudio.com/src/contrib/purrr_0.2.3.tar.gz'
Content type 'application/x-gzip' length 126170 bytes (123 KB)
=================================================downloaded 123 KB
trying URL 'https://cran.rstudio.com/src/contrib/readr_1.1.1.tar.gz'
Content type 'application/x-gzip' length 233793 bytes (228 KB)
=================================================downloaded 228 KB
trying URL 'https://cran.rstudio.com/src/contrib/readxl_1.0.0.tar.gz'
Content type 'application/x-gzip' length 1936302 bytes (1.8 MB)
=================================================downloaded 1.8 MB
trying URL 'https://cran.rstudio.com/src/contrib/stringr_1.2.0.tar.gz'
Content type 'application/x-gzip' length 94095 bytes (91 KB)
=================================================downloaded 91 KB
trying URL 'https://cran.rstudio.com/src/contrib/tibble_1.3.3.tar.gz'
Content type 'application/x-gzip' length 91511 bytes (89 KB)
=================================================downloaded 89 KB
trying URL 'https://cran.rstudio.com/src/contrib/rvest_0.3.2.tar.gz'
Content type 'application/x-gzip' length 1597137 bytes (1.5 MB)
=================================================downloaded 1.5 MB
trying URL 'https://cran.rstudio.com/src/contrib/tidyr_0.7.0.tar.gz'
Content type 'application/x-gzip' length 368687 bytes (360 KB)
=================================================downloaded 360 KB
trying URL 'https://cran.rstudio.com/src/contrib/xml2_1.1.1.tar.gz'
Content type 'application/x-gzip' length 244643 bytes (238 KB)
=================================================downloaded 238 KB
trying URL 'https://cran.rstudio.com/src/contrib/tidyverse_1.1.1.tar.gz'
Content type 'application/x-gzip' length 23452 bytes (22 KB)
=================================================downloaded 22 KB
* installing *source* package ?colorspace? ...
** package ?colorspace? successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c colorspace.c -o colorspace.o
gcc: error: unrecognized command line option '-fstack-protector-strong'
gcc: error: unrecognized command line option '-Wdate-time'
/usr/lib/R/etc/Makeconf:159: recipe for target 'colorspace.o' failed
make: *** [colorspace.o] Error 1
ERROR: compilation failed for package ?colorspace?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/colorspace?
Warning in install.packages :
installation of package ?colorspace? had non-zero exit status
* installing *source* package ?psych? ...
** package ?psych? successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error : objects ?rmnorm?, ?sadmvn?, ?dmnorm? are not exported by
'namespace:mnormt'
ERROR: lazy loading failed for package ?psych?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/psych?
Warning in install.packages :
installation of package ?psych? had non-zero exit status
* installing *source* package ?Rcpp? ...
** package ?Rcpp? successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c Date.cpp -o Date.o
g++: error: unrecognized command line option '-fstack-protector-strong'
g++: error: unrecognized command line option '-Wdate-time'
/usr/lib/R/etc/Makeconf:168: recipe for target 'Date.o' failed
make: *** [Date.o] Error 1
ERROR: compilation failed for package ?Rcpp?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/Rcpp?
Warning in install.packages :
installation of package ?Rcpp? had non-zero exit status
* installing *source* package ?digest? ...
** package ?digest? successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c aes.c -o aes.o
gcc: error: unrecognized command line option '-fstack-protector-strong'
gcc: error: unrecognized command line option '-Wdate-time'
/usr/lib/R/etc/Makeconf:159: recipe for target 'aes.o' failed
make: *** [aes.o] Error 1
ERROR: compilation failed for package ?digest?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/digest?
Warning in install.packages :
installation of package ?digest? had non-zero exit status
* installing *source* package ?curl? ...
** package ?curl? successfully unpacked and MD5 sums checked
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGSUsing PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
* deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
* rpm: libcurl-devel (Fedora, CentOS, RHEL)
* csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ?curl?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/curl?
Warning in install.packages :
installation of package ?curl? had non-zero exit status
* installing *source* package ?openssl? ...
** package ?openssl? successfully unpacked and MD5 sums checked
Found pkg-config cflags and libs!
Using PKG_CFLAGSUsing PKG_LIBS=-lssl -lcrypto
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because openssl was not found. Try installing:
* deb: libssl-dev (Debian, Ubuntu, etc)
* rpm: openssl-devel (Fedora, CentOS, RHEL)
* csw: libssl_dev (Solaris)
* brew: openssl at 1.1 (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ?openssl?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/openssl?
Warning in install.packages :
installation of package ?openssl? had non-zero exit status
* installing *source* package ?stringi? ...
** package ?stringi? successfully unpacked and MD5 sums checked
checking for local ICUDT_DIR... icu55/data
checking for R_HOME... /usr/lib/R
checking for R... /usr/lib/R/bin/R
checking for R >= 3.1.0 for C++11 use... yes
checking for R < 3.4.0 for CXX1X flag use... no
checking for cat... /bin/cat
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... no
configure: error: in `/tmp/Rtmpu3553h/R.INSTALL28ffe0ce527/stringi':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ?stringi?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/stringi?
Warning in install.packages :
installation of package ?stringi? had non-zero exit status
* installing *source* package ?jsonlite? ...
** package ?jsonlite? successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o
gcc: error: unrecognized command line option '-fstack-protector-strong'
gcc: error: unrecognized command line option '-Wdate-time'
/usr/lib/R/etc/Makeconf:159: recipe for target 'base64.o' failed
make: *** [base64.o] Error 1
ERROR: compilation failed for package ?jsonlite?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/jsonlite?
Warning in install.packages :
installation of package ?jsonlite? had non-zero exit status
ERROR: dependency ?colorspace? is not available for package ?munsell?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/munsell?
Warning in install.packages :
installation of package ?munsell? had non-zero exit status
ERROR: dependency ?Rcpp? is not available for package ?plyr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/plyr?
Warning in install.packages :
installation of package ?plyr? had non-zero exit status
ERROR: dependency ?Rcpp? is not available for package ?bindrcpp?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/bindrcpp?
Warning in install.packages :
installation of package ?bindrcpp? had non-zero exit status
ERROR: dependency ?Rcpp? is not available for package ?tidyselect?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/tidyselect?
Warning in install.packages :
installation of package ?tidyselect? had non-zero exit status
ERROR: dependencies ?jsonlite?, ?curl?, ?openssl? are not available for
package ?httr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/httr?
Warning in install.packages :
installation of package ?httr? had non-zero exit status
ERROR: dependency ?stringi? is not available for package ?stringr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/stringr?
