I recently updated R to the latest release: 3.4.0. R is installed on a network location H:/. Now something weird is happening when I try to install a local binary package:
filename <- paste0("R:/path/independeR_", versions, ".zip")
install.packages(filename,
repos = NULL, type = "source",
lib = gsub("\\\\\\\\networkpath/home/[[:alpha:]]*/",
"H:/", .libPaths()[1]))
Both H:/ and R:/ are network locations. In .libPaths() the default location is in the H:/ location, but it shows with the entire network adress. In the call to install.packages I substituted this.
The code above fails, with the following output:
'\\networkpath\home\JDUB~PN6\DOCU~UZL\R\R-34~TN4.0' is not recognized as an internal or external command,
operable program or batch file.
Warning in install.packages :
running command '"//networkpath/home/JDUB~PN6/DOCU~UZL/R/R-34~TN4.0/bin/x64/R" CMD INSTALL -l "H:\Documents\R\R-3.4.0\library" "R:/path/independeR_0.1.8.zip"' had status 1
Warning in install.packages :
installation of package ‘R:/path/independeR_0.1.8.zip’ had non-zero exit status
There is two things that surprise me here. The directorynames are all jumbled up (DOCU~UZL instead of Documents etc), but for some reason Command promt seems fine with that. The more interesting thing is the following:
When I try to put the command "//networkpath/home/JDUB~PN6/DOCU~UZL/R/R-34~TN4.0/bin/x64/R" CMD INSTALL -l "H:\Documents\R\R-3.4.0\library" "R:/path/independeR_0.1.8.zip" directly into Command Prompt, the output is very similar:
C:\Users\jdubbeldam>"//networkpath/home/JDUB~PN6/DOCU~UZL/R/R-34~TN4.0/b
in/x64/R" CMD INSTALL -l "H:\Documents\R\R-3.4.0\library" "R:/path/independeR_0.1.8.zip"
'\\networkpath\home\JDUB~PN6\DOCU~UZL\R\R-34~TN4.0' is not recognized as
an internal or external command,
operable program or batch file.
For some reason CMD seems to cut off the path to the command halfway through. I guess that this is because the command is too long. When I try the same command, but with H:/Documents/R/R-3.4.0/bin/x64/R, the installation goes just fine.
I would like to be able to automatically install this package from a script, so I would like a solution to this problem from within R. Is there a way to get R to use the shorter H:/Documents/R/R-3.4.0/bin/x64/R?
I was having problems with updating packages, while searching I found that there is a reported bug affecting getting the timestamps from files in Windows 10:
https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=17261
Starting in R 3.4.0, file.info sometimes returns for mtime,
atime and ctime for directories. It seems to have something to do
with sharing. This affects functions that use file.mtime like
update.packages.
Reproduce:
Try file.info() with a random directory. If it returns a legitimate
file time, open a windows explorer window and navigate to the
directory, then run the call again and it will return s.
In some cases it returns s even if the directory is not open (or
in the path of an open explorer window), but this is not consistent.
With a comment of Tomas Kalibera:
Thank you for the report, this is a known bug that has been fixed
recently in R-devel
I found that when I closed the file explorer windows the timestamps worked correctly and didn't show up as NA's.
This may be a lead for why your code isn't working.
I managed to make the following work. However, I think it is extremely ugly, and would still like to see if it is possible to do it someway else.
filename <- paste0("R:/path/independeR_", versions, ".zip")
cmd <- file.path(gsub("//networkpath/home/[[:alnum:]]*/", "H:/",
gsub("//networkpath/home/[[:alnum:]]*~[[:alnum:]]*/",
"H:/", R.home())), "bin/x64/R")
libname <- gsub("\\\\\\\\networkpath/home/[[:alpha:]]*/",
"H:/", .libPaths()[1])
call <- paste(paste0('"', cmd, '"'),
"CMD",
"INSTALL",
"-l",
paste0('"', libname, '"'),
"--no-lock",
paste0('"', filename, '"'),
sep = " ")
system(call)
Related
I am running Red Hat Enterprise Linux (RHEL) 8.5 with Linux kernel 4.18 and Gnome 3.32.2. In this system, I've got R 4.1.2 compiled with the tool asdf with shared libraries enabled. On top of that, I installed RStudio 2021.09.01-372 from an RPM from the official RStudio website.
