RStudio: Problem installing tibble as dependency for Bchron - r

I've been trying to install Bchron for use with my dissertation data, and tibble is apparently one of the dependencies it needs. I'm fairly new to R so don't understand most of this, but I get pretty much the same error whether I try to install Bchron, tidyverse, or just tibble alone. Here's the error text (apologies if it's not conventionally formatted); any help would be appreciated:
Installing tibble [3.1.1] ...
FAILED
Error installing package 'tibble':
==================================
* installing to library ‘/Users/timdennehymac/Dropbox (Personal)/Dissertation/Chronology/Bchron3_TY/renv/staging/1’
* installing *source* package ‘tibble’ ...
** package ‘tibble’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘tibble’
* removing ‘/Users/timdennehymac/Dropbox
(Personal)/Dissertation/Chronology/Bchron3_TY/renv/staging/1/tibble’
Error: install of package 'tibble' failed [error code 1]
In addition: Warning messages:
1: /usr/bin/xcrun --find --show-sdk-path returned exit code 1
2: In system2(R(), args, stdout = TRUE, stderr = TRUE) :
running command ''/Library/Frameworks/R.framework/Resources/bin/R' CMD config CC 2>&1' had status 1
3: In if (eval(cond, envir = environment(dot))) return(eval(expr, envir = environment(dot))) :
the condition has length > 1 and only the first element will be used
4: In if (eval(cond, envir = environment(dot))) return(eval(expr, envir = environment(dot))) :
the condition has length > 1 and only the first element will be used

The tibble package was updated yesterday to version 3.1.1.
There is not yet any binary available for this version, even on the Rstudio CRAN mirror so you will need to compile the package yourself.
Since you appear to be running MacOS, you will need to install the Xcode command line tools in order to be able to build packages.
Open terminal.app and type the following command:
xcode-select --install
Follow the on screen prompts.
Once the command line utilities have been installed. Close R, restart and try again.

Related

Fail to install R kernel for Jupyter in Mac

I use the following lines:
install.packages('devtools')
devtools::install_github('IRkernel/IRkernel')
but get warnings:
installing source package ‘IRkernel’ ...
Warning in as.POSIXlt.POSIXct(x, tz) :
unknown timezone 'default/America/Los_Angeles'
** R
** inst
** tests
** preparing package for lazy loading
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
Warning: running command '/usr/bin/otool -L /Library/Frameworks/R.framework/Versions/3.4/Resources/library/pbdZMQ/libs/pbdZMQ.so' had status 1
Error : .onLoad failed in loadNamespace() for 'pbdZMQ', details:
call: if (org != fn.libzmq.4.dylib) {
error: missing value where TRUE/FALSE needed
ERROR: lazy loading failed for package ‘IRkernel’
removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/IRkernel’
I try to solve this problem by
xcode-select --install
but get
Error: object 'xcode' not found
Late answer, but this just happened to me and I got the
Error: object 'xcode' not found
because I was still running R in Terminal. Make sure you quit R with
quit()
and then run
xcode-select --install
again (using Bash/Terminal, not R from within Terminal).

Unable to Install RMarkdown

I am trying to install Rmarkdown on Rstudio.
install.packages("rmarkdown")
I receive error messages that include:
configure: error: in `/private/var/folders/z6/pjv553zn1bb39ldgph2klbt40000gn/T/RtmplQkOZY/R.INSTALL7213 13a123d/stringi':
configure: error: no acceptable C compiler found in $PATH
See `config.log' for more details
ERROR: configuration failed for package ‘stringi’
(I also receive other error terms such as
Warning in install.packages :
installation of package ‘stringi’ had non-zero exit status
ERROR: dependency ‘stringi’ is not available for package ‘stringr’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/stringr’
There are a few of these that would take up too much space in this question post.)
I have a Mac OS X Lion 10.7.5, and downloaded an xcode on my computer that should have supplied the C compiler, but is not read in rstudio.
Sir try this:
install.packages("stringi", dependencies=TRUE, INSTALL_opts = c('--no-lock'))
install.packages("stringr", dependencies=TRUE, INSTALL_opts = c('--no-lock'))
Then rerun the install.packages("rmarkdown", dependencies=TRUE)

Installing local package on R 3.2.2 failed

Installing an old version of caret on my custom R version was a burden.
I tried using the RStudio installation tool, but failed
I tried the command:
pathToFile <- "C:/Users/Fsociety/Desktop/caret_5.17-7.tar"
install.packages(pathToFile,repos = NULL, type = "source")
I got this error:
Warning: invalid package 'C:/Users/Fsociety/Desktop/caret_5.17-7.tar'
Error: ERROR: no packages specified
Warning in install.packages :
running command '"C:/PROGRA~1/RRO/RRO-32~1.0/R-32~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Fsociety\Documents\R\win-library\3.2" "C:/Users/Fsociety/Desktop/caret_5.17-7.tar"' had status 1
Warning in install.packages :
installation of package ‘C:/Users/Fsociety/Desktop/caret_5.17-7.tar’ had non-zero exit status
Is there any thing wrong with the install.package that I can fix?

