Add _R_CHECK_SUGGESTS_ONLY_=true to Renviron.bioc

3.17/Renviron.bioc

@@ -37,6 +37,19 @@ _R_CHECK_LENGTH_1_LOGIC2_=package:_R_CHECK_PACKAGE_NAME_,abort,verbose
 _R_CHECK_S3_METHODS_NOT_REGISTERED_=true
 #_R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_=true
 #_R_CLASS_MATRIX_ARRAY_=true
+
+# _R_CHECK_SUGGESTS_ONLY_=true will allow 'R CMD check' to expose undeclared package dependencies.
+# Note that:
+# - The setting is effective **only** if base and recommended packages are installed in
+#   <R_HOME>/library and all other packages are installed somewhere else (e.g. in
+#   <R_HOME>/site-library). An easy way to achieve this setup is by creating the
+#   <R_HOME>/site-library folder right after installing R and **before** installing any
+#   package.
+# - Only the Bioconductor **Linux** builders use the above setup at the moment (i.e. all
+#   packages except base and recommended packages are installed in <R_HOME>/site-library).
+#   This means that 'R CMD check' can only expose undeclared dependencies on the Bioconductor
+#   Linux builders. It will NOT expose them on the Bioconductor Windows or Mac builders.
+_R_CHECK_SUGGESTS_ONLY_=true
 R_DEFAULT_INTERNET_TIMEOUT=600
 
 # Package code can use this to detect that it's running on a Bioconductor

3.17/report.css

@@ -81,7 +81,6 @@ TABLE.grid_layout DIV.hscrollable {
 DIV.motd {
     padding-top: 10px;
     padding-bottom: 0px;
-    text-align: center;
     /*font-weight: bold;*/
 }
 DIV.motd TABLE {

BBS-report.py

@@ -112,18 +112,21 @@ def write_notes_to_developer(out, pkg):
         prefix = ''
     if BBSvars.buildtype == "bioc":
         url = 'https://bioconductor.org/developers/how-to/troubleshoot-build-report/'
-        out.write('%sPlease allow up to 24 hours (and sometimes ' % prefix)
+        out.write('%sAllow up to 24 hours (and sometimes ' % prefix)
         out.write('48 hours) for your latest push to ')
         out.write('git@git.bioconductor.org:packages/%s.git ' % pkg)
-        out.write('to<BR>reflect on this report. ')
-        out.write('See <A href="%s">How and When does the builder ' % url)
-        out.write('pull? When will my changes propagate?</A> ')
-        out.write('for more information.<BR>\n')
+        out.write('to reflect on this report. ')
+        out.write('See <A href="%s">Troubleshooting Build Report</A> ')
+        out.write('for more information.<BR><BR>\n')
     if os.path.exists('Renviron.bioc'):
-        out.write('%sMake sure to ' % prefix)
-        out.write('<A href="../%s">use the following ' % 'Renviron.bioc')
-        out.write('settings</A> in order to reproduce any error ')
-        out.write('or warning you see on this page.<BR>\n')
+        out.write('%sUse the following ' % prefix)
+        out.write('<A href="../%s">Renviron settings</A> ' % 'Renviron.bioc')