Warning in install.packages :
installation of package ?stringr? had non-zero exit status
ERROR: dependency ?Rcpp? is not available for package ?tibble?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/tibble?
Warning in install.packages :
installation of package ?tibble? had non-zero exit status
ERROR: dependency ?Rcpp? is not available for package ?xml2?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/xml2?
Warning in install.packages :
installation of package ?xml2? had non-zero exit status
ERROR: dependencies ?plyr?, ?stringr?, ?Rcpp? are not available for package
?reshape2?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/reshape2?
Warning in install.packages :
installation of package ?reshape2? had non-zero exit status
ERROR: dependencies ?plyr?, ?munsell?, ?Rcpp? are not available for package
?scales?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/scales?
Warning in install.packages :
installation of package ?scales? had non-zero exit status
ERROR: dependency ?tibble? is not available for package ?cellranger?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/cellranger?
Warning in install.packages :
installation of package ?cellranger? had non-zero exit status
ERROR: dependency ?stringr? is not available for package ?selectr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/selectr?
Warning in install.packages :
installation of package ?selectr? had non-zero exit status
ERROR: dependencies ?bindrcpp?, ?Rcpp?, ?tibble? are not available for
package ?dplyr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/dplyr?
Warning in install.packages :
installation of package ?dplyr? had non-zero exit status
ERROR: dependency ?tibble? is not available for package ?forcats?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/forcats?
Warning in install.packages :
installation of package ?forcats? had non-zero exit status
ERROR: dependency ?stringr? is not available for package ?lubridate?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/lubridate?
Warning in install.packages :
installation of package ?lubridate? had non-zero exit status
ERROR: dependency ?tibble? is not available for package ?purrr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/purrr?
Warning in install.packages :
installation of package ?purrr? had non-zero exit status
ERROR: dependencies ?Rcpp?, ?tibble? are not available for package ?readr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/readr?
Warning in install.packages :
installation of package ?readr? had non-zero exit status
ERROR: dependencies ?digest?, ?plyr?, ?reshape2?, ?scales?, ?tibble? are
not available for package ?ggplot2?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/ggplot2?
Warning in install.packages :
installation of package ?ggplot2? had non-zero exit status
ERROR: dependencies ?Rcpp?, ?readr?, ?tibble?, ?forcats? are not available
for package ?haven?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/haven?
Warning in install.packages :
installation of package ?haven? had non-zero exit status
ERROR: dependencies ?cellranger?, ?Rcpp?, ?tibble? are not available for
package ?readxl?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/readxl?
Warning in install.packages :
installation of package ?readxl? had non-zero exit status
ERROR: dependencies ?xml2?, ?httr?, ?selectr? are not available for package
?rvest?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/rvest?
Warning in install.packages :
installation of package ?rvest? had non-zero exit status
ERROR: dependencies ?dplyr?, ?purrr?, ?Rcpp?, ?stringi?, ?tibble?,
?tidyselect? are not available for package ?tidyr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/tidyr?
Warning in install.packages :
installation of package ?tidyr? had non-zero exit status
ERROR: dependencies ?plyr?, ?dplyr?, ?tidyr?, ?psych?, ?stringr?,
?reshape2? are not available for package ?broom?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/broom?
Warning in install.packages :
installation of package ?broom? had non-zero exit status
ERROR: dependencies ?purrr?, ?tibble?, ?broom?, ?dplyr?, ?tidyr? are not
available for package ?modelr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/modelr?
Warning in install.packages :
installation of package ?modelr? had non-zero exit status
ERROR: dependencies ?broom?, ?dplyr?, ?forcats?, ?ggplot2?, ?haven?,
?httr?, ?jsonlite?, ?lubridate?, ?modelr?, ?purrr?, ?readr?, ?readxl?,
?stringr?, ?tibble?, ?rvest?, ?tidyr?, ?xml2? are not available for package
?tidyverse?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/tidyverse?
Warning in install.packages :
installation of package ?tidyverse? had non-zero exit status
The downloaded source packages are in
?/tmp/RtmplZrBGp/downloaded_packages?
Warning message:
R graphics engine version 12 is not supported by this version of RStudio.
The Plots tab will be disabled until a newer version of RStudio is
installed.> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 17.04
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.7.0
LAPACK: /usr/lib/lapack/liblapack.so.3.7.0
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
loaded via a namespace (and not attached):
[1] compiler_3.4.1 tools_3.4.1
[[alternative HTML version deleted]]
John Kane
2017-Aug-17 11:42 UTC
[R] How to install Tidyverse on Ubuntu 17.04? Getting gcc errors for -fstack-protector-strong and -Wdate-time
No idea what the problem is but I am running Ubuntu 17.04 with R 3.4.1 and
tidyverse seems to be working well.
On Thursday, August 17, 2017, 7:10:42 AM EDT, Jocelyn Ireson-Paine via R-help
<r-help at r-project.org> wrote:
I'm running Ubuntu 17.04 and R 3.4.1. I installed the latter yesterday, so
I presume it's the latest version. I want to install Tidyverse, which
I've
spent many happy hours with under Windows. But when I do
install.packages("tidyverse") , I get errors about unrecognized
command
line options to gcc. These start when the install hits the colorspace and
munsell packages. I'll show an example at the end of this post.
I've not found anyone else who had exactly that problem on Ubuntu 17.04.
But posts from people with similar problems suggest that my gcc might be a
version that's too old to recognise the options -fstack-protector-strong
and -Wdate-time.
Possible work-arounds that I've thought of:
1) Find an older version of Tidyverse that doesn't need those compiler
options.
2) Upgrade my Ubuntu's gcc so that whichever one Tidyverse needs becomes
the default. But I don't know whether that would nuke other software on my
machine that expects an older gcc. And I don't know exactly what software
the installer expects, so I'd have to keep installing different gccs until
I found one that worked.
(A suggestion: it would be excellent if the installer could detect such
errors, then fetch and install needed software for itself. If it can't do
that, couldn't it at least tell me which version it wants, instead of
making me deduce it from the compiler options it's using?)
3) Install a new gcc just for Tidyverse, and somehow play with paths to
fool the installer into calling it. Perhaps by following the advice in
https://askubuntu.com/questions/466651/how-do-i-use-the-latest-gcc-on-ubuntu
. But that sounds risky.
4) Change operating systems? I know Tidyverse works on Windows straight out
of the box. Maybe it's not designed to work on Ubuntu. Anyone know?
Here's an install that failed:
R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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("tidyverse")
Installing package into ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4?
