In my rocker/rstudio-derived docker container, I'm engulfed in a quagmire surrounding the yearly TexLive update and the R package tinytex.
I have gone through a plethora of iterations of tinytex::install_tinytex(), tinytex::uninstall_tinytex(), tinytex::reinstall(), etc.
I have installed the most current version via remotes::install_github("yiuhi/tinytex").
I have experimented with different (up to date) mirrors of CTAN.
When using a up to date mirror and having installed/reinstalled tinytex properly, I keep getting this behavior:
> tinytex::tinytex_root()
[1] "/home/rstudio/.TinyTeX"
> tinytex::pdflatex("<MYFILE>.tex")
tlmgr: package repository http://vesta.informatik.rwth-aachen.de/ftp/pub/mirror/ctan/systems/texlive/tlnet (verified)
[1/1, ??:??/??:??] install: koma-script [13745k]
running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /home/rstudio/.TinyTeX/texmf-var/web2c/tlmgr.log
... 6 more successful package installs ...
tlmgr: package repository http://vesta.informatik.rwth-aachen.de/ftp/pub/mirror/ctan/systems/texlive/tlnet (verified)
[1/1, ??:??/??:??] install: babel-english [3k]
running mktexlsr ...
done running mktexlsr.
tlmgr: package log updated: /home/rstudio/.TinyTeX/texmf-var/web2c/tlmgr.log
! LaTeX Error: This NFSS system isn't set up properly.
! sh: 1: pdflatex: not found
Error: LaTeX failed to compile <MYFILE>.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See <MYFILE>.log for more info.
In addition: Warning messages:
1: In system2(..., stdout = if (use_file_stdout()) f1 else FALSE, stderr = f2) :
error in running command
2: In system2("tlmgr", args, ...) : error in running command
> tinytex::tinytex_root()
[1] ""
After this, ~/.TinyTeX (which was present before) is literally GONE from the file system!?
Can anybody shed light on why 1) tinytex appears to install, 2) it appears to properly process my *.tex file and pulling in the appropriate packages from CTAN and than 3) proceeds in one of those package installations to delete it's entire own installation!?
The observed behavior was a bug in the tinytex R package and has since been resolved (https://github.com/yihui/tinytex/issues/197).
Until the CRAN-available version is >= 0.21.5, one may remedy the behavior by installing directly from the author's repository by:
install.packages("remotes")
remotes::install_github("yihui/tinytex")
Related
I recently had to have a new laptop build at work and therefore reinstalled R and R Studio through a designated 'Company Portal' that did the software installation for me (this might be the problem). When now trying to install and load packages for use, I am running in to the below error for packages (in this case for tidyverse):
Warning message: In options(stringsAsFactors = TRUE) :
'options(stringsAsFactors = TRUE)' is deprecated and will be
disabled Error in setwd("C:/R/WorkingDir") : cannot change working
directory Execution halted Warning in install.packages :
installation of package ‘tidyselect’ had non-zero exit status
I also had this error when I first loaded R up that seems to be reappearing due any attempt to install packages:
Error in setwd("C:/R/WorkingDir") :
cannot change working directory
I've never had this issue before using RStudio across numerous machines and software versions, can anyone advise what is going on? My name (and thus C:\ user file path(s)) does have an apostrophe in it, if that matters - but it has never been an issue before. Is some key installation setting now misaligned and if yes, can anyone advise how to resolve?
I am trying to install an R package along with its dependencies. But it is throwing error.
$ install.packages(rvest_0.3.5.tar.gz, dependencies=True)
-bash: syntax error near unexpected token `rvest_0.3.5.tar.gz,'
I am new to R please help me how can I download this along with it dependencies.
Before this, I tried following
$ R CMD INSTALL rvest_0.3.5.tar.gz
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
ERROR: dependencies ‘httr’, ‘magrittr’, ‘selectr’ are not available for package ‘rvest’
But it failed with dependent packages are missing error. And obviously it is cumbersome to install the dependent packages manually. Hence I tried package.install
You need to run it with quotes and capital TRUE:
install.packages("rvest_0.3.5.tar.gz", dependencies = TRUE)
Note this will only work if you have unix-like system and the file is located in your current working directory (check with running getwd() from your R session). Otherwise you need to provide full path to the file (like "~/somefolder/mydata/rvest_0.3.5.tar.gz").
If you run Windows, then you need .zip file instead of .tar.gz.
If you are connected to internet, just run:
install.packages("rvest")
I am using Anaconda to manage my R-installation. It works great for packages available in the R-channels provided by Anaconda, but I am having troubles installing packages not contained in the Anaconda repos.
I have tried a few different approaches, all listed below together with their error output.
1. install.packages('rafalib')
Suggested to work here conda - How to install R packages that are not available in "R-essentials"?. My .libPaths() points to '/home/user/anaconda2/lib/R/library'.
