Error in file(con, "w") : cannot open the connection

[xfim]

Hi,

I've just tried DataExplorer and have followed the minimal example:

library(DataExplorer)
GenerateReport(iris)

It seems that the knitr part runs OK, but then it stops at the end with error:

Error in file(con, "w") : cannot open the connection
In addition: Warning message:
In file(con, "w") :  cannot open file 'report.knit.md': Permission denied

I have also tried the diamonds example with the same result.

Any hint on what may happen?

Thank you,

> sessionInfo()
R version 3.2.4 (2016-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Gentoo/Linux

locale:
 [1] LC_CTYPE=ca_AD.UTF8        LC_NUMERIC=C               LC_TIME=ca_AD.UTF8         LC_COLLATE=C               LC_MONETARY=ca_AD.UTF8     LC_MESSAGES=ca_AD.UTF8     LC_PAPER=ca_AD.UTF8
 [8] LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=ca_AD.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] ggplot2_2.1.0      DataExplorer_0.2.4 vimcom_1.2-6       setwidth_1.0-4     colorout_1.0-3

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.3      knitr_1.12.3     magrittr_1.5     munsell_0.4.3    colorspace_1.2-6 stringr_1.0.0    plyr_1.8.3       tools_3.2.4      grid_3.2.4       data.table_1.9.6 gtable_0.2.0     htmltools_0.3.5
[13] yaml_2.1.13      digest_0.6.9     gridExtra_2.2.1  reshape2_1.4.1   formatR_1.3      evaluate_0.8.3   rmarkdown_0.9.5  labeling_0.3     stringi_1.0-1    scales_0.4.0     chron_2.3-47
>

[boxuancui]

According to your error message, I think this is the cause: In file(con, "w") : cannot open file 'report.knit.md': Permission denied.

You are probably in a directory that you do not have write permission. Please check the file/directory permission in your getwd(), e.g.,

1. Run getwd() in R.
2. In your Linux shell, type cd $YOUR_GETWD_DIRECTORY && ls -l.
3. Make sure you have at least -rw-r--r--, or chmod -r 644 $YOUR_GETWD_DIRECTORY.

Alternatively, as suggested in this SO post, you may set the working directory in your R session and do it from somewhere you have write permission.

[boxuancui]

In addition, I see you are running DataExplorer_0.2.4. I fixed a number of bugs in the new version, so it is advised to use the latest version on master branch.

library(devtools)
install_github("boxuancui/DataExplorer")

[xfim]

Thank you for your suggestions, @boxuancui . But I don't think that a pure permission issue is going on here. I'm in fact in my home directory ($HOME), where I have write permissions. In addition, the knitr part works until the end, which means that a directory "report_files" is created (which if it was a permission issue would not work).
Then, if I run it with su permissions it works.
Using the development version doesn't solve it neither.

[boxuancui]

So is there a report.html file generated in your home directory? If so, when you manually open it, does it render in your browser?

[xfim]

When running with su permission, it does appear the report. But when being a regular user, it does not. But let me stress it out again that when being regular user the "report_files" directory is created. So probably it has to do whith the temporal place where the md file is stored or knitted.

[xfim]

Hi again,

Another weird signal: The development version works if I clone the git repository and run load_all("DataExplorer") from the local machine, but it does not work when installing it via library(devtools); install_github("boxuancui/DataExplorer", force = TRUE).

So I am sure quite certain that we can discard anything related to permissions.

[xfim]

OK, I think I have found the error. I've used inotify to check which files are touched in the filesystem when GenerateReport() run. And it turns out that when looking at the package installation directory it does the following:

./rmd_template/report.knit.md CREATE
./rmd_template/report.utf8.md CREATE
./rmd_template/report.knit.md DELETE
./rmd_template/report.utf8.md DELETE

The problem is when the R packages are not in a library writable by the user, which is not uncommon. Then GenerateReport() creates and deletes two files.

I think that the more reasonable solution is to generate the files in the working directory.