(as ?lib? is unspecified)
also installing the dependencies ?colorspace?, ?munsell?, ?plyr?, ?psych?,
?reshape2?, ?bindrcpp?, ?Rcpp?, ?digest?, ?scales?, ?curl?, ?openssl?,
?cellranger?, ?stringi?, ?selectr?, ?tidyselect?, ?broom?, ?dplyr?,
?forcats?, ?ggplot2?, ?haven?, ?httr?, ?jsonlite?, ?lubridate?, ?modelr?,
?purrr?, ?readr?, ?readxl?, ?stringr?, ?tibble?, ?rvest?, ?tidyr?, ?xml2?
trying URL
'https://cran.rstudio.com/src/contrib/colorspace_1.3-2.tar.gz'
Content type 'application/x-gzip' length 293433 bytes (286 KB)
=================================================downloaded 286 KB
trying URL 'https://cran.rstudio.com/src/contrib/munsell_0.4.3.tar.gz'
Content type 'application/x-gzip' length 97244 bytes (94 KB)
=================================================downloaded 94 KB
trying URL 'https://cran.rstudio.com/src/contrib/plyr_1.8.4.tar.gz'
Content type 'application/x-gzip' length 392451 bytes (383 KB)
=================================================downloaded 383 KB
trying URL 'https://cran.rstudio.com/src/contrib/psych_1.7.5.tar.gz'
Content type 'application/x-gzip' length 3219737 bytes (3.1 MB)
=================================================downloaded 3.1 MB
trying URL 'https://cran.rstudio.com/src/contrib/reshape2_1.4.2.tar.gz'
Content type 'application/x-gzip' length 34688 bytes (33 KB)
=================================================downloaded 33 KB
trying URL 'https://cran.rstudio.com/src/contrib/bindrcpp_0.2.tar.gz'
Content type 'application/x-gzip' length 8089 bytes
=================================================downloaded 8089 bytes
trying URL 'https://cran.rstudio.com/src/contrib/Rcpp_0.12.12.tar.gz'
Content type 'application/x-gzip' length 2421289 bytes (2.3 MB)
=================================================downloaded 2.3 MB
trying URL 'https://cran.rstudio.com/src/contrib/digest_0.6.12.tar.gz'
Content type 'application/x-gzip' length 120337 bytes (117 KB)
=================================================downloaded 117 KB
trying URL 'https://cran.rstudio.com/src/contrib/scales_0.4.1.tar.gz'
Content type 'application/x-gzip' length 57703 bytes (56 KB)
=================================================downloaded 56 KB
trying URL 'https://cran.rstudio.com/src/contrib/curl_2.8.1.tar.gz'
Content type 'application/x-gzip' length 409743 bytes (400 KB)
=================================================downloaded 400 KB
trying URL 'https://cran.rstudio.com/src/contrib/openssl_0.9.6.tar.gz'
Content type 'application/x-gzip' length 1239339 bytes (1.2 MB)
=================================================downloaded 1.2 MB
trying URL
'https://cran.rstudio.com/src/contrib/cellranger_1.1.0.tar.gz'
Content type 'application/x-gzip' length 63857 bytes (62 KB)
=================================================downloaded 62 KB
trying URL 'https://cran.rstudio.com/src/contrib/stringi_1.1.5.tar.gz'
Content type 'application/x-gzip' length 3645872 bytes (3.5 MB)
=================================================downloaded 3.5 MB
trying URL 'https://cran.rstudio.com/src/contrib/selectr_0.3-1.tar.gz'
Content type 'application/x-gzip' length 42098 bytes (41 KB)
=================================================downloaded 41 KB
trying URL
'https://cran.rstudio.com/src/contrib/tidyselect_0.1.1.tar.gz'
Content type 'application/x-gzip' length 18670 bytes (18 KB)
=================================================downloaded 18 KB
trying URL 'https://cran.rstudio.com/src/contrib/broom_0.4.2.tar.gz'
Content type 'application/x-gzip' length 1388242 bytes (1.3 MB)
=================================================downloaded 1.3 MB
trying URL 'https://cran.rstudio.com/src/contrib/dplyr_0.7.2.tar.gz'
Content type 'application/x-gzip' length 692952 bytes (676 KB)
=================================================downloaded 676 KB
trying URL 'https://cran.rstudio.com/src/contrib/forcats_0.2.0.tar.gz'
Content type 'application/x-gzip' length 95288 bytes (93 KB)
=================================================downloaded 93 KB
trying URL 'https://cran.rstudio.com/src/contrib/ggplot2_2.2.1.tar.gz'
Content type 'application/x-gzip' length 2213308 bytes (2.1 MB)
=================================================downloaded 2.1 MB
trying URL 'https://cran.rstudio.com/src/contrib/haven_1.1.0.tar.gz'
Content type 'application/x-gzip' length 184056 bytes (179 KB)
=================================================downloaded 179 KB
trying URL 'https://cran.rstudio.com/src/contrib/httr_1.3.0.tar.gz'
Content type 'application/x-gzip' length 147567 bytes (144 KB)
=================================================downloaded 144 KB
trying URL 'https://cran.rstudio.com/src/contrib/jsonlite_1.5.tar.gz'
Content type 'application/x-gzip' length 1096810 bytes (1.0 MB)
=================================================downloaded 1.0 MB
trying URL 'https://cran.rstudio.com/src/contrib/lubridate_1.6.0.tar.gz'
Content type 'application/x-gzip' length 317672 bytes (310 KB)
=================================================downloaded 310 KB
trying URL 'https://cran.rstudio.com/src/contrib/modelr_0.1.1.tar.gz'
Content type 'application/x-gzip' length 83629 bytes (81 KB)
=================================================downloaded 81 KB
trying URL 'https://cran.rstudio.com/src/contrib/purrr_0.2.3.tar.gz'
Content type 'application/x-gzip' length 126170 bytes (123 KB)
=================================================downloaded 123 KB
trying URL 'https://cran.rstudio.com/src/contrib/readr_1.1.1.tar.gz'
Content type 'application/x-gzip' length 233793 bytes (228 KB)
=================================================downloaded 228 KB
trying URL 'https://cran.rstudio.com/src/contrib/readxl_1.0.0.tar.gz'
Content type 'application/x-gzip' length 1936302 bytes (1.8 MB)
=================================================downloaded 1.8 MB
trying URL 'https://cran.rstudio.com/src/contrib/stringr_1.2.0.tar.gz'
Content type 'application/x-gzip' length 94095 bytes (91 KB)
=================================================downloaded 91 KB
trying URL 'https://cran.rstudio.com/src/contrib/tibble_1.3.3.tar.gz'
Content type 'application/x-gzip' length 91511 bytes (89 KB)
=================================================downloaded 89 KB
trying URL 'https://cran.rstudio.com/src/contrib/rvest_0.3.2.tar.gz'
Content type 'application/x-gzip' length 1597137 bytes (1.5 MB)
=================================================downloaded 1.5 MB
trying URL 'https://cran.rstudio.com/src/contrib/tidyr_0.7.0.tar.gz'
Content type 'application/x-gzip' length 368687 bytes (360 KB)
=================================================downloaded 360 KB
trying URL 'https://cran.rstudio.com/src/contrib/xml2_1.1.1.tar.gz'
Content type 'application/x-gzip' length 244643 bytes (238 KB)
=================================================downloaded 238 KB
trying URL 'https://cran.rstudio.com/src/contrib/tidyverse_1.1.1.tar.gz'
Content type 'application/x-gzip' length 23452 bytes (22 KB)
=================================================downloaded 22 KB
* installing *source* package ?colorspace? ...
