Why R packages are removed after updating them? - r

I was trying to update some R packages since RStudio showed they could be updated. After updating, two packages are simply removed. (rgdal and spatstat). The same thing has happened several times recently. What is happening here?
> install.packages(c("data.table", "rgdal", "spatstat"))
Installing packages into ‘C:/Users/Patrick/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
also installing the dependency ‘spatstat.data’
There is a binary version available but the source version is later:
binary source needs_compilation
spatstat.data 1.1-0 1.1-1 FALSE
trying URL 'https://mirror.las.iastate.edu/CRAN/bin/windows/contrib/3.4/data.table_1.10.4-1.zip'
Content type 'application/zip' length 1577319 bytes (1.5 MB)
downloaded 1.5 MB
trying URL 'https://mirror.las.iastate.edu/CRAN/bin/windows/contrib/3.4/rgdal_1.2-13.zip'
Content type 'application/zip' length 30475771 bytes (29.1 MB)
downloaded 29.1 MB
trying URL 'https://mirror.las.iastate.edu/CRAN/bin/windows/contrib/3.4/spatstat_1.53-2.zip'
Content type 'application/zip' length 14521163 bytes (13.8 MB)
downloaded 13.8 MB
package ‘data.table’ successfully unpacked and MD5 sums checked
package ‘rgdal’ successfully unpacked and MD5 sums checked
Warning in install.packages :
cannot remove prior installation of package ‘rgdal’
package ‘spatstat’ successfully unpacked and MD5 sums checked
Warning in install.packages :
cannot remove prior installation of package ‘spatstat’
The downloaded binary packages are in
C:\Users\Patrick\AppData\Local\Temp\RtmpeaKi0Y\downloaded_packages
installing the source package ‘spatstat.data’
trying URL 'https://mirror.las.iastate.edu/CRAN/src/contrib/spatstat.data_1.1-1.tar.gz'
Content type 'application/x-gzip' length 2837063 bytes (2.7 MB)
downloaded 2.7 MB
* installing *source* package 'spatstat.data' ...
** package 'spatstat.data' successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (spatstat.data)
The downloaded source packages are in
‘C:\Users\Patrick\AppData\Local\Temp\RtmpeaKi0Y\downloaded_packages’
> library(rgdal)
Error in library(rgdal) : there is no package called ‘rgdal’
> library(spatstat)
Error in library(spatstat) : there is no package called ‘spatstat’

You can find the directory that contains your installed packages with
.libPaths()
Which should give you something like:
"/Library/Frameworks/R.framework/Versions/3.3/Resources/library"
If you see rgdal or spatstat there I would delete them and then try installing again.