When I start Rstudio, the first line of output after the usual R startup is an error:
Error in tools::startDynamicHelp() : internet routines cannot be loaded
I am unable to figure out what's causing this error, and with it I can't run things like refresh CRAN or update packages. But if I start a pure R session from the terminal (instead of Rstudio) this error does not occur.
Some things I tried:
Install the krb5 and libssh2 packages on my host system: Didn't help.
Starting a "pure" R session (both with and without the --vanilla argument) from the Terminal tab within Rstudio also gives this error. If I try to run update.packages() from this session, it pops up a window to select a CRAN mirror then fails with the following:
Warning: failed to download mirrors file (internet routines cannot be loaded); using local file '/home/[my username]/.asdf/installs/R/4.1.2/lib64/R/doc/CRAN_mirrors.csv'
Warning: unable to access index for repository https://cloud.r-project.org/src/contrib:
internet routines cannot be loaded
Warning message:
In download.file(url, destfile = f, quiet = TRUE) :
unable to load shared object '/home/penyuan/.asdf/installs/R/4.1.2/lib64/R/modules//internet.so':
/lib64/libssh.so.4: undefined symbol: EVP_KDF_ctrl, version OPENSSL_1_1_1b
But like I said, the strange thing is if I start an R session outside of Rstudio, these errors don't happen.
Within RStudio, the only workaround I can find is to run this command upon startup (suggested in this thread):
options(download.file.method="wget")
Once this is done, everything else seems to work, such as package updates.
However, I don't want to manually do this every time I start RStudio. So I tried to put it into ~/.Rprofile including a test print() as follows:
print("This is `~/.Rprofile`")
options(download.file.method="wget")
When I open RStudio, I can see the output from the print() call, but the options() command is not run because the original error shows up again. I still have to manually enter options(download.file.method="wget") every time.
I also tried to fold everything into a .First function in ~/.Rprofile as follows:
.First <- function() {
options(download.file.method="wget")
print("This is the `.First` function in `~/.Rprofile`")
}
Unfortunately, same result as before: print()'s output is seen, but options() is not run.
I also made sure that my ~/.Rprofile includes a trailing newline as discussed here. But this didn't help.
The above are the steps I've tried so far.
Why does this error only occur when running RStudio or a terminal within Rstudio? Why doesn't it happen if I start R from a terminal outside of Rstudio?
Is there a way to solve the problem so that the error doesn't happen in the first place? If it can't be solved, how do I set up my ~/.Rprofile so that options(download.file.method="wget") will be run?
Thank you.
I am using R on my work computer inside of our Network. Naturally, I do not have admin rights and It would be hard to convince my IT Department to make an exception for me installing Rtools on my computer.
My main issue with not having Rtools is, that I cannot use the saveWorkbook command from openxlsx, which would allow me to save data as Excel table objects.
The Error of the command implies that I could use an alternative zip application:
Please make sure Rtools is installed or a zip application is available to R
Would this be possible? Our work Computers have 7-zip for instance.
In line with the comment of #Tung and others I copied a Folder of Rtools from my private Computer to my work Computer. I tried the following to no avail
Rtools.bin="C:\\Rtools\\bin"
sys.path = Sys.getenv("PATH")
if (Sys.which("zip") == "" ) {
system(paste("setx PATH \"", Rtools.bin, ";", sys.path, "\"", sep = ""))
}
I also tried using Sys.setenv("R_ZIPCMD" = "C:/Program Files/7-Zip/7zG.exe") to use 7 zip but then I get an error messan Incorrect Switch postfix: -r1
I am specifally trying to replicate the writeDataTable example from openxlsx
Trying to use the awesome gganimate package in R, but was having trouble getting my animation to run. Reverted to trying to run the base example but couldn't get it to link up with ImageMagick.
