Merge branch 'release/0.16.1'

Author: HenrikBengtsson

.github/workflows/shellcheck.yml

@@ -23,9 +23,9 @@ jobs:
       run: |
         sudo apt-get install -y shellcheck
         shellcheck --version
-        curl -L -O https://github.com/koalaman/shellcheck/releases/download/v0.9.0/shellcheck-v0.9.0.linux.x86_64.tar.xz
-        tar Jxf shellcheck-v0.9.0.linux.x86_64.tar.xz
-        mv shellcheck-v0.9.0/shellcheck bin
+        curl -L -O https://github.com/koalaman/shellcheck/releases/download/v0.10.0/shellcheck-v0.10.0.linux.x86_64.tar.xz
+        tar Jxf shellcheck-v0.10.0.linux.x86_64.tar.xz
+        mv shellcheck-v0.10.0/shellcheck bin
         PATH="bin:$PATH" shellcheck --version
 
     - name: ShellCheck

NEWS.md

@@ -1,3 +1,26 @@
+## Version 0.16.1 [2024-08-20]
+
+### Miscellaneous
+
+ * Now the error message that `rsc stop` produces when it failed to
+   stop an RStudio Server instance running on another machine, will
+   report on both the machine where it thinks RStudio is running and
+   the current machine.
+ 
+ * Now `rsc` assert that all files it creates are non-empty. This
+   helps troubleshooting obscure errors, e.g. when user runs out of
+   disk space.
+
+### Bug Fixes
+
+ * `rsc start --debug` could give an `operand expected (error token is
+   "<pid>")` error on some systems.
+
+### Deprecated and defunct
+
+ * `--port=random` and `--port=uid` are defunct.
+
+
 ## Version 0.16.0 [2024-02-01]
 
 ### New Features

README.md

@@ -333,20 +333,20 @@ As before, the RStudio Server is available at
 
 ```sh
 $ cd /path/to/software
-$ curl -L -O https://github.com/UCSF-CBI/rstudio-server-controller/archive/refs/tags/0.16.0.tar.gz
-$ tar xf 0.16.0.tar.gz
-$ PATH=/path/to/softwarerstudio-server-controller-0.16.0/bin:$PATH
+$ curl -L -O https://github.com/UCSF-CBI/rstudio-server-controller/archive/refs/tags/0.16.1.tar.gz
+$ tar xf 0.16.1.tar.gz
+$ PATH=/path/to/softwarerstudio-server-controller-0.16.1/bin:$PATH
 $ export PATH
 $ rsc --version
-0.16.0
+0.16.1
 ```
 
 To verify that the tool can find R and the RStudio Server executables,
 call:
 
 ```sh
 $ rsc --version --full
-rsc: 0.16.0
+rsc: 0.16.1
 RStudio Server: 2023.06.2+561 (Mountain Hydrangea) for Linux [/path/to/rstudio-server/bin/rstudio-server]
 R: 4.3.1 (2023-06-16) -- "Shortstop Beagle" [/path/to/R/bin/R]
 ```

bin/incl/asserts.sh

@@ -8,6 +8,14 @@ function assert_file_exists {
     [[ -f "$1" ]] || error "No such file: '$1' (working directory '${PWD}')"
 }
 
+## Usage: assert_file_is_not_empty /path/to/file
+function assert_file_is_not_empty {
+    [[ $# -ne 1 ]] && error "${FUNCNAME[0]}() requires a single argument: $#"
+    [[ -n "$1" ]] || error "File name must be non-empty: '$1'"
+    [[ -f "$1" ]] || error "No such file: '$1' (working directory '${PWD}')"
+    [[ -s "$1" ]] || error "The file is empty: '$1' (working directory '${PWD}')"
+}
+
 function assert_link_exists {
     [[ $# -ne 1 ]] && error "${FUNCNAME[0]}() requires a single argument: $#"
     [[ -n "$1" ]] || error "File name must be non-empty: '$1'"

bin/incl/conditions.sh

@@ -123,5 +123,5 @@ function relay_condition {
 
 
 function prune_debug {
-    printf "%s\n" "$@" | sed '/DEBUG:/d' | sed -E 's/\x1b(\[[0-9;]*m|\(B)//g'
+    printf "%s\n" "$@" | sed '/DEBUG:/d' | sed 's/\x1b\[[0-9;]*m\x0f//g' | sed -E 's/\x1b(\[[0-9;]*m|\(B)//g'
 }

bin/rsc

@@ -63,7 +63,7 @@
 ###  rsc config --full
 ###  rsc log
 ###
-### Version: 0.16.0
+### Version: 0.16.1
 ### Copyright: Henrik Bengtsson (2022-2024) and Harry Putnam (2022)
 ### License: ISC
 
@@ -284,6 +284,7 @@ function acquire_lock_file {
         error "${msg}"
     fi
     echo "${PPID}" > "${lockfile}"
+    assert_file_is_not_empty "${lockfile}"
 }
 
 function remove_lock_file {
@@ -388,7 +389,7 @@ function remove_stray_pid_file {
     warn_if_check_pid_needs_ssh "${rserver_hostname}"
     mapfile -t res < <(check_pid "${pid}" "${rserver_hostname}" 2>&1)
     okay=$?
-    mdebug " - checkpid('${pid}', '${rserver_hostname}') exit code: ${okay}"
+    mdebug " - check_pid('${pid}', '${rserver_hostname}') exit code: ${okay}, output='$(printf "%q" "${res[*]}")'"
     relay_condition "${res[@]}"
     mapfile -t res < <(prune_debug "${res[@]}")
 
