Can not write csv file in rocker

[freshnemo]

Hi, when I install the rocker/tidyverse by the following commend "sudo docker run -d --name kanglin_rstudio -v /internal/khsieh/:/internal/khsieh -e ROOT=TRUE -e PASSWORD=kanglin -p 7776:8787 rocker/tidyverse"

I can read the file but can not write a file, I got following alarms

"Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file '/internal/kangrstudio/all_dataset/CCLE/CCLE_RNAseq_genes_counts_20180929.gct.gz': No such file or directory"

Error in file(file, ifelse(append, "a", "w")) : cannot open the connection In addition: Warning message: In file(file, ifelse(append, "a", "w")) : cannot open file 'try.csv': Permission denied

How can I solve this issue?

[cboettig]

When mapping volumes you will need to be sure user ID numbers match between host and container, see https://www.rocker-project.org/use/managing_users/.

[freshnemo]

so the user id should b the same with host and container?

[eddelbuettel]

Yes, ideally. Which makes it host dependent. On Ubuntu I have an alias (among several) setting 1000:1000 which is what I am on this machine. One can generalise it to user-lookup via id(1) etc but I didn't need this here:

alias dkrr='docker run --rm -ti -u1000:1000 -v$(pwd):/work -w /work'
alias dkrrr='docker run --rm -ti -v$(pwd):/work -w /work'
alias dkrrx='docker run --rm -it -u1000:1000 -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix'

[freshnemo]

This is the current error I have Commend sudo docker run -d --name kanglin_rstudio -v /internal/khsieh/:/internal/khsieh --user khsieh -e PASSWORD=kanglin -p 7776:8787 rocker/tidyverse bash Response 50534921e0857f6b00835474e193f18612aaf79e9151e4858eeb66cb05dd7cc8 docker: Error response from daemon: unable to find user khsieh: no matching entries in passwd file.

[eddelbuettel]

Simplify it:

edd@rob:~$ ls -l demo.csv                                                            # no file yet
ls: cannot access 'demo.csv': No such file or directory
edd@rob:~$ dkrr r-base Rscript -e 'write.csv(mtcars, file="demo.csv")'               # using alias from above
edd@rob:~$ ls -l demo.csv    
-rw-r--r-- 1 edd edd 1783 Jan 14 11:56 demo.csv
edd@rob:~$ head demo.csv 
"","mpg","cyl","disp","hp","drat","wt","qsec","vs","am","gear","carb"
"Mazda RX4",21,6,160,110,3.9,2.62,16.46,0,1,4,4
"Mazda RX4 Wag",21,6,160,110,3.9,2.875,17.02,0,1,4,4
"Datsun 710",22.8,4,108,93,3.85,2.32,18.61,1,1,4,1
"Hornet 4 Drive",21.4,6,258,110,3.08,3.215,19.44,1,0,3,1
"Hornet Sportabout",18.7,8,360,175,3.15,3.44,17.02,0,0,3,2
"Valiant",18.1,6,225,105,2.76,3.46,20.22,1,0,3,1
"Duster 360",14.3,8,360,245,3.21,3.57,15.84,0,0,3,4
"Merc 240D",24.4,4,146.7,62,3.69,3.19,20,1,0,4,2
"Merc 230",22.8,4,140.8,95,3.92,3.15,22.9,1,0,4,2
edd@rob:~$ 

Minimally working proof that yes, I can write a file in a container 'as me' so that I use later, as well as the inverse. You are setting yourself up for a more complicated situatoin and it is that situation ("where do I validate my password against?") where you fail. Carl pointed you to our general documentation for managing IDs which is still your best bet. Good luck!