Input:
library(gapminder)
b = ggplot(gapminder, aes(gdpPercap, lifeExp, size = pop, color = continent, frame = year))+ geom_point() +scale_x_log10()
gg_animate(b)
And the output:
I cannot find ImageMagick with convert = "convert"
Error in file(file, "rb") : cannot open the connection
In addition: Warning messages:
1: running command 'C:\windows\system32\cmd.exe /c convert --version' had status 4
2: In find_magic() : ImageMagick not installed yet!
3: In im.convert(img.files, output = movie.name, convert = convert, :
Please install ImageMagick first or put its bin path into the system PATH variable
4: In normalizePath(path.expand(path), winslash, mustWork) :
path[1]="filed42411bd2b88.gif": The system cannot find the file specified
From the research I have done it seems that the issue has something to do with declaring convert.exe and the windows path, I'm just not sure what to fix to get this code to work.
I have installed ImageMagick-7.0.2-Q16 for Windows (I am running Windows 7).
What am I missing?
You don't need to declare convert.exe; Windows has a native cli tool with the same name to convert a FAT partition into an NTFS partition, not what you want.
(NB: I forget to which directory IM installs itself in windows, so please verify the path I provide before blindly using this code.)
If this is a one-time thing, you can make it available with something like:
Sys.setenv(PATH = paste("c:/Program Files/ImageMagick/bin",
Sys.getenv("PATH"), sep = ";"))
If you want a more permanent solution, you have two options:
Save the above code in a .Rprofile file, either in your home directory (affects all of your future R sessions) or in the directory of your R project needing this tool. (You either need to also run this code on the console or restart the R session for the change to be noticed in your code.)
Add it to the windows path. There are lots of places to find help with this, including https://stackoverflow.com/a/28545224/3358272.
Edit: it came to my attention that the windows install no longer provides the convenience applications (e.g., convert.exe, mogrify.exe) that the unixy install does. (I'm using IM on windows installed via msys2, so I guess it's preferring the unixy-method ... I should have known.) So that suggests a third option:
Since gapminder is using gganimate which is calling animation::im.convert, its source says you can specify the command executable via something like ani.options(convert = shQuote('c:/program files/imagemagick/magick.exe')).
I am downloading data from data.gov website and I get following two types of errors in the process:
fileUrl <- "http://catalog.data.gov/dataset/expenditures-on-children-by-families"
download.file(fileUrl,destfile=".data/studentdata.csv",method="curl")
Warning message:
In download.file(fileUrl, destfile = ".data/studentdata.csv", method = "curl") :
download had nonzero exit status
I tried to remove the method="curl" as suggested in other forum, but again I get this new error
download.file(fileUrl,destfile=".data/studentdata.csv")
Error in download.file(fileUrl, destfile = ".data/studentdata.csv") :
cannot open destfile '.data/studentdata.csv', reason 'No such file or directory'
I think there are two major factors why your curl doesn't work well.
First, the problem is on your URL. fileUrl <- "http://catalog.data.gov/dataset/expenditures-on-children-by-families". In your URL, it is not referred to a csv file. So, they won't work even if you set the destination into a csv file such as destfile = ".data/studentdata.csv"
I have an example of getting a csv dataset using the same code (different dataset):
DataURL<- "https://data.baltimorecity.gov/api/views/dz54-2aru/rows.csv?accessType=DOWNLOAD" (This link refers to a rows.csv file)
download.file(DataURL, destfile="./data/rows.csv", method="curl") (The method is quite same, using curl)
Second, previously I had the same problem that the curl does not work, even I used a proper URL that refers to a csv file. However, when I diagnosed a bit deeper, I found something interesting fact about why my curl method cannot work properly. It was my R session program. I used a 32-bit R, in which the error occurs. Later then, I tried to change the session into a 64-bit R. Amazingly, and the download status was running at that time. To see your R session architecture (whether you are using 32-bit or 64-bit), type in your R:
sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-w64-ming32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
You have to switch your R, from 32-bit to 64-bit to avoid 'curl' call had nonzero exit status. You go to your R directory folder, and then you run a 64-bit R.