@@ -413,6 +414,7 @@ function make_database_conf {
         ## Default: /var/lib/rstudio-server
         echo "directory=${workdir}/lib"
     } > "${workdir}/database.conf"
+    assert_file_is_not_empty "${workdir}/database.conf"
 }
 
 function make_rserver_conf {
@@ -481,6 +483,7 @@ function make_rserver_conf {
         ## The web port for the RStudio Server
         echo "www-port=${port:?}"
     } > "${workdir}/rserver.conf"
+    assert_file_is_not_empty "${workdir}/rserver.conf"
 
     mdebug "make_rserver_conf() ... done"
 }
@@ -683,8 +686,9 @@ function rs_process_status {
 	warn_if_check_pid_needs_ssh "${hostname}"
         mapfile -t res < <(check_pid "${pid}" "${rserver_hostname}" 2>&1)
         okay=$?
-        mdebug " - checkpid('${pid}', '${rserver_hostname}') exit code: ${okay}"
+        mdebug " - check_pid('${pid}', '${rserver_hostname}') exit code: ${okay}, output='$(printf "%q" "${res[*]}")'"
         mapfile -t res < <(prune_debug "${res[@]}")
+        mdebug " - prune_debug(): '$(printf "%q" "${res[*]}")'"
         if [[ -n "${res[0]}" ]]; then
             pid="${res[0]}"
         else
@@ -757,6 +761,7 @@ function make_rsession_envs {
     mv "${outfile}.tmp.tmp" "${outfile}"
     rm -f "${outfile}.tmp"
     mdebug "Created: ${outfile} [$(wc -l "${outfile}" | cut -d ' ' -f 1) variables: $(sed -E 's/(^declare -x |=.*$)//g' "${outfile}" | tr $'\n' ' ' | sed -E 's/ $//' | sed 's/ /, /g')]"
+    assert_file_is_not_empty "${outfile}"
 }
 
 function make_rsession_conf {
@@ -772,6 +777,7 @@ function make_rsession_conf {
         ## The default R_LIBS_USER folder that the R session will use
         echo "r-libs-user=${R_LIBS_USER:?}"
     } > "${workdir}/rsession.conf"
+    assert_file_is_not_empty "${workdir}/rsession.conf"
 }
 
 
@@ -837,6 +843,7 @@ set -x
 
 exec rsession "\${@}"
 END
+  assert_file_is_not_empty "${workdir}/rsession.sh"
 
   chmod +x "${workdir}/rsession.sh"
 }
@@ -1099,7 +1106,9 @@ function launch_rserver {
     assert_dir_exists "${workdir}"
 
     hostname > "${workdir}/rserver.hostname"
+    assert_file_is_not_empty "${workdir}/rserver.hostname"
     grep -E "www-port=" "$(config_dir)/rserver.conf" | sed 's/www-port=//' > "${workdir}/rserver.port"
+    assert_file_is_not_empty "${workdir}/rserver.port"
 
     port=$(rserver_port)
     assert_port_free "${port}"
@@ -1114,6 +1123,7 @@ function launch_rserver {
     fi
     rs_pid=$!
     echo "${rs_pid}" > "${pid_file}"
+    assert_file_is_not_empty "${pid_file}"
     rs_pid=$(rserver_pid)
     mdebug "RStudio Server started (PID ${rs_pid})"
 }
@@ -1265,6 +1275,7 @@ function launch_rserver_monitor {
     fi
     pid=$!
     echo "${pid}" > "${pid_file}"
+    assert_file_is_not_empty "${pid_file}"
 
     pid=$(rserver_pid)
     mdebug "rserver monitor started (PID ${pid})"
@@ -1563,10 +1574,10 @@ fi
 ## Validate 'port':
 if [[ "${port}" == "random" ]]; then
     port="port4me"
-    warn "--port=random is deprecated in favor of --port=port4me (default)"
+    error "--port=random is defunct in favor of --port=port4me (default)"
 elif [[ "${port}" == "uid" ]]; then
     port="port4me"
-    warn "--port=uid is deprecated in favor of --port=port4me (default)"
+    error "--port=uid is defunct in favor of --port=port4me (default)"
 elif [[ "${port}" != "port4me" ]]; then
     assert_port "${port}"
 fi
@@ -1781,7 +1792,7 @@ elif [[ "${action}" == "stop" ]]; then
     lockfile=${workdir}/pid.lock
     ## If running, make sure we're stopping from the correct machine
     if [[ -f "${lockfile}" ]] && [[ "$(hostname)" != "$(rserver_hostname)" ]]; then
-        error "Stopping the RStudio Server can only be made from the machine ($(rserver_hostname)) where it was started from"
+        error "Stopping the RStudio Server can only be made from the machine ($(rserver_hostname)) where it was started from - not from $(hostname)"
     fi
 
     ## Terminate rsession
@@ -1914,10 +1925,12 @@ elif [[ "${action}" == "start" ]]; then
         else
             mdebug "ssh -o ConnectTimeout=\"$(ssh_timeout)\" -N -R \"${rev_spec}\" \"${rev_hostname}\""
             printf "%s\n%s\n" "${rev_hostname}" "${rev_port}" > "$(ssh_revtunnel_spec_file)"
+            assert_file_is_not_empty "$(ssh_revtunnel_spec_file)"
             ssh -o ConnectTimeout="$(ssh_timeout)" -N -R "${rev_spec}" "${rev_hostname}" &
         fi
         ssh_pid=$!
         echo "${ssh_pid}" > "${pid_file}"
+        assert_file_is_not_empty "${pid_file}"
         ssh_pid=$(ssh_revtunnel_pid false)
         mdebug "Reverse SSH tunnel started (PID ${ssh_pid})"
         pids+=("${ssh_pid}")