** package ?colorspace? successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG? ? ? -fpic? -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g? -c colorspace.c -o colorspace.o
gcc: error: unrecognized command line option '-fstack-protector-strong'
gcc: error: unrecognized command line option '-Wdate-time'
/usr/lib/R/etc/Makeconf:159: recipe for target 'colorspace.o' failed
make: *** [colorspace.o] Error 1
ERROR: compilation failed for package ?colorspace?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/colorspace?
Warning in install.packages :
? installation of package ?colorspace? had non-zero exit status
* installing *source* package ?psych? ...
** package ?psych? successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error : objects ?rmnorm?, ?sadmvn?, ?dmnorm? are not exported by
'namespace:mnormt'
ERROR: lazy loading failed for package ?psych?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/psych?
Warning in install.packages :
? installation of package ?psych? had non-zero exit status
* installing *source* package ?Rcpp? ...
** package ?Rcpp? successfully unpacked and MD5 sums checked
** libs
g++? -I/usr/share/R/include -DNDEBUG -I../inst/include/? ? -fpic? -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g? -c Date.cpp -o Date.o
g++: error: unrecognized command line option '-fstack-protector-strong'
g++: error: unrecognized command line option '-Wdate-time'
/usr/lib/R/etc/Makeconf:168: recipe for target 'Date.o' failed
make: *** [Date.o] Error 1
ERROR: compilation failed for package ?Rcpp?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/Rcpp?
Warning in install.packages :
? installation of package ?Rcpp? had non-zero exit status
* installing *source* package ?digest? ...
** package ?digest? successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG? ? ? -fpic? -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g? -c aes.c -o aes.o
gcc: error: unrecognized command line option '-fstack-protector-strong'
gcc: error: unrecognized command line option '-Wdate-time'
/usr/lib/R/etc/Makeconf:159: recipe for target 'aes.o' failed
make: *** [aes.o] Error 1
ERROR: compilation failed for package ?digest?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/digest?
Warning in install.packages :
? installation of package ?digest? had non-zero exit status
* installing *source* package ?curl? ...
** package ?curl? successfully unpacked and MD5 sums checked
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGSUsing PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
* deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
* rpm: libcurl-devel (Fedora, CentOS, RHEL)
* csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ?curl?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/curl?
Warning in install.packages :
? installation of package ?curl? had non-zero exit status
* installing *source* package ?openssl? ...
** package ?openssl? successfully unpacked and MD5 sums checked
[[elided Yahoo spam]]
Using PKG_CFLAGSUsing PKG_LIBS=-lssl -lcrypto
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because openssl was not found. Try installing:
* deb: libssl-dev (Debian, Ubuntu, etc)
* rpm: openssl-devel (Fedora, CentOS, RHEL)
* csw: libssl_dev (Solaris)
* brew: openssl at 1.1 (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ?openssl?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/openssl?
Warning in install.packages :
? installation of package ?openssl? had non-zero exit status
* installing *source* package ?stringi? ...
** package ?stringi? successfully unpacked and MD5 sums checked
checking for local ICUDT_DIR... icu55/data
checking for R_HOME... /usr/lib/R
checking for R... /usr/lib/R/bin/R
checking for R >= 3.1.0 for C++11 use... yes
checking for R < 3.4.0 for CXX1X flag use... no
checking for cat... /bin/cat
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... no
configure: error: in `/tmp/Rtmpu3553h/R.INSTALL28ffe0ce527/stringi':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ?stringi?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/stringi?
Warning in install.packages :
? installation of package ?stringi? had non-zero exit status
* installing *source* package ?jsonlite? ...
** package ?jsonlite? successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api? ? -fpic? -g -O2
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g? -c base64.c -o base64.o
gcc: error: unrecognized command line option '-fstack-protector-strong'
gcc: error: unrecognized command line option '-Wdate-time'
/usr/lib/R/etc/Makeconf:159: recipe for target 'base64.o' failed
make: *** [base64.o] Error 1
ERROR: compilation failed for package ?jsonlite?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/jsonlite?
Warning in install.packages :
? installation of package ?jsonlite? had non-zero exit status
ERROR: dependency ?colorspace? is not available for package ?munsell?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/munsell?
Warning in install.packages :
? installation of package ?munsell? had non-zero exit status
ERROR: dependency ?Rcpp? is not available for package ?plyr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/plyr?
Warning in install.packages :
? installation of package ?plyr? had non-zero exit status
ERROR: dependency ?Rcpp? is not available for package ?bindrcpp?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/bindrcpp?
Warning in install.packages :
? installation of package ?bindrcpp? had non-zero exit status
ERROR: dependency ?Rcpp? is not available for package ?tidyselect?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/tidyselect?
Warning in install.packages :
? installation of package ?tidyselect? had non-zero exit status
ERROR: dependencies ?jsonlite?, ?curl?, ?openssl? are not available for
package ?httr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/httr?
Warning in install.packages :
? installation of package ?httr? had non-zero exit status
ERROR: dependency ?stringi? is not available for package ?stringr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/stringr?
Warning in install.packages :
? installation of package ?stringr? had non-zero exit status
ERROR: dependency ?Rcpp? is not available for package ?tibble?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/tibble?
Warning in install.packages :
? installation of package ?tibble? had non-zero exit status
ERROR: dependency ?Rcpp? is not available for package ?xml2?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/xml2?
Warning in install.packages :
? installation of package ?xml2? had non-zero exit status
ERROR: dependencies ?plyr?, ?stringr?, ?Rcpp? are not available for package
?reshape2?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/reshape2?