Out:
--- Please select a CRAN mirror for use in this session ---
Error in download.file(url, destfile = f, quiet = TRUE) :
unsupported URL scheme
Error: .onLoad failed in loadNamespace() for 'tcltk', details:
call: fun(libname, pkgname)
error: Can't find a usable init.tcl in the following directories:
/opt/anaconda1anaconda2anaconda3/lib/tcl8.5 ./lib/tcl8.5 ./lib/tcl8.5 ./library ./library ./tcl8.5.18/library ./tcl8.5.18/library
This probably means that Tcl wasn't installed properly.
I installed tcl from the conda channel r-old, but install.packages() still threw the same error message.
2. options(menu.graphics=FALSE) and then install.packages('rafalib')
I got a list of mirrors and chose one.
Out:
Selection: 15
trying URL 'http://cran.utstat.utoronto.ca/src/contrib/rafalib_1.0.0.tar.gz'
Content type 'application/x-gzip' length 11798 bytes (11 KB)
==================================================
downloaded 11 KB
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
The downloaded source packages are in
‘/tmp/Rtmphwpta0/downloaded_packages’
Warning message:
In install.packages("rafalib") :
installation of package ‘rafalib’ had non-zero exit status
Both 2 and 3 are from Disable/suppress tcltk popup for CRAN mirror selection in R
3. Setting the mirror in ~/.Rprofile
Before trying install.packages(), I added the following to my ~/.Rprofile.
## Default repo
local({r <- getOption("repos");
r["CRAN"] <- "http://cran.us.r-project.org";
options(repos=r)})
Out:
trying URL 'http://cran.us.r-project.org/src/contrib/rafalib_1.0.0.tar.gz'
Content type 'application/x-gzip' length 11798 bytes (11 KB)
==================================================
downloaded 11 KB
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
The downloaded source packages are in
‘/tmp/RtmppIz9rT/downloaded_packages’
Warning message:
In install.packages("rafalib") :
installation of package ‘rafalib’ had non-zero exit status
4. Setting the download method to 'curl' or 'wget'.
While keeping the new ~/.Rprofile configuration. I guess this wasn't necessary since the package seems to be downloading fine now, but I tested it just in case.
Out:
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ‘rafalib’ failed
Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
download had nonzero exit status
5. Manual download of rafalib
install.packages('../Downloads/rafalib_1.0.0.tar.gz', repos=NULL, type='source')
Out:
sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook
Warning message:
In install.packages("../Downloads/rafalib_1.0.0.tar.gz", repos = NULL, :
installation of package ‘../Downloads/rafalib_1.0.0.tar.gz’ had non-zero exit status
6. Building a conda package from rafalib
I opened a separate issue for this Errors building R-packages for conda. In short, it complains about missing dependencies that I already have installed. Update I got a round the dependency problem and I am now stuck at the same rl_signal_event_hook-error as for my other approaches.
7. sudo ln /usr/lib/libncursesw.so.6 /usr/lib/libncursesw.so.5
As per https://github.com/conda/conda/issues/1679, but it didn't fix the issue for me.
So it seems like I can now download the package fine, but installing it fails. I have seen the error message sh: symbol lookup error: sh: undefined symbol: rl_signal_event_hook previously when using R with irkernel in the Jupyter Notebook, but it has never obstructed my work. I have never seen anything relating to that error message when running python through anaconda.
I'm out of ideas. Does anyone know how I can install R-packages not provided by anaconda, such as rafalib or swirl?
I am on Linux (Antergos, an Arch derivative) with kernel 4.4.5-1-ARCH.
UPDATE 2016/04/15
There is some related discussion in this thread. I have tried to get around this error by installing different versions of ncurses, including this patched version, and I have tried to link the readline libraries, as suggested here, but I keep running into the same error. I'm quite lost at this point and any help to solve this would be greatly appreciated.
Detailed post on managing packages that are and are not in Anaconda R: http://ihrke.github.io/conda.html
Essentially is using commands:
conda skeleton cran <package_name>
conda build <package_name>
If the package has dependencies that are also not in Anaconda:
conda skeleton cran <dependency1>
conda skeleton cran <dependency2>
conda build <package_name>
Essentially I would agree with this post in saying that I don't understand how install.packages() works with Anaconda. What I seem to see is that Anaconda creates a R environment where all the packages installed from install.packages() are kept.
Whenever I am working in Jupyter with R, I use this environment and am able to access all the packages that I have installed with install.packages()
In the end, I got around the rl_event_hookproblems by following the approach recommended here and symlinking anaconda's libreadline to the system one:
mv ~/anaconda3/lib/libreadline.s.6.2 ~/anaconda3/lib/libreadline.s.6.2.bak
ln -s /usr/lib/libreadline.so.6.3 ~/anaconda3/lib/libreadline.s.6.2
I am still having troubles installing some dependency heavy R-packages due to failure to load shared objects when using install.packages() from withing R. However, simpler packages work fine and I can get most of the dependency heavy packages from anacondas R-repositories.