If you are using a Windows OS and installing the R in a default path folder, you can run this C:\Program Files\R\R-3.5.3\bin\x64\R.exe. (I used a version of 3.5.3, so it may be different with your version)
If you are using R-studio, you can switch the R session on the menubar Tools -> Global Options -> R version -> Change -> Use your machine's default version of R64 (64-bit) -> OK. Then restart your R-studio.
However, it depends on your OS architecture. If you are using a 32-bit OS, hence you have to find another way to solve this.
So looking at the code for download.file(...), if you specify method="curl" the function tries to use the curl shell command. If this command does not exist on your system, you will get the error above.
If you do not specify a method, the default is to use an internal R method to download, which evidently works on your system. In that case, the function is trying to put the file in .data/studentdata.csv but evidently there is not .data directory. Try taking out the ..
When this download works, you will get a text/html file, not a csv file. Your url points to a web page, not a download link. That page does have a download link, but unfortunately it is a pdf, not a csv.
Finally, if your goal is to have the data in R (is it?), and if the link actually produces a csv file, you could more easily use
df <- read.csv(fileUrl)
If I'm not very much mistaken you just have a simple typo here. I suspect you have a "data" directory, not a ".data" directory - in which case your only problem is that your destfile string needs to begin "./data", not ".data".
I was having the same problem.
Then I realized that I forget to create the "data" directory!
So try adding this above your fileURL line to create the directory first.
if(!file.exists("data")){
dir.create("data")
}
Also, if you are running a Mac, then you want to keep method="curl" when downloading a https file. I don't believe Windows has that problem hence the suggestions to remove it.
Try this:
file<-'http://catalog.data.gov/dataset/expenditures-on-children-by-families'
file<- read.csv(file)
I wanted to run this example script: http://mazamascience.com/WorkingWithData/?p=912 from Windows command line. So I opened the command line and typed Rscript tryCatch.R 1. However, I keep getting the error message Error: R not found. I did set the PATH environment variable as C:\Programme\R\R-3.0.1\bin. If I just type R.exe, it does start R, but it cannot find the packages that are to be loaded at start (e.g. package 'utils' in options<"defaultPackages"> was not found). I guess I have to set another path to the libraries somewhere, but I haven't got any idea where to do this.
UPDATE: After explicitly typing PATH C:\Programme\R\R-3.0.1\bin (rather than just adding this to the value of the environment variable PATH) it seems that R is found. However, a new problem occurs: In normalizePath<path.expand(path), winslash, mustWork>: path[2] = "C:/Programme/R/R-3.0.1/library": Access denied, the same than for the methods library. Then: Calls: .First ... library -> .getRequiredPackages2 -> library -> normalizePath Execution stopped. I'm using Windows 7 and I do have administrator rights.
Rscript is very handy (R CMD BATCH is the old way to ) specially under windows, But generally under I create a batch file to avoid all path's headache.
For example say launcher.bat:
#echo off
C:
PATH C:\Programme\R\R-3.0.1\bin;%path%
cd PATH_TO_YOUR_RSCRIPT
Rscript tryCatch.R 1
pause
And open a console(using cmd) , go where you have stored your launcher.bat and launch it. Or from the R cosnole using shell:
shell('path_to_launcher\launcher.bat')
I've found out that it was a language-specific problem on Windows 7, similar to what is described here: https://stat.ethz.ch/pipermail/r-help/2011-May/276932.html
After changing PATH to C:\Program Files\R\R-3.0.1\bin the script is properly executed from the command prompt.
Thanks to everyone who tried to help!
I ran into this problem under windows 7, apparently, when setting environment variables>user variables the path is not added into the PATH, so the user must add this path in system variables > PATH
at the end just add the path to your .EXE files and voila.