Warning in install.packages :
? installation of package ?reshape2? had non-zero exit status
ERROR: dependencies ?plyr?, ?munsell?, ?Rcpp? are not available for package
?scales?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/scales?
Warning in install.packages :
? installation of package ?scales? had non-zero exit status
ERROR: dependency ?tibble? is not available for package ?cellranger?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/cellranger?
Warning in install.packages :
? installation of package ?cellranger? had non-zero exit status
ERROR: dependency ?stringr? is not available for package ?selectr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/selectr?
Warning in install.packages :
? installation of package ?selectr? had non-zero exit status
ERROR: dependencies ?bindrcpp?, ?Rcpp?, ?tibble? are not available for
package ?dplyr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/dplyr?
Warning in install.packages :
? installation of package ?dplyr? had non-zero exit status
ERROR: dependency ?tibble? is not available for package ?forcats?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/forcats?
Warning in install.packages :
? installation of package ?forcats? had non-zero exit status
ERROR: dependency ?stringr? is not available for package ?lubridate?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/lubridate?
Warning in install.packages :
? installation of package ?lubridate? had non-zero exit status
ERROR: dependency ?tibble? is not available for package ?purrr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/purrr?
Warning in install.packages :
? installation of package ?purrr? had non-zero exit status
ERROR: dependencies ?Rcpp?, ?tibble? are not available for package ?readr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/readr?
Warning in install.packages :
? installation of package ?readr? had non-zero exit status
ERROR: dependencies ?digest?, ?plyr?, ?reshape2?, ?scales?, ?tibble? are
not available for package ?ggplot2?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/ggplot2?
Warning in install.packages :
? installation of package ?ggplot2? had non-zero exit status
ERROR: dependencies ?Rcpp?, ?readr?, ?tibble?, ?forcats? are not available
for package ?haven?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/haven?
Warning in install.packages :
? installation of package ?haven? had non-zero exit status
ERROR: dependencies ?cellranger?, ?Rcpp?, ?tibble? are not available for
package ?readxl?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/readxl?
Warning in install.packages :
? installation of package ?readxl? had non-zero exit status
ERROR: dependencies ?xml2?, ?httr?, ?selectr? are not available for package
?rvest?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/rvest?
Warning in install.packages :
? installation of package ?rvest? had non-zero exit status
ERROR: dependencies ?dplyr?, ?purrr?, ?Rcpp?, ?stringi?, ?tibble?,
?tidyselect? are not available for package ?tidyr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/tidyr?
Warning in install.packages :
? installation of package ?tidyr? had non-zero exit status
ERROR: dependencies ?plyr?, ?dplyr?, ?tidyr?, ?psych?, ?stringr?,
?reshape2? are not available for package ?broom?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/broom?
Warning in install.packages :
? installation of package ?broom? had non-zero exit status
ERROR: dependencies ?purrr?, ?tibble?, ?broom?, ?dplyr?, ?tidyr? are not
available for package ?modelr?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/modelr?
Warning in install.packages :
? installation of package ?modelr? had non-zero exit status
ERROR: dependencies ?broom?, ?dplyr?, ?forcats?, ?ggplot2?, ?haven?,
?httr?, ?jsonlite?, ?lubridate?, ?modelr?, ?purrr?, ?readr?, ?readxl?,
?stringr?, ?tibble?, ?rvest?, ?tidyr?, ?xml2? are not available for package
?tidyverse?
* removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/tidyverse?
Warning in install.packages :
? installation of package ?tidyverse? had non-zero exit status
The downloaded source packages are in
? ? ?/tmp/RtmplZrBGp/downloaded_packages?
Warning message:
R graphics engine version 12 is not supported by this version of RStudio.
The Plots tab will be disabled until a newer version of RStudio is
installed.> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 17.04
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.7.0
LAPACK: /usr/lib/lapack/liblapack.so.3.7.0
locale:
[1] LC_CTYPE=en_GB.UTF-8? ? ? LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8? ? ? ? LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8? ? LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8? ? ? LC_NAME=C
[9] LC_ADDRESS=C? ? ? ? ? ? ? LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats? ? graphics? grDevices utils? ? datasets? methods
[7] base
loaded via a namespace (and not attached):
[1] compiler_3.4.1 tools_3.4.1
??? [[alternative HTML version deleted]]
______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
Ista Zahn
2017-Aug-17 15:25 UTC
[R] How to install Tidyverse on Ubuntu 17.04? Getting gcc errors for -fstack-protector-strong and -Wdate-time
Note also that this is not the best place to ask questions about installation on Ubuntu -- please post any future Ubuntu-specific questions to the r-sig-debian mailing list. Subscription info at https://stat.ethz.ch/mailman/listinfo/r-sig-debian The tidyverse suite of packages gennerally installs just fine on Ubuntu Zesty. How did you install R? If you didn't follow the instructions at https://cran.r-project.org/bin/linux/ubuntu/ I suggest uninstalling and re-installing as described there. Make sure you install r-base-dev? Ubuntu zesty comes with gcc6, which is fine for compiling R packages. What does "gcc --version" say? You will also need some additional dependencies, including libxml2-dev, libcurl4-openssl-dev, and libssl-dev, according to https://stackoverflow.com/questions/43592316/warning-in-install-packages-installation-of-package-tidyverse-had-non-zero-e#43649793 Best, Ista On Thu, Aug 17, 2017 at 5:26 AM, Jocelyn Ireson-Paine via R-help <r-help at r-project.org> wrote:> I'm running Ubuntu 17.04 and R 3.4.1. I installed the latter yesterday, so > I presume it's the latest version. I want to install Tidyverse, which I've > spent many happy hours with under Windows. But when I do > install.packages("tidyverse") , I get errors about unrecognized command > line options to gcc. These start when the install hits the colorspace and > munsell packages. I'll show an example at the end of this post. > > I've not found anyone else who had exactly that problem on Ubuntu 17.04. > But posts from people with similar problems suggest that my gcc might be a > version that's too old to recognise the options -fstack-protector-strong > and -Wdate-time. > > Possible work-arounds that I've thought of: > > 1) Find an older version of Tidyverse that doesn't need those compiler > options. > > 2) Upgrade my Ubuntu's gcc so that whichever one Tidyverse needs becomes > the default. But I don't know whether that would nuke other software on my > machine that expects an older gcc. And I don't know exactly what software > the installer expects, so