"Installation failed: Command failed (1)": Username read incorrectly

[rempsyc]

Hi there,

I'm getting an error message when trying the install instructions. I believe my username is read incorrectly because of French accents.

Downloading GitHub repo Frostarella/DSUR.noof@master
from URL https://api.github.com/repos/Frostarella/DSUR.noof/zipball/master
Installing DSUR.noof
"C:/PROGRA1/R/R-341.2/bin/x64/R" --no-site-file --no-environ --no-save
--no-restore --quiet CMD INSTALL "C:/Users/Xéxx
Xxéxxxxxx/AppData/Local/Temp/Rtmp4292Jy/devtools3a005dfd5c11/Frostarella-DSUR.noof-2c5b53a"
--library="C:/Users/Xéxx Xxéxxxxxx/Documents/R/win-library/3.4" --install-tests

• installing source package 'DSUR.noof' ...
  Warning in file(file, if (append) "a" else "w") :
  cannot open file 'C:/Users/Xixx Xxixxxxxx/Documents/R/win-library/3.4/DSUR.noof/DESCRIPTION': No such file or directory
  Error in file(file, if (append) "a" else "w") :
  cannot open the connection
  ERROR: installing package DESCRIPTION failed for package 'DSUR.noof'
• removing 'C:/Users/Xéxx Xxéxxxxxx/Documents/R/win-library/3.4/DSUR.noof'
  Installation failed: Command failed (1)

Any way to fix this without changing my username?

[Frostarella]

I'm terribly sorry for not getting back to you. Unfortunately I don't see a way to fix this from my side right now.
Have you tried installing the package from source instead of using devtools?

[rempsyc]

I have tried:

> install.packages("DSUR.noof", repos = "https://github.com/Frostarella/DSUR.noof", type="source")
Installing package into ‘C:/Users/Xéxx Xxéxxxxxx/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
  unable to access index for repository https://github.com/Frostarella/DSUR.noof/src/contrib:
  cannot open URL 'https://github.com/Frostarella/DSUR.noof/src/contrib/PACKAGES'
Warning in install.packages :
  package ‘DSUR.noof’ is not available (for R version 3.4.2)

I have also tried downloading the .zip file to my C drive and installing from there:

> install.packages("C:\\DSUR.noof-master.zip", repos = NULL, type="source")
Installing package into ‘C:/Users/Xéxx Xxéxxxxxx/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)

But it gives me no further output and no confirmation that it installed correctly (or incorrectly). If I try to load the library, I get:

> library(DSUR.noof)
Error in library(DSUR.noof) : there is no package called ‘DSUR.noof’

If I try to test one of the command, I get:

> meanOfVariable(c(1,2,3))
Error in meanOfVariable(c(1, 2, 3)) : 
  could not find function "meanOfVariable"

Can you please tell me if I tried to install from source incorrectly? Thanks

[Frostarella]

It looks like you're doing everything right.

I'm running MacOS and R version 3.5.1, so it's hard for me to test; the installation using devtools worked fine for me, can you try updating to R version 3.5.x?
If this also fails, you could try using the githubinstall-package or try downloading the R-file containing the functions (see here) and simply loading that file using the source() command (see here for further explanation) for now.

I'm sorry it's all a little hacky, but I can't make time to find a decent fix for this right now.

[rempsyc]

Thanks for coming back to me. I have tried the githubinstall package:

> githubinstall("DSUR.noof")
Suggestion:
 - Frostarella/DSUR.noof  R package substitute for the package mentioned in 'Discovering Statistics Using R'
Do you want to install the package (Y/n)?  y
Downloading GitHub repo Frostarella/DSUR.noof@master
    ERROR
   cannot change to directory 'C:\Users\X?xx Xx?xxxxxx\AppData\Local\Temp\RtmpCEGuUV\remotes5c029c27180\Frostarella-DSUR.noof-2c5b53a'
Error in run(bin, args = real_cmdargs, stdout_line_callback = real_callback(stdout),  : 
  System command error

From source after downloading the functions:

> setwd("XXX/XXX")
> source("DSUR_functions.r")
Error in source("DSUR_functions.r") : 
  DSUR_functions.r:7:1: unexpected '<'
6: 
7: <
   ^

I then updated to R version 3.5.1, and then tried the original install_github method:

> install_github("Frostarella/DSUR.noof")
Downloading GitHub repo Frostarella/DSUR.noof@master
√  checking for file 'C:\Users\Xéxx Xxéxxxxxx\AppData\Local\Temp\RtmpmWMlh3\remotes3dfc7435d03\Frostarella-DSUR.noof-2c5b53a/DESCRIPTION' ...
-  preparing 'DSUR.noof':
√  checking DESCRIPTION meta-information ... 
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  building 'DSUR.noof_0.1.1.tar.gz'
   