Related

Cannot load in ggplot2 or seemingly anything

So I haven't used R since I finished my masters.
I deleted a bunch of files back then.
Anyway I tried to work on things again but ggplot2 was not loading. I've tried now deleting RStudio and reinstalling fully, deleting win-library completely. Nothing seems to work:
install.packages("ggplot2")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/Ahsan/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
also installing the dependencies ‘cli’, ‘colorspace’, ‘utf8’, ‘farver’, ‘labeling’, ‘lifecycle’, ‘munsell’, ‘R6’, ‘RColorBrewer’, ‘viridisLite’, ‘fansi’, ‘magrittr’, ‘pillar’, ‘pkgconfig’, ‘vctrs’, ‘digest’, ‘glue’, ‘gtable’, ‘isoband’, ‘rlang’, ‘scales’, ‘tibble’, ‘withr’
There are binary versions available but the source versions are later:
binary source needs_compilation
cli 2.0.2 3.4.1 TRUE
colorspace 1.4-1 2.0-3 TRUE
utf8 1.1.4 1.2.2 TRUE
farver 2.0.3 2.1.1 TRUE
labeling 0.3 0.4.2 FALSE
lifecycle 0.2.0 1.0.3 FALSE
R6 2.4.1 2.5.1 FALSE
RColorBrewer 1.1-2 1.1-3 FALSE
viridisLite 0.3.0 0.4.1 FALSE
fansi 0.4.1 1.0.3 TRUE
magrittr 1.5 2.0.3 TRUE
pillar 1.4.3 1.8.1 FALSE
vctrs 0.2.4 0.4.2 TRUE
digest 0.6.25 0.6.29 TRUE
glue 1.4.0 1.6.2 TRUE
gtable 0.3.0 0.3.1 FALSE
isoband 0.2.1 0.2.6 TRUE
rlang 0.4.5 1.0.6 TRUE
scales 1.1.0 1.2.1 FALSE
tibble 3.0.1 3.1.8 TRUE
withr 2.2.0 2.5.0 FALSE
ggplot2 3.3.0 3.3.6 FALSE
Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/cli_2.0.2.zip'
Content type 'application/zip' length 397120 bytes (387 KB)
downloaded 387 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/colorspace_1.4-1.zip'
Content type 'application/zip' length 2549008 bytes (2.4 MB)
downloaded 2.4 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/utf8_1.1.4.zip'
Content type 'application/zip' length 214574 bytes (209 KB)
downloaded 209 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/farver_2.0.3.zip'
Content type 'application/zip' length 1910691 bytes (1.8 MB)
downloaded 1.8 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/munsell_0.5.0.zip'
Content type 'application/zip' length 244203 bytes (238 KB)
downloaded 238 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/fansi_0.4.1.zip'
Content type 'application/zip' length 222782 bytes (217 KB)
downloaded 217 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/magrittr_1.5.zip'
Content type 'application/zip' length 155738 bytes (152 KB)
downloaded 152 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/pkgconfig_2.0.3.zip'
Content type 'application/zip' length 22161 bytes (21 KB)
downloaded 21 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/vctrs_0.2.4.zip'
Content type 'application/zip' length 1018801 bytes (994 KB)
downloaded 994 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/digest_0.6.25.zip'
Content type 'application/zip' length 248623 bytes (242 KB)
downloaded 242 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/glue_1.4.0.zip'
Content type 'application/zip' length 157284 bytes (153 KB)
downloaded 153 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/isoband_0.2.1.zip'
Content type 'application/zip' length 3303519 bytes (3.2 MB)
downloaded 3.2 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/rlang_0.4.5.zip'
Content type 'application/zip' length 1115838 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/tibble_3.0.1.zip'
Content type 'application/zip' length 407904 bytes (398 KB)
downloaded 398 KB
package ‘cli’ successfully unpacked and MD5 sums checked
package ‘colorspace’ successfully unpacked and MD5 sums checked
package ‘utf8’ successfully unpacked and MD5 sums checked
package ‘farver’ successfully unpacked and MD5 sums checked
package ‘munsell’ successfully unpacked and MD5 sums checked
package ‘fansi’ successfully unpacked and MD5 sums checked
package ‘magrittr’ successfully unpacked and MD5 sums checked
package ‘pkgconfig’ successfully unpacked and MD5 sums checked
package ‘vctrs’ successfully unpacked and MD5 sums checked
package ‘digest’ successfully unpacked and MD5 sums checked
package ‘glue’ successfully unpacked and MD5 sums checked
package ‘isoband’ successfully unpacked and MD5 sums checked
package ‘rlang’ successfully unpacked and MD5 sums checked
package ‘tibble’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\Ahsan\AppData\Local\Temp\RtmpURKnmJ\downloaded_packages
installing the source packages ‘labeling’, ‘lifecycle’, ‘R6’, ‘RColorBrewer’, ‘viridisLite’, ‘pillar’, ‘gtable’, ‘scales’, ‘withr’, ‘ggplot2’
trying URL 'https://cran.rstudio.com/src/contrib/labeling_0.4.2.tar.gz'
Content type 'application/x-gzip' length 10156 bytes
downloaded 10156 bytes
trying URL 'https://cran.rstudio.com/src/contrib/lifecycle_1.0.3.tar.gz'
Content type 'application/x-gzip' length 106854 bytes (104 KB)
downloaded 104 KB
trying URL 'https://cran.rstudio.com/src/contrib/R6_2.5.1.tar.gz'
Content type 'application/x-gzip' length 63422 bytes (61 KB)
downloaded 61 KB
trying URL 'https://cran.rstudio.com/src/contrib/RColorBrewer_1.1-3.tar.gz'
Content type 'application/x-gzip' length 11638 bytes (11 KB)
downloaded 11 KB
trying URL 'https://cran.rstudio.com/src/contrib/viridisLite_0.4.1.tar.gz'
Content type 'application/x-gzip' length 1267090 bytes (1.2 MB)
downloaded 1.2 MB
trying URL 'https://cran.rstudio.com/src/contrib/pillar_1.8.1.tar.gz'