I'd have to keep installing different gccs until > I found one that worked. > > (A suggestion: it would be excellent if the installer could detect such > errors, then fetch and install needed software for itself. If it can't do > that, couldn't it at least tell me which version it wants, instead of > making me deduce it from the compiler options it's using?) > > 3) Install a new gcc just for Tidyverse, and somehow play with paths to > fool the installer into calling it. Perhaps by following the advice in > https://askubuntu.com/questions/466651/how-do-i-use-the-latest-gcc-on-ubuntu > . But that sounds risky. > > 4) Change operating systems? I know Tidyverse works on Windows straight out > of the box. Maybe it's not designed to work on Ubuntu. Anyone know? > > Here's an install that failed: > R version 3.4.1 (2017-06-30) -- "Single Candle" > Copyright (C) 2017 The R Foundation for Statistical Computing > Platform: x86_64-pc-linux-gnu (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("tidyverse") > Installing package into ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4? > (as ?lib? is unspecified) > also installing the dependencies ?colorspace?, ?munsell?, ?plyr?, ?psych?, > ?reshape2?, ?bindrcpp?, ?Rcpp?, ?digest?, ?scales?, ?curl?, ?openssl?, > ?cellranger?, ?stringi?, ?selectr?, ?tidyselect?, ?broom?, ?dplyr?, > ?forcats?, ?ggplot2?, ?haven?, ?httr?, ?jsonlite?, ?lubridate?, ?modelr?, > ?purrr?, ?readr?, ?readxl?, ?stringr?, ?tibble?, ?rvest?, ?tidyr?, ?xml2? > > trying URL 'https://cran.rstudio.com/src/contrib/colorspace_1.3-2.tar.gz' > Content type 'application/x-gzip' length 293433 bytes (286 KB) > =================================================> downloaded 286 KB > > trying URL 'https://cran.rstudio.com/src/contrib/munsell_0.4.3.tar.gz' > Content type 'application/x-gzip' length 97244 bytes (94 KB) > =================================================> downloaded 94 KB > > trying URL 'https://cran.rstudio.com/src/contrib/plyr_1.8.4.tar.gz' > Content type 'application/x-gzip' length 392451 bytes (383 KB) > =================================================> downloaded 383 KB > > trying URL 'https://cran.rstudio.com/src/contrib/psych_1.7.5.tar.gz' > Content type 'application/x-gzip' length 3219737 bytes (3.1 MB) > =================================================> downloaded 3.1 MB > > trying URL 'https://cran.rstudio.com/src/contrib/reshape2_1.4.2.tar.gz' > Content type 'application/x-gzip' length 34688 bytes (33 KB) > =================================================> downloaded 33 KB > > trying URL 'https://cran.rstudio.com/src/contrib/bindrcpp_0.2.tar.gz' > Content type 'application/x-gzip' length 8089 bytes > =================================================> downloaded 8089 bytes > > trying URL 'https://cran.rstudio.com/src/contrib/Rcpp_0.12.12.tar.gz' > Content type 'application/x-gzip' length 2421289 bytes (2.3 MB) > =================================================> downloaded 2.3 MB > > trying URL 'https://cran.rstudio.com/src/contrib/digest_0.6.12.tar.gz' > Content type 'application/x-gzip' length 120337 bytes (117 KB) > =================================================> downloaded 117 KB > > trying URL 'https://cran.rstudio.com/src/contrib/scales_0.4.1.tar.gz' > Content type 'application/x-gzip' length 57703 bytes (56 KB) > =================================================> downloaded 56 KB > > trying URL 'https://cran.rstudio.com/src/contrib/curl_2.8.1.tar.gz' > Content type 'application/x-gzip' length 409743 bytes (400 KB) > =================================================> downloaded 400 KB > > trying URL 'https://cran.rstudio.com/src/contrib/openssl_0.9.6.tar.gz' > Content type 'application/x-gzip' length 1239339 bytes (1.2 MB) > =================================================> downloaded 1.2 MB > > trying URL 'https://cran.rstudio.com/src/contrib/cellranger_1.1.0.tar.gz' > Content type 'application/x-gzip' length 63857 bytes (62 KB) > =================================================> downloaded 62 KB > > trying URL 'https://cran.rstudio.com/src/contrib/stringi_1.1.5.tar.gz' > Content type 'application/x-gzip' length 3645872 bytes (3.5 MB) > =================================================> downloaded 3.5 MB > > trying URL 'https://cran.rstudio.com/src/contrib/selectr_0.3-1.tar.gz' > Content type 'application/x-gzip' length 42098 bytes (41 KB) > =================================================> downloaded 41 KB > > trying URL 'https://cran.rstudio.com/src/contrib/tidyselect_0.1.1.tar.gz' > Content type 'application/x-gzip' length 18670 bytes (18 KB) > =================================================> downloaded 18 KB > > trying URL 'https://cran.rstudio.com/src/contrib/broom_0.4.2.tar.gz' > Content type 'application/x-gzip' length 1388242 bytes (1.3 MB) > =================================================> downloaded 1.3 MB > > trying URL 'https://cran.rstudio.com/src/contrib/dplyr_0.7.2.tar.gz' > Content type 'application/x-gzip' length 692952 bytes (676 KB) > =================================================> downloaded 676 KB > > trying URL 'https://cran.rstudio.com/src/contrib/forcats_0.2.0.tar.gz' > Content type 'application/x-gzip' length 95288 bytes (93 KB) > =================================================> downloaded 93 KB > > trying URL 'https://cran.rstudio.com/src/contrib/ggplot2_2.2.1.tar.gz' > Content type 'application/x-gzip' length 2213308 bytes (2.1 MB) > =================================================> downloaded 2.1 MB > > trying URL 'https://cran.rstudio.com/src/contrib/haven_1.1.0.tar.gz' > Content type 'application/x-gzip' length 184056 bytes (179 KB) > =================================================> downloaded 179 KB > > trying URL 'https://cran.rstudio.com/src/contrib/httr_1.3.0.tar.gz' > Content type 'application/x-gzip' length 147567 bytes (144 KB) > =================================================> downloaded 144 KB > > trying URL 'https://cran.rstudio.com/src/contrib/jsonlite_1.5.tar.gz' > Content type 'application/x-gzip' length 1096810 bytes (1.0 MB) > =================================================> downloaded 1.0 MB > > trying URL 'https://cran.rstudio.com/src/contrib/lubridate_1.6.0.tar.gz' > Content type 'application/x-gzip' length 317672 bytes (310 KB) > =================================================> downloaded 310 KB > > trying URL 'https://cran.rstudio.com/src/contrib/modelr_0.1.1.tar.gz' > Content type 'application/x-gzip' length 83629 bytes (81 KB) > =================================================> downloaded 81 KB > > trying URL 'https://cran.rstudio.com/src/contrib/purrr_0.2.3.tar.gz' > Content type 'application/x-gzip' length 126170 bytes (123 KB) > =================================================> downloaded 123 KB > > trying URL 'https://cran.rstudio.com/src/contrib/readr_1.1.1.tar.gz' > Content type 'application/x-gzip' length 233793 bytes (228 KB) > =================================================> downloaded 228 KB > > trying URL 'https://cran.rstudio.com/src/contrib/readxl_1.0.0.tar.gz' > Content type 'application/x-gzip' length 1936302 bytes (1.8 MB) > =================================================> downloaded 1.8 MB > > trying URL 'https://cran.rstudio.com/src/contrib/stringr_1.2.0.tar.gz' > Content