Publish of rmarkdown documents fails (or document cannot be loaded)

[fereshtehRS]

RStudio IDE 0.99.1189
rmarkdown 0.9.6.9 (from github)

Publish to radixu server or beta server; 2 different behaviours:

1- Static rmarkdown document:
Deployment fails with this error:

2016/05/23 18:29:31.080224611 Error in tools::file_path_as_absolute(output_file) :
2016/05/23 18:29:31.080231689   file '/opt/rstudio-connect/mnt/report/test-rmarkdown-github.html' does not exist
2016/05/23 18:29:31.080241673 Calls: local ... eval -> eval -> do.call -> <Anonymous> -> <Anonymous>
2016/05/23 18:29:31.080305316 In addition: Warning message:
2016/05/23 18:29:31.080456029 In file.rename(pandoc_output_tmp, output) :
2016/05/23 18:29:31.080476812   cannot rename file '/opt/rstudio-connect/mnt/app/pandoc7dcb665f7558.html' to '/opt/rstudio-connect/mnt/report/test-rmarkdown-github.html', reason 'Invalid cross-device link'
2016/05/23 18:29:31.084151982 Execution halted
Document deployment failed with error: exit status 1

2- Shiny Rmarkdown
Deployment is successful, but then loading the document gives this error:

05/23 18:31:46.896Warning in file.rename(pandoc_output_tmp, output) :
05/23 18:31:46.896 cannot rename file '/opt/rstudio-connect/mnt/app/pandoc7ef16193a75e.html' to '/tmp/RtmphOLdFC/file7ef167446add.html', reason 'Invalid cross-device link'
05/23 18:31:46.896Warning in file(con, "r") :
05/23 18:31:46.896 cannot open file '/tmp/RtmphOLdFC/file7ef167446add.html': No such file or directory
05/23 18:31:46.907Warning: Error in file: cannot open the connection
05/23 18:31:46.941Stack trace (innermost first):

[jjallaire]

This is due to the file.rename introduced in this change: df18647

@kevinushey file.rename doesn't work across volumes and in the case of Connect the output_file is on another volume. Could you revise this to use file.copy when the files aren't in the same exact directory? (it's not enough to check if they are apparently on the same volume as Linux could have volumes mounted anywhere on the filesystem).

@aronatkins

[kevinushey]

Thanks for catching that; I'll make that change.

[kevinushey]

This should hopefully resolve the issue: 0d7143f

We attempt a plain file.rename first; if that fails we fall back to a file.copy. (This does assume that file.rename reports FALSE when the rename fails; which is hopefully the case here)

[kevinushey]

I added a bit more cleanup on master (making sure we remove the temporary file on exit).

@fereshtehRS, can you give current master of rmarkdown a shot and let me know if the issue is resolved?

[aronatkins]

Initial testing from here looks good; I'll let Fereshteh confirm with the original test case.

[fereshtehRS]

Different error now (for static document):

2016/05/23 20:46:00.286687252 Error in convert(output_file, run_citeproc) :
2016/05/23 20:46:00.286703134   failed to copy rendered pandoc artefact to '/opt/rstudio-connect/mnt/report/testing-5-23.html'
2016/05/23 20:46:00.286715274 Calls: local ... eval -> eval -> eval -> do.call -> <Anonymous> -> convert
2016/05/23 20:46:00.298722461 Execution halted
Document deployment failed with error: exit status 1

[fereshtehRS]

@aronatkins Were you testing this locally or on dogfood?

[fereshtehRS]

Case 2 (shiny rmarkdown) is working fine now.

[fereshtehRS]

No more issues with the latest fixes from @kevinushey

[aronatkins]

@kevinushey Any issue with us marking this closed? Was there more work planned? Someone else just hit this and they were unclear about status since the bug was still open.

[kevinushey]

I think this can be closed -- any issues should be resolved as long as users are using the latest version of rmarkdown from GitHub. (sorry for the temporary breakage!)

[github-actions]

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