Content type 'application/x-gzip' length 479977 bytes (468 KB)
downloaded 468 KB
trying URL 'https://cran.rstudio.com/src/contrib/gtable_0.3.1.tar.gz'
Content type 'application/x-gzip' length 92733 bytes (90 KB)
downloaded 90 KB
trying URL 'https://cran.rstudio.com/src/contrib/scales_1.2.1.tar.gz'
Content type 'application/x-gzip' length 270609 bytes (264 KB)
downloaded 264 KB
trying URL 'https://cran.rstudio.com/src/contrib/withr_2.5.0.tar.gz'
Content type 'application/x-gzip' length 102089 bytes (99 KB)
downloaded 99 KB
trying URL 'https://cran.rstudio.com/src/contrib/ggplot2_3.3.6.tar.gz'
Content type 'application/x-gzip' length 3061989 bytes (2.9 MB)
downloaded 2.9 MB
installing source package 'labeling' ...
** package 'labeling' successfully unpacked and MD5 sums checked
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'labeling'
finding HTML links ... done
extended html
extended.figures html
gnuplot html
heckbert html
labeling-internal html
labeling-package html
matplotlib html
nelder html
rpretty html
sparks html
thayer html
wilkinson html
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
DONE (labeling)
In R CMD INSTALL
installing source package 'lifecycle' ...
** package 'lifecycle' successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace 'rlang' 0.4.5 is being loaded, but >= 1.0.6 is required
ERROR: lazy loading failed for package 'lifecycle'
removing 'C:/Users/Ahsan/Documents/R/win-library/3.5/lifecycle'
In R CMD INSTALL
Warning in install.packages :
installation of package ‘lifecycle’ had non-zero exit status
installing source package 'R6' ...
** package 'R6' successfully unpacked and MD5 sums checked
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'R6'
finding HTML links ... done
R6Class html
as.list.R6 html
is.R6 html
*** copying figures
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
DONE (R6)
In R CMD INSTALL
installing source package 'RColorBrewer' ...
** package 'RColorBrewer' successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RColorBrewer'
finding HTML links ... done
ColorBrewer html
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
DONE (RColorBrewer)
In R CMD INSTALL
installing source package 'viridisLite' ...
** package 'viridisLite' successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'viridisLite'
finding HTML links ... done
viridis html
viridis.map html
*** copying figures
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
DONE (viridisLite)
In R CMD INSTALL
installing source package 'gtable' ...
** package 'gtable' successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'gtable'
finding HTML links ... done
bind html
gtable-package html
gtable html
gtable_add_cols html
gtable_add_grob html
gtable_add_padding html
gtable_add_rows html
gtable_add_space html
gtable_col html
gtable_filter html
Rd warning: C:/Users/Ahsan/AppData/Local/Temp/RtmpSqbjMI/R.INSTALL7ee849be739a/gtable/man/gtable_filter.Rd:12: file link 'regular expression' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/Ahsan/AppData/Local/Temp/RtmpSqbjMI/R.INSTALL7ee849be739a/gtable/man/gtable_filter.Rd:15: file link 'as.character' in package 'base' does not exist and so has been treated as a topic
gtable_height html
gtable_matrix html
gtable_row html
gtable_show_layout html
gtable_spacer html
gtable_trim html
gtable_width html
is.gtable html
print.gtable html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
DONE (gtable)
In R CMD INSTALL
installing source package 'withr' ...
** package 'withr' successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'withr'
finding HTML links ... done
defer html
devices html
Rd warning: C:/Users/Ahsan/AppData/Local/Temp/Rtmpi2NkSE/R.INSTALL75e85eba3949/withr/man/devices.Rd:228: file link 'X11' in package 'grDevices' does not exist and so has been treated as a topic
makevars_user html
set_makevars html
with_ html
with_collate html
with_connection html
with_db_connection html
with_dir html
with_envvar html
with_file html
with_gctorture2 html
with_language html
with_libpaths html
with_locale html
with_makevars html
with_options html
with_package html
Rd warning: C:/Users/Ahsan/AppData/Local/Temp/Rtmpi2NkSE/R.INSTALL75e85eba3949/withr/man/with_package.Rd:68: file link '.libPaths' in package 'base' does not exist and so has been treated as a topic
with_par html
with_path html
with_rng_version html
with_seed html
with_sink html
with_temp_libpaths html
with_tempfile html
with_timezone html
withr html
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
DONE (withr)
In R CMD INSTALL
ERROR: dependency 'lifecycle' is not available for package 'pillar'
removing 'C:/Users/Ahsan/Documents/R/win-library/3.5/pillar'
In R CMD INSTALL
Warning in install.packages :
installation of package ‘pillar’ had non-zero exit status
ERROR: dependency 'lifecycle' is not available for package 'scales'
removing 'C:/Users/Ahsan/Documents/R/win-library/3.5/scales'
In R CMD INSTALL
Warning in install.packages :
installation of package ‘scales’ had non-zero exit status
ERROR: dependency 'scales' is not available for package 'ggplot2'
removing 'C:/Users/Ahsan/Documents/R/win-library/3.5/ggplot2'
In R CMD INSTALL
Warning in install.packages :
installation of package ‘ggplot2’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\Ahsan\AppData\Local\Temp\RtmpURKnmJ\downloaded_packages’