Installing package into ‘C:/Users/Xéxx Xxéxxxxxx/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
* installing *source* package 'DSUR.noof' ...
Warning in file(file, if (append) "a" else "w") :
  cannot open file 'C:/Users/Xixx Xxixxxxxx/Documents/R/win-library/3.5/DSUR.noof/DESCRIPTION': No such file or directory
Error in file(file, if (append) "a" else "w") : 
  cannot open the connection
ERROR: installing package DESCRIPTION failed for package 'DSUR.noof'
* removing 'C:/Users/Xéxx Xxéxxxxxx/Documents/R/win-library/3.5/DSUR.noof'
In R CMD INSTALL
Error in i.p(...) : 
  (converted from warning) installation of package ‘C:/Users/XXXXXX~1/AppData/Local/Temp/RtmpmWMlh3/file3dfc4e51c81/DSUR.noof_0.1.1.tar.gz’ had non-zero exit status

Then from source:

> install.packages("DSUR.noof", repos = "https://github.com/Frostarella/DSUR.noof", type="source")
Installing package into ‘C:/Users/Xéxx Xxéxxxxxx/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
Warning in install.packages :
  unable to access index for repository https://github.com/Frostarella/DSUR.noof/src/contrib:
  cannot open URL 'https://github.com/Frostarella/DSUR.noof/src/contrib/PACKAGES'
Warning in install.packages :
  package ‘DSUR.noof’ is not available (for R version 3.5.1)

Then from local source:

> install.packages("C:\\DSUR.noof-master.zip", repos = NULL, type="source")
Installing package into ‘C:/Users/Xéxx Xxéxxxxxx/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
In R CMD INSTALL
> library(DSUR.noof)
Error in library(DSUR.noof) : there is no package called ‘DSUR.noof’

Then from githubinstall() again:

> githubinstall("DSUR.noof")
Suggestion:
 - Frostarella/DSUR.noof  R package substitute for the package mentioned in 'Discovering Statistics Using R'
Do you want to install the package (Y/n)?  y
Downloading GitHub repo Frostarella/DSUR.noof@master
√  checking for file 'C:\Users\Xéxx Xxéxxxxxx\AppData\Local\Temp\RtmpmWMlh3\remotes3dfc595f24e7\Frostarella-DSUR.noof-2c5b53a/DESCRIPTION' ...
-  preparing 'DSUR.noof':
√  checking DESCRIPTION meta-information ... 
-  checking for LF line-endings in source and make files and shell scripts
-  checking for empty or unneeded directories
-  building 'DSUR.noof_0.1.1.tar.gz'
   
Installing package into ‘C:/Users/Xéxx Xxéxxxxxx/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
* installing *source* package 'DSUR.noof' ...
Warning in file(file, if (append) "a" else "w") :
  cannot open file 'C:/Users/Xixx Xxixxxxxx/Documents/R/win-library/3.5/DSUR.noof/DESCRIPTION': No such file or directory
Error in file(file, if (append) "a" else "w") : 
  cannot open the connection
ERROR: installing package DESCRIPTION failed for package 'DSUR.noof'
* removing 'C:/Users/Xéxx Xxéxxxxxx/Documents/R/win-library/3.5/DSUR.noof'
In R CMD INSTALL
Error in i.p(...) : 
  (converted from warning) installation of package ‘C:/Users/XXXXXX~1/AppData/Local/Temp/RtmpmWMlh3/file3dfc7b6c6d80/DSUR.noof_0.1.1.tar.gz’ had non-zero exit status
In addition: Warning message:
In fread(download_url, sep = "\t", header = FALSE, stringsAsFactors = FALSE,  :
  Found and resolved improper quoting out-of-sample. First healed line 4848: <<Puriney	honfleuR	"Evening, honfleuR" by Seurat>>. If the fields are not quoted (e.g. field separator does not appear within any field), try quote="" to avoid this warning.

And finally, the source() command gave me the same results again.

But it's ok, don't worry about it, I think I can managed without! Thanks for trying though :3

[rempsyc]

Hi Frostarella, just to let you know that I've found a workaround because I encountered this problem with yet another R package! Looking online I found that the workaround is to create a symbolic link (junction) between the real file path name and the wrong file path name that is being used:

1. Open an elevated command prompt
2. Change to the user directory
3. Create a directory junction targeting the real name of the user directory, e.g.,

C:
CD\Users
MKLINK /J Jeremy Jérémy

Then, I was able to install your package. Source: https://superuser.com/a/986487/1034460

[Frostarella]

Thanks for following up on this! Sounds good, I'm glad you found a way to make it work :)