I am trying to load RQuantLib but I get the following error:
> require(RQuantLib)
Loading required package: RQuantLib
Error : .onLoad failed in loadNamespace() for 'RQuantLib', details:
call: if (is.character(qc) && nchar(qc) > 1) {
error: missing value where TRUE/FALSE needed
In addition: Warning message:
running command 'bash -c 'type -p quantlib-config' 2>/dev/null' had status 1
I am pretty new to programming in general so I am not sure what this means. I am working in an Mac OS Maverick environment, I downloaded the latest version of RQuantLib (0.3.12) and the "R Package Installer" says it is installed. (I installed RQuantLib from the terminal using "R CMD INSTALL RQuantLib" as using install.packages() from within R did not work - it gave me an error saying QuantLib was not configured, although it was running fine in from the terminal.) I am running R from the R console. QuantLib works fine and so does Rcpp.
I checked the "NAMESPACE" document in the RQuantLib folder and it says:
import(methods)
importFrom(Rcpp, Rcpp.plugin.maker)
useDynLib(RQuantLib)
exportPattern("*.default")
export(
##--arrays.R
"oldEuropeanOptionArrays",
"EuropeanOptionArrays",
"plotOptionSurface",
##--asian.R
"AsianOption",
##--bermudan.R
"BermudanSwaption",
"summary.G2Analytic",
"summary.HWAnalytic",
"summary.HWTree",
"summary.BKTree",
##--bond.R
"ZeroCouponBond",
"ZeroPriceByYield",
"ZeroYield",
"FixedRateBond",
"FixedRateBondYield",
"FixedRateBondPriceByYield",
"FloatingRateBond",
"ConvertibleZeroCouponBond",
"ConvertibleFixedCouponBond",
"ConvertibleFloatingCouponBond",
"CallableBond",
"FittedBondCurve",
##--calendars.R
"isBusinessDay", "businessDay",
"isHoliday",
"isWeekend",
"isEndOfMonth",
"getEndOfMonth", "endOfMonth",
"adjust",
"advance",
"businessDaysBetween",
"getHolidayList", "holidayList",
"setCalendarContext",
##--dayCounter.R
"dayCount",
"yearFraction",
"setEvaluationDate",
##--discount.R
"DiscountCurve",
"plot.DiscountCurve",
##--implied.R
"EuropeanOptionImpliedVolatility",
"AmericanOptionImpliedVolatility",
"BinaryOptionImpliedVolatility",
##--option.R
"EuropeanOption",
"AmericanOption",
"AmericanOption.default",
"BinaryOption",
"BarrierOption"
)
S3method("plot", "Option")
S3method("print", "Option")
S3method("summary", "Option")
S3method("plot", "Bond")
S3method("print", "Bond")
S3method("summary", "Bond")
If I try to specify the path where the Terminal wrote that it installed RQuantLib while requiring it I get the following error:
> require('RQuantLib', lib.loc = "C:/Users/dealmer/Library/R/3.1/library/RQuantLib/libs")
Loading required package: RQuantLib
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
no library trees found in 'lib.loc'
So, do I need to move something from there to where the other R libraries are? (There is already a folder named "RQuantLib" in the folder where the other R library folders are, that's where I found the NAMESPACE doc for example) The path that the Terminal gave me I can't follow in the Finder window however because it doesn't show the "Library" folder and I don't know how to make it do that.)
This is what .libPaths() gives me:
> .libPaths()
[1] "/Users/dealmer/Library/R/3.1/library"
[2] "/Library/Frameworks/R.framework/Versions/3.1/Resources/library"
The R libraries are in [2].
I've tried googling but I can't find anything that seems helpful. Any help will be very appreciated. Thank you
- Dom
I think the issue is that on Linux we have quantlib-config in the $PATH:
edd#max:~$ quantlib-config --help
Usage: quantlib-config [--prefix[=DIR]] [--exec-prefix[=DIR]] [--version] \
[--libs] [--cflags]
edd#max:~$ quantlib-config --version
1.4
edd#max:~$
I don't own an OS X box, so I depend on someone like you help with a better configure setup. It should just work if you copy (or soft-link) quantlib-config into your path (eg /usr/local/bin), or adjust $PATH otherwise to include the directory it is in.
I had the same issue and after some hours of struggle I manage to use something not very rigorous but it works!
It seems that R has some issues evaluating system("bash -c 'type -p quantlib-config'").
After having installed QuantLib, typing the command bash -c 'type -p quantlib-config' in Terminal gives us the path of our quantlib-config which is for me /opt/local/bin/quantlib-config.