ggplot not installing - tried everything

I'm out of options to install ggplot. I tried installing from Tools, from the console itself, indicating the cran source, indicating the local dir that the ggplot.gz file appears in. None of them works. I tried installing devtools first but same issue with that package too. I still get the error as follows:
install.packages("ggplot2")
Installing package into ‘\\corp.bloomberg.com/ny-dfs/Users/asadeghi8/R/win-library/3.5’
(as ‘lib’ is unspecified)
also installing the dependencies ‘lifecycle’, ‘rlang’, ‘scales’, ‘withr’
There are binary versions available but the source versions are later:
binary source needs_compilation
lifecycle 0.2.0 1.0.1 FALSE
rlang 0.4.5 1.0.2 TRUE
scales 1.1.0 1.2.0 FALSE
withr 2.2.0 2.5.0 FALSE
ggplot2 3.3.0 3.3.6 FALSE
Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/rlang_0.4.5.zip'
Content type 'application/zip' length 1115838 bytes (1.1 MB)
downloaded 1.1 MB
package ‘rlang’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\asadeghi8\AppData\Local\Temp\RtmpY96UwM\downloaded_packages
installing the source packages ‘lifecycle’, ‘scales’, ‘withr’, ‘ggplot2’
trying URL 'https://cran.rstudio.com/src/contrib/lifecycle_1.0.1.tar.gz'
Content type 'application/x-gzip' length 99716 bytes (97 KB)
downloaded 97 KB
trying URL 'https://cran.rstudio.com/src/contrib/scales_1.2.0.tar.gz'
Content type 'application/x-gzip' length 270188 bytes (263 KB)
downloaded 263 KB
trying URL 'https://cran.rstudio.com/src/contrib/withr_2.5.0.tar.gz'
Content type 'application/x-gzip' length 102089 bytes (99 KB)
downloaded 99 KB
trying URL 'https://cran.rstudio.com/src/contrib/ggplot2_3.3.6.tar.gz'
Content type 'application/x-gzip' length 3061989 bytes (2.9 MB)
downloaded 2.9 MB
* installing *source* package 'lifecycle' ...
** package 'lifecycle' successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace 'rlang' 0.4.5 is being loaded, but >= 0.4.10 is required
ERROR: lazy loading failed for package 'lifecycle'
* removing '\\corp.bloomberg.com/ny-dfs/Users/asadeghi8/R/win-library/3.5/lifecycle'
In R CMD INSTALL
Warning in install.packages :
installation of package ‘lifecycle’ had non-zero exit status
* installing *source* package 'withr' ...
** package 'withr' successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'withr'
finding HTML links ... done
defer html
devices html
Rd warning: C:/Users/asadeghi8/AppData/Local/Temp/RtmpIN8vq1/R.INSTALL987c3eca7587/withr/man/devices.Rd:228: file link 'X11' in package 'grDevices' does not exist and so has been treated as a topic
makevars_user html
set_makevars html
with_ html
with_collate html
with_connection html
with_db_connection html
with_dir html
with_envvar html
with_file html
with_gctorture2 html
with_language html
with_libpaths html
with_locale html
with_makevars html
with_options html
with_package html
Rd warning: C:/Users/asadeghi8/AppData/Local/Temp/RtmpIN8vq1/R.INSTALL987c3eca7587/withr/man/with_package.Rd:68: file link '.libPaths' in package 'base' does not exist and so has been treated as a topic
with_par html
with_path html
with_rng_version html
with_seed html
with_sink html
with_temp_libpaths html
with_tempfile html
with_timezone html
withr html
*** copying figures
** building package indices
** installing vignettes
Warning in file(con, "w") :
cannot open file '\\corp.bloomberg.com/ny-dfs/Users/asadeghi8/R/win-library/3.5/withr/doc/index.html': No such file or directory
Error in file(con, "w") : cannot open the connection
ERROR: installing vignettes failed
* removing '\\corp.bloomberg.com/ny-dfs/Users/asadeghi8/R/win-library/3.5/withr'
In R CMD INSTALL
Warning in install.packages :
installation of package ‘withr’ had non-zero exit status
ERROR: dependency 'lifecycle' is not available for package 'scales'
* removing '\\corp.bloomberg.com/ny-dfs/Users/asadeghi8/R/win-library/3.5/scales'
In R CMD INSTALL
Warning in install.packages :
installation of package ‘scales’ had non-zero exit status
ERROR: dependencies 'scales', 'withr' are not available for package 'ggplot2'
* removing '\\corp.bloomberg.com/ny-dfs/Users/asadeghi8/R/win-library/3.5/ggplot2'
In R CMD INSTALL
Warning in install.packages :
installation of package ‘ggplot2’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\asadeghi8\AppData\Local\Temp\RtmpY96UwM\downloaded_packages’
> library("ggplot")
Error in library("ggplot") : there is no package called ‘ggplot’
I tried to update the rlang package but it when I install it again, it's the same version. This is how it's installed:
> install.packages("rlang")
Installing package into ‘\\corp.bloomberg.com/ny-dfs/Users/asadeghi8/R/win-library/3.5’
(as ‘lib’ is unspecified)
There is a binary version available but the source version is later:
binary source needs_compilation
rlang 0.4.5 1.0.2 TRUE
Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/rlang_0.4.5.zip'
Content type 'application/zip' length 1115838 bytes (1.1 MB)
downloaded 1.1 MB
package ‘rlang’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\asadeghi8\AppData\Local\Temp\RtmpwpTtFm\downloaded_packages