gpclibPermit() is FALSE, cannot install gpclib

I have similar problem as this user, How to turn gpclibPermit() to TRUE
Solution was to install gpclib, but I get error
> install.packages("gpclib")
Package which is only available in source form, and may need compilation of C/C++/Fortran:
‘gpclib’
These will not be installed
Then I download gpclib_1.5-5.tar.gz from http://cran.r-project.org/web/packages/gpclib/index.html and extract to library folder, i.e D:\R\R-3.2.0\library.
When I execute the following, I still get the errors:
> install.packages("gpclib")
Package which is only available in source form, and may need compilation of C/C++/Fortran:
‘gpclib’
These will not be installed
> gpclibPermitStatus()
[1] FALSE
Thanks
Update
I tried
> install.packages("D:/R/gpclib_1.5-5.tar.gz", repos = NULL, type = "source")
and got error
* installing *source* package 'gpclib' ...
** package 'gpclib' successfully unpacked and MD5 sums checked
** libs
*** arch - i386
Warning: running command 'make -f "D:/R/R-3.2.0/etc/i386/Makeconf" -f "D:/R/R-3.2.0/share/make/winshlib.mk" SHLIB="gpclib.dll" OBJECTS="Rgpc.o gpc.o"' had status 127
ERROR: compilation failed for package 'gpclib'
* removing 'D:/R/R-3.2.0/library/gpclib'
Warning in install.packages :
running command '"D:/R/R-3.2.0/bin/x64/R" CMD INSTALL -l "D:\R\R-3.2.0\library" "D:/R/gpclib_1.5-5.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘D:/R/gpclib_1.5-5.tar.gz’ had non-zero exit status
"Extract[ing] to library folder" is not the correct way to install a source package (the .tar.gz you downloaded). Inside R execute
install.packages(path_to_file, repos = NULL, type="source")
More details and approaches can be found at How do I install an R package from source?

Build R package on Mac for Windows

I develop a package under Mac and want to distribute it to my colleagues. I can build the package under Mac and can install it under Mac and 'most' of my colleagues Windows PCs. Some of these are Windows 7 and some are Windows 8. All of them use RStudio and different R Versions all above 3.1.
I have now one big Problem with one computer and can not figure out what to do.
When I try to install the package, I get the following message
install.packages("C:/Users/ncasasvi/Downloads/imbproteomicsr_0.1.6.tar.gz", repos = NULL, type = "source", lib="\\fs02/ncasasvi$/Dokumente/R/R-3.1.2/library")
Warning in install.packages :
'lib = "\fs02/ncasasvi$/Dokumente/R/R-3.1.2/library"' is not writable
'\\fs02\ncasasvi$\Dokumente'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
'\\fs02\ncasasvi$\DOKUME~1\R\R-31~1.2' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
running command '"//fs02/ncasasvi$/DOKUME~1/R/R-31~1.2/bin/x64/R" CMD INSTALL -l "\\fs02\ncasasvi$\Dokumente\R\win-library\3.1" "C:/Users/ncasasvi/Downloads/imbproteomicsr_0.1.6.tar.gz"' had status 1
Warning in install.packages :
installation of package 'C:/Users/ncasasvi/Downloads/imbproteomicsr_0.1.6.tar.gz' had non-zero exit status
I copied now the complete package source, so all folders and files, to a Windows machine, installed Rtools and devtools there and build the package on the windows machine with the same problem...
Is there a way to geht a more precise error message, not just status one? I have no further Ideas.
I also sensed my file to win builder. It reported no error messages, but I also didn't got a 'new build package' from the website.
Hope some of you have some suggestions. Thanks in advance!
EDIT:
After changing the path to something without \\ at the beginning and trying to get rid of all the other error messages, I got this message:
> install.packages("C:/Users/ncasasvi/Downloads/imbproteomicsr_latest.tar.gz", repos = NULL, type = "source", lib=('U:/Dokumente/R/win-library/'))
Error: ERROR: no packages specified
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-31~1.2/bin/x64/R" CMD INSTALL -l "U:\Dokumente\R\win-library\" "C:/Users/ncasasvi/Downloads/imbproteomicsr_latest.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘C:/Users/ncasasvi/Downloads/imbproteomicsr_latest.tar.gz’ had non-zero exit status
In between, I had a partly success, but it still could not install the package. This was the output in between:
> install.packages("C:/Users/ncasasvi/Downloads/imbproteomicsr_latest (2).tar.gz", repos = NULL, type = "source")
Installing package into ‘\\fs02/ncasasvi$/Dokumente/R/win-library/3.1’
(as ‘lib’ is unspecified)
'\\fs02\ncasasvi$\Dokumente'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* installing *source* package 'imbproteomicsr' ...
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) :
no library trees found in 'lib.loc'
Error: loading failed
Execution halted
*** arch - x64
Warning in library(pkg_name, lib.loc = lib, character.only = TRUE, logical.return = TRUE) :
no library trees found in 'lib.loc'
Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'
* removing '\\fs02/ncasasvi$/Dokumente/R/win-library/3.1/imbproteomicsr'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-31~1.2/bin/x64/R" CMD INSTALL -l "\\fs02\ncasasvi$\Dokumente\R\win-library\3.1" "C:/Users/ncasasvi/DOWNLO~1/imbproteomicsr_latest (2).tar.gz"' had status 1
Warning in install.packages :
installation of package ‘C:/Users/ncasasvi/DOWNLO~1/imbproteomicsr_latest (2).tar.gz’ had non-zero exit status

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