minor doc fixes

README.md

@@ -165,8 +165,8 @@ Contributions are welcome and they come in many different forms, shapes, and
 sizes. These include, but are not limited to:
 
 * Questions beyond the [User
-  Guide](https://mschubert.github.io/clustermq/articles/userguide.html): Please
-  post your questions on the [Github Discussion](https://github.com/mschubert/clustermq/discussions)
+  Guide](https://mschubert.github.io/clustermq/articles/userguide.html): Ask on
+  the [Github Discussions](https://github.com/mschubert/clustermq/discussions)
   board. If you are an advanced user, please also consider answering them.
 * Bug reports: [File an issue](https://github.com/mschubert/clustermq/issues)
   if something does not work as expected. Be sure to
@@ -179,10 +179,9 @@ sizes. These include, but are not limited to:
   in, I'm happy to help you get started.
 
 > [!TIP]
-> For any questions and issues, please check the
-> [User](https://mschubert.github.io/clustermq/articles/userguide.html) and the
-> [FAQ](https://mschubert.github.io/clustermq/articles/faq.html)
-> guides first
+> For any questions or issues, please check the
+> [User Guide](https://mschubert.github.io/clustermq/articles/userguide.html) and the
+> [FAQ](https://mschubert.github.io/clustermq/articles/faq.html) first
 
 Citation
 --------

vignettes/userguide.Rmd

@@ -108,9 +108,9 @@ processing. This will work in most, but not all cases.
 
 To set up a scheduler explicitly, see the following links:
 
-* [LSF](#lsf) - *should work without setup*
-* [SGE](#sge) - *should work without setup*
 * [SLURM](#slurm) - *should work without setup*
+* [LSF](#lsf) - *should work without setup*
+* [SGE](#sge) - *may require configuration*
 * [PBS](#pbs)/[Torque](#torque) - *needs* `options(clustermq.scheduler="PBS"/"Torque")`
 * you can suggest another scheduler by [opening an
   issue](https://github.com/mschubert/clustermq/issues/new)
@@ -308,21 +308,19 @@ time after you restart R.
       and populated with logging information regarding the SSH connection
       (e.g. `"~/cmq_ssh.log"`); helpful for debugging purposes
 * `clustermq.ssh.timeout` - The amount of time to wait (in seconds) for a SSH
-      start-up connection before timing out (default is 5 seconds)
+      start-up connection before timing out (default is `10` seconds)
 * `clustermq.worker.timeout` - The amount of time to wait (in seconds) for
-      master-worker communication before timing out (default is 600 seconds)
-* `clustermq.error.timeout` - The amount of time to wait (in seconds), in case
-      of a worker error, for the remaining workers to finish their computations
-      and shut down cleanly (default is `min(timeout, 30)` seconds)
+      master-worker communication before timing out (default is to wait
+      indefinitely)
 * `clustermq.template` - Path to a [template file](#scheduler-templates) for
       submitting HPC jobs; only necessary if using your own template, otherwise
-      the default template will be used (default depends on
+      the default template will be used (default depends on set or inferred
       `clustermq.scheduler`)
 * `clustermq.data.warning` - The threshold for the size of the common data (in
-      Mb) before `clustermq` throws a warning (default is 1000)
+      Mb) before `clustermq` throws a warning (default is `1000`)
 * `clustermq.defaults` - A named-list of default values for the HPC template;
       this takes precedence over defaults specified in the template file
-      (default is an empty list (i.e. `list()`))
+      (default is an empty list)
 
 ## Debugging workers
 
@@ -546,9 +544,6 @@ CMQ_AUTH={{ auth }} R --no-save --no-restore -e 'clustermq:::worker("{{ master }
 
 In this file, `#SBATCH` defines command-line arguments to the `sbatch` program.
 
-* Queue: ``. Use the queue with name *default*. This
-  will most likely not exist on your system, so choose the right name (or
-  comment out this line with an additional `#`)
 * Partition: `SBATCH --partition default`. Use the queue with name *default*.
   This will most likely not exist on your system, so choose the right name and
   uncomment by removing the additional `#`
@@ -646,8 +641,8 @@ manually connecting to the HPC environment.
 ```{r eval=FALSE}
 options(clustermq.scheduler = "ssh",
 		clustermq.ssh.host = "myhost", # set this up in your local ~/.ssh/config
-        clustermq.ssh.log = "~/ssh_proxy.log", # log file on your HPC
-        clustermq.ssh.timeout = 30, # if changing the default connection timeout
+        clustermq.ssh.log = "~/ssh_proxy.log",     # log file on your HPC
+        clustermq.ssh.timeout = 30,    # if changing the default connection timeout
         clustermq.template = "/path/to/file/below" # if using your own template
 )
 ```