cannot authenticate r shinyapps account with rsconnect

Trying to install reconnect and authenticate it with R-shiny. However, it seems unable to find the function file size.
Here is the installation:
> install.packages("rsconnect", type = "source", dependencies = TRUE, repos = "http://cran.rstudio.com/")
Installing package into ‘/Users/~/Library/R/3.1/library’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/rsconnect_0.8.8.tar.gz'
Content type 'application/x-gzip' length 245177 bytes (239 Kb)
opened URL
==================================================
downloaded 239 Kb
* installing *source* package ‘rsconnect’ ...
** package ‘rsconnect’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (rsconnect)
The downloaded source packages are in
/private/VAb/downloaded_packages
Here is the error when I try to register my account.
rsconnect::setAccountInfo(name='me',
+ token='token',
+ secret='pass')
Error in inferCertificateContents(system.file("cert/shinyapps.io.pem", :
could not find function "file.size"

macos: configure: error: C compiler cannot create executables while install R pachage

I was facing this problem while installing R package devtools. My R studio is in Anaconda, and it's the latest version. The code is this:
install.packages("devtools")
And I got response as follows:
also installing the dependency ‘git2r’
trying URL 'https://cran.rstudio.com/src/contrib/git2r_0.21.0.tar.gz'
Content type 'application/x-gzip' length 1155512 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/src/contrib/devtools_1.13.5.tar.gz'
Content type 'application/x-gzip' length 486555 bytes (475 KB)
==================================================
downloaded 475 KB
* installing *source* package ‘git2r’ ...
** package ‘git2r’ successfully unpacked and MD5 sums checked
checking build system type... x86_64-apple-darwin17.6.0
checking host system type... x86_64-apple-darwin17.6.0
checking for gcc... x86_64-apple-darwin13.4.0-clang
checking whether the C compiler works... no
configure: error: in `/private/var/folders/mh/df2k68vs4g3714qyztvg2y980000gn/T/RtmppuLmjL/R.INSTALL8f6b17805a/git2r':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘git2r’
* removing ‘/Users/nora/anaconda3/lib/R/library/git2r’
Warning in install.packages :
installation of package ‘git2r’ had non-zero exit status
ERROR: dependency ‘git2r’ is not available for package ‘devtools’
* removing ‘/Users/nora/anaconda3/lib/R/library/devtools’
Warning in install.packages :
installation of package ‘devtools’ had non-zero exit status
The downloaded source packages are in
‘/private/var/folders/mh/df2k68vs4g3714qyztvg2y980000gn/T/Rtmpyjv9BV/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
To fix this problem, I've tried the following but nothing changed:
check Xcode and command line tools, and make surethe command line tools is the latest version.
update all the anaconda package.
update homebrew
update gcc
restart my laptop.
Now I've installed this package by using this code in terminal:
conda install -c r r-devtools
when I type install.packages("devtools") in my R console, nothing seems wrong and I saw feedback as following:
trying URL 'https://cran.rstudio.com/src/contrib/devtools_1.13.5.tar.gz'
Content type 'application/x-gzip' length 486555 bytes (475 KB)
==================================================
downloaded 475 KB
* installing *source* package ‘devtools’ ...
** package ‘devtools’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (devtools)
The downloaded source packages are in
‘/private/var/folders/mh/df2k68vs4g3714qyztvg2y980000gn/T/Rtmpyjv9BV/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
But I'm not sure whether I still have C compiler problem. If so, I still want to fix that for future's convenience. And still, I don't know why I countered this problem in the first place.

Error when library ggplot2 and survminer

I have the following error when I'm using the ggplot2 and survminer packages.
I really have no idea why the warning appeared.
> install.packages(c("survival", "survminer", "ggplot2"))
Installing packages into ‘C:/Users/xu081/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://mirrors.tongji.edu.cn/CRAN/bin/windows/contrib/3.4/survival_2.42-3.zip'
Content type 'application/zip' length 4584781 bytes (4.4 MB)
downloaded 4.4 MB
trying URL 'https://mirrors.tongji.edu.cn/CRAN/bin/windows/contrib/3.4/survminer_0.4.2.zip'
Content type 'application/zip' length 2849057 bytes (2.7 MB)
downloaded 2.7 MB
trying URL 'https://mirrors.tongji.edu.cn/CRAN/bin/windows/contrib/3.4/ggplot2_2.2.1.zip'
Content type 'application/zip' length 2784778 bytes (2.7 MB)
downloaded 2.7 MB
package ‘survival’ successfully unpacked and MD5 sums checked
Warning in install.packages :
cannot remove prior installation of package ‘survival’
package ‘survminer’ successfully unpacked and MD5 sums checked
package ‘ggplot2’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\xu081\AppData\Local\Temp\RtmpuOtZaF\downloaded_packages
> library(survival)
> library(ggplot2)
Error in UseMethod("conditionCall") :
no applicable method for 'conditionCall' applied to an object of class "character"
> library(survminer)
载入需要的程辑包:ggplot2
Error in UseMethod("conditionCall") :
no applicable method for 'conditionCall' applied to an object of class "character"
> install.packages("devtools")
Installing package into ‘C:/Users/xu081/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
trying URL'https://mirrors.tongji.edu.cn/CRAN/bin/windows/contrib/3.4/devtools_1.13.5.zip'
Content type 'application/zip' length 443954 bytes (433 KB)
downloaded 433 KB
package ‘devtools’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\xu081\AppData\Local\Temp\Rtmpa62LXv\downloaded_packages
> library(devtools)
> devtools::install_github("tidyverse/ggplot2")
Downloading GitHub repo tidyverse/ggplot2#master
from URL https://api.github.com/repos/tidyverse/ggplot2/zipball/master
Installing ggplot2
"C:/PROGRA~1/R/R-34~1.4/bin/x64/R" --no-site-file --no-environ --no-save no-restore --quiet CMD INSTALL \
"C:/Users/xu081/AppData/Local/Temp/Rtmpa62LXv/devtools1dac50bf8ef/tidyverse-ggplot2-4463da6" \
--library="C:/Users/xu081/Documents/R/win-library/3.4" --install-tests
* installing *source* package 'ggplot2' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** preparing package for lazy loading
Error in UseMethod("conditionCall") :
"conditionCall"没有适用于"character"目标对象的方法
* removing 'C:/Users/xu081/Documents/R/win-library/3.4/ggplot2'
* restoring previous 'C:/Users/xu081/Documents/R/win-library/3.4/ggplot2'
In R CMD INSTALL
Error in UseMethod("conditionMessage") :
no applicable method for 'conditionMessage' applied to an object of class
"character"
I really appreciate your answers.

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