So I went back to my source folder for RQuantLib (version 0.4.0) and replaced qc in file R/inline.Rby:
qc <- as.character("/opt/local/bin/quantlib-config")
and rebuilt the package using the terminal command R CMD install RQuantLib/.
As I said, not very sexy but it works.
A restart of R and Rstudio is necessary.
Hope it helps!
I'm trying to install development version of ggbiplotfrom Github. During installation I'm getting the following error message:
library(devtools)
install_github("ggbiplot", "vqv")
Installing github repo(s) ggbiplot/master from vqv
Installing ggbiplot.zip from https://github.com/vqv/ggbiplot/zipball
Installing ggbiplot
* checking for file 'C:\Users\Muhammad Yaseen\AppData\Local\Temp\Rtmpsx4n5u\vqv-ggbiplot-2623d7c/DESCRIPTION' ... OK
* preparing 'ggbiplot':
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a 'data/datalist' file should be added
* building 'ggbiplot_0.5.tar.gz'
cygwin warning:
MS-DOS style path detected: C:/Users/MUHAMM~1/AppData/Local/Temp/Rtmpsx4n5u/ggbiplot_0.5.tar.gz
Preferred POSIX equivalent is: /cygdrive/c/Users/MUHAMM~1/AppData/Local/Temp/Rtmpsx4n5u/ggbiplot_0.5.tar.gz
CYGWIN environment variable option "nodosfilewarning" turns off this warning.
Consult the user's guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
Warning: invalid package 'Yaseen/R/win-library/2.14'
Error: ERROR: cannot cd to directory 'C:/Users/Muhammad'
Error: Command failed (1)
In addition: Warning message:
running command '"C:/PROGRA~1/R/R-214~1.2/bin/i386/R" CMD INSTALL C:\Users\MUHAMM~1\AppData\Local\Temp\Rtmpsx4n5u/ggbiplot_0.5.tar.gz --library=C:/Users/Muhammad Yaseen/R/win-library/2.14' had status 1
Any idea to figure out this problem. Thanks in advance for your help and time.
Edit
After downloading from Github, also tried
install.packages("vqv-ggbiplot-2623d7c.tar.gz", repos=NULL, type="source")
which produced this error message
Installing package(s) into ‘C:/Users/Muhammad Yaseen/R/win-library/2.14’
(as ‘lib’ is unspecified)
Error in untar2(tarfile, files, list, exdir) : unsupported entry type 'g'
Warning messages:
1: running command 'C:/PROGRA~1/R/R-214~1.2/bin/i386/R CMD INSTALL -l "C:/Users/Muhammad Yaseen/R/win-library/2.14" "vqv-ggbiplot-2623d7c.tar.gz"' had status 1
2: In install.packages("vqv-ggbiplot-2623d7c.tar.gz", repos = NULL, :
installation of package ‘vqv-ggbiplot-2623d7c.tar.gz’ had non-zero exit status
It's because your Rlib path has a space in it: C:/Users/Muhammad Yasseen/R/win-library/2.14.
See how in the first error log the warning message was
running command '"C:/PROGRA~1/R/R-214~1.2/bin/i386/R" CMD INSTALL
C:\Users\MUHAMM~1\AppData\Local\Temp\Rtmpsx4n5u/ggbiplot_0.5.tar.gz
--library=C:/Users/Muhammad Yaseen/R/win-library/2.14'
had status 1
In particular, the --library=C:/Users/Muhammad Yaseen/R/win-library/2.14.
This should be --library="C:/Users/Muhammad Yaseen/R/win-library/2.14" to deal with the space.
Using install.packages takes care of the quotes for you - see how your second warning message (when you used install.packages) was
running command 'C:/PROGRA~1/R/R-214~1.2/bin/i386/R CMD INSTALL
-l "C:/Users/Muhammad Yaseen/R/win-library/2.14"
"vqv-ggbiplot-2623d7c.tar.gz"' had status 1
The -l "C:/Users/Muhammad Yasseen/R/win-library/2.14" has quote marks around it, so you don't get the same error.
I had a quick look at the install-github sources, and it constructs the R CMD INSTALL command via:
paste("CMD INSTALL ", built_path, " --library=", .libPaths()[1], sep="")
See how it doesn't surround .libPaths()[1] by double quotes in case of spaces? I'd guess that's your problem.
As to a fix - there seems to be an error using install.packages() on a tar file generated by git (as reported here). So, you can either:
change your R library location to somewhere without spaces
unzip the .tar.gz file (I don't know what software does this on Windows) and install from the extracted directories rather than the .tar.gz.
You can't unzip the .tar.gz because it cleans up that file quicker than you can grab it (I've watched it appear and get deleted again). Correct me if I'm wrong, but I also can't get devtools from github for teh same reason :S