type 'application/x-gzip' length 94095 bytes (91 KB) > =================================================> downloaded 91 KB > > trying URL 'https://cran.rstudio.com/src/contrib/tibble_1.3.3.tar.gz' > Content type 'application/x-gzip' length 91511 bytes (89 KB) > =================================================> downloaded 89 KB > > trying URL 'https://cran.rstudio.com/src/contrib/rvest_0.3.2.tar.gz' > Content type 'application/x-gzip' length 1597137 bytes (1.5 MB) > =================================================> downloaded 1.5 MB > > trying URL 'https://cran.rstudio.com/src/contrib/tidyr_0.7.0.tar.gz' > Content type 'application/x-gzip' length 368687 bytes (360 KB) > =================================================> downloaded 360 KB > > trying URL 'https://cran.rstudio.com/src/contrib/xml2_1.1.1.tar.gz' > Content type 'application/x-gzip' length 244643 bytes (238 KB) > =================================================> downloaded 238 KB > > trying URL 'https://cran.rstudio.com/src/contrib/tidyverse_1.1.1.tar.gz' > Content type 'application/x-gzip' length 23452 bytes (22 KB) > =================================================> downloaded 22 KB > > * installing *source* package ?colorspace? ... > ** package ?colorspace? successfully unpacked and MD5 sums checked > ** libs > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -g -c colorspace.c -o colorspace.o > gcc: error: unrecognized command line option '-fstack-protector-strong' > gcc: error: unrecognized command line option '-Wdate-time' > /usr/lib/R/etc/Makeconf:159: recipe for target 'colorspace.o' failed > make: *** [colorspace.o] Error 1 > ERROR: compilation failed for package ?colorspace? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/colorspace? > Warning in install.packages : > installation of package ?colorspace? had non-zero exit status > * installing *source* package ?psych? ... > ** package ?psych? successfully unpacked and MD5 sums checked > ** R > ** data > *** moving datasets to lazyload DB > ** inst > ** preparing package for lazy loading > Error : objects ?rmnorm?, ?sadmvn?, ?dmnorm? are not exported by > 'namespace:mnormt' > ERROR: lazy loading failed for package ?psych? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/psych? > Warning in install.packages : > installation of package ?psych? had non-zero exit status > * installing *source* package ?Rcpp? ... > ** package ?Rcpp? successfully unpacked and MD5 sums checked > ** libs > g++ -I/usr/share/R/include -DNDEBUG -I../inst/include/ -fpic -g -O2 > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -g -c Date.cpp -o Date.o > g++: error: unrecognized command line option '-fstack-protector-strong' > g++: error: unrecognized command line option '-Wdate-time' > /usr/lib/R/etc/Makeconf:168: recipe for target 'Date.o' failed > make: *** [Date.o] Error 1 > ERROR: compilation failed for package ?Rcpp? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/Rcpp? > Warning in install.packages : > installation of package ?Rcpp? had non-zero exit status > * installing *source* package ?digest? ... > ** package ?digest? successfully unpacked and MD5 sums checked > ** libs > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -g -c aes.c -o aes.o > gcc: error: unrecognized command line option '-fstack-protector-strong' > gcc: error: unrecognized command line option '-Wdate-time' > /usr/lib/R/etc/Makeconf:159: recipe for target 'aes.o' failed > make: *** [aes.o] Error 1 > ERROR: compilation failed for package ?digest? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/digest? > Warning in install.packages : > installation of package ?digest? had non-zero exit status > * installing *source* package ?curl? ... > ** package ?curl? successfully unpacked and MD5 sums checked > Package libcurl was not found in the pkg-config search path. > Perhaps you should add the directory containing `libcurl.pc' > to the PKG_CONFIG_PATH environment variable > No package 'libcurl' found > Package libcurl was not found in the pkg-config search path. > Perhaps you should add the directory containing `libcurl.pc' > to the PKG_CONFIG_PATH environment variable > No package 'libcurl' found > Using PKG_CFLAGS> Using PKG_LIBS=-lcurl > ------------------------- ANTICONF ERROR --------------------------- > Configuration failed because libcurl was not found. Try installing: > * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc) > * rpm: libcurl-devel (Fedora, CentOS, RHEL) > * csw: libcurl_dev (Solaris) > If libcurl is already installed, check that 'pkg-config' is in your > PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config > is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: > R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' > -------------------------------------------------------------------- > ERROR: configuration failed for package ?curl? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/curl? > Warning in install.packages : > installation of package ?curl? had non-zero exit status > * installing *source* package ?openssl? ... > ** package ?openssl? successfully unpacked and MD5 sums checked > Found pkg-config cflags and libs! > Using PKG_CFLAGS> Using PKG_LIBS=-lssl -lcrypto > ------------------------- ANTICONF ERROR --------------------------- > Configuration failed because openssl was not found. Try installing: > * deb: libssl-dev (Debian, Ubuntu, etc) > * rpm: openssl-devel (Fedora, CentOS, RHEL) > * csw: libssl_dev (Solaris) > * brew: openssl at 1.1 (Mac OSX) > If openssl is already installed, check that 'pkg-config' is in your > PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config > is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: > R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' > -------------------------------------------------------------------- > ERROR: configuration failed for package ?openssl? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/openssl? > Warning in install.packages : > installation of package ?openssl? had non-zero exit status > * installing *source* package ?stringi? ... > ** package ?stringi? successfully unpacked and MD5 sums checked > checking for local ICUDT_DIR... icu55/data > checking for R_HOME... /usr/lib/R > checking for R... /usr/lib/R/bin/R > checking for R >= 3.1.0 for C++11 use... yes > checking for R < 3.4.0 for CXX1X flag use... no > checking for cat... /bin/cat > checking for gcc... gcc -std=gnu99 > checking whether the C compiler works... no > configure: error: in `/tmp/Rtmpu3553h/R.INSTALL28ffe0ce527/stringi': > configure: error: C compiler cannot create executables > See `config.log' for more details > ERROR: configuration failed for package ?stringi? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/stringi? > Warning in install.packages : > installation of package ?stringi? had non-zero exit status > * installing *source* package ?jsonlite? ... > ** package ?jsonlite? successfully unpacked and MD5 sums checked > ** libs > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 > -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time > -D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o > gcc: error: unrecognized command line option '-fstack-protector-strong' > gcc: error: unrecognized command line option '-Wdate-time' > /usr/lib/R/etc/Makeconf:159: recipe for target 'base64.o' failed > make: *** [base64.o] Error 1 > ERROR: compilation failed for package ?jsonlite? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/jsonlite? > Warning in install.packages : > installation of package ?jsonlite? had non-zero exit status > ERROR: dependency ?colorspace? is not available for package ?munsell? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/munsell? > Warning in install.packages : > installation of package ?munsell? had non-zero exit status > ERROR: dependency ?Rcpp? is not available for package ?plyr? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/plyr? > Warning in install.packages : > installation of package ?plyr? had non-zero exit status > ERROR: dependency ?Rcpp? is not available for package ?bindrcpp? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/bindrcpp? > Warning in install.packages : > installation of package ?bindrcpp? had non-zero exit status > ERROR: dependency ?Rcpp? is not available for package ?tidyselect? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/tidyselect? > Warning in install.packages : > installation of package ?tidyselect? had non-zero exit status > ERROR: dependencies ?jsonlite?, ?curl?, ?openssl? are not available for > package ?httr? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/httr? > Warning in install.packages : > installation of package ?httr? had non-zero exit status > ERROR: dependency ?stringi? is not available for package ?stringr? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/stringr? > Warning in install.packages : > installation of package ?stringr? had non-zero exit status > ERROR: dependency ?Rcpp? is not available for package ?tibble? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/tibble? > Warning in install.packages : > installation of package ?tibble? had non-zero exit status > ERROR: dependency ?Rcpp? is not available for package ?xml2? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/xml2? > Warning in install.packages : > installation of package ?xml2? had non-zero exit status > ERROR: dependencies ?plyr?, ?stringr?, ?Rcpp? are not available for package > ?reshape2? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/reshape2? > Warning in install.packages : > installation of package ?reshape2? had non-zero exit status > ERROR: dependencies ?plyr?, ?munsell?, ?Rcpp? are not available for package > ?scales? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/scales? > Warning in install.packages : > installation of package ?scales? had non-zero exit status > ERROR: dependency ?tibble? is not available for package ?cellranger? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/cellranger? > Warning in install.packages : > installation of package ?cellranger? had non-zero exit status > ERROR: dependency ?stringr? is not available for package ?selectr? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/selectr? > Warning in install.packages : > installation of package ?selectr? had non-zero exit status > ERROR: dependencies ?bindrcpp?, ?Rcpp?, ?tibble? are not available for > package ?dplyr? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/dplyr? > Warning in install.packages : > installation of package ?dplyr? had non-zero exit status > ERROR: dependency ?tibble? is not available for package ?forcats? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/forcats? > Warning in install.packages : > installation of package ?forcats? had non-zero exit status > ERROR: dependency ?stringr? is not available for package ?lubridate? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/lubridate? > Warning in install.packages : > installation of package ?lubridate? had non-zero exit status > ERROR: dependency ?tibble? is not available for package ?purrr? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/purrr? > Warning in install.packages : > installation of package ?purrr? had non-zero exit status > ERROR: dependencies ?Rcpp?, ?tibble? are not available for package ?readr? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/readr? > Warning in install.packages : > installation of package ?readr? had non-zero exit status > ERROR: dependencies ?digest?, ?plyr?, ?reshape2?, ?scales?, ?tibble? are > not available for package ?ggplot2? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/ggplot2? > Warning in install.packages : > installation of package ?ggplot2? had non-zero exit status > ERROR: dependencies ?Rcpp?, ?readr?, ?tibble?, ?forcats? are not available > for package ?haven? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/haven? > Warning in install.packages : > installation of package ?haven? had non-zero exit status > ERROR: dependencies ?cellranger?, ?Rcpp?, ?tibble? are not available for > package ?readxl? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/readxl? > Warning in install.packages : > installation of package ?readxl? had non-zero exit status > ERROR: dependencies ?xml2?, ?httr?, ?selectr? are not available for package > ?rvest? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/rvest? > Warning in install.packages : > installation of package ?rvest? had non-zero exit status > ERROR: dependencies ?dplyr?, ?purrr?, ?Rcpp?, ?stringi?, ?tibble?, > ?tidyselect? are not available for package ?tidyr? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/tidyr? > Warning in install.packages : > installation of package ?tidyr? had non-zero exit status > ERROR: dependencies ?plyr?, ?dplyr?, ?tidyr?, ?psych?, ?stringr?, > ?reshape2? are not available for package ?broom? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/broom? > Warning in install.packages : > installation of package ?broom? had non-zero exit status > ERROR: dependencies ?purrr?, ?tibble?, ?broom?, ?dplyr?, ?tidyr? are not > available for package ?modelr? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/modelr? > Warning in install.packages : > installation of package ?modelr? had non-zero exit status > ERROR: dependencies ?broom?, ?dplyr?, ?forcats?, ?ggplot2?, ?haven?, > ?httr?, ?jsonlite?, ?lubridate?, ?modelr?, ?purrr?, ?readr?, ?readxl?, > ?stringr?, ?tibble?, ?rvest?, ?tidyr?, ?xml2? are not available for package > ?tidyverse? > * removing ?/home/popx/R/x86_64-pc-linux-gnu-library/3.4/tidyverse? > Warning in install.packages : > installation of package ?tidyverse? had non-zero exit status > > The downloaded source packages are in > ?/tmp/RtmplZrBGp/downloaded_packages? > Warning message: > R graphics engine version 12 is not supported by this version of RStudio. > The Plots tab will be disabled until a newer version of RStudio is > installed. >> sessionInfo() > R version 3.4.1 (2017-06-30) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 17.04 > > Matrix products: default > BLAS: /usr/lib/libblas/libblas.so.3.7.0 > LAPACK: /usr/lib/lapack/liblapack.so.3.7.0 > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods > [7] base > > loaded via a namespace (and not attached): > [1] compiler_3.4.1 tools_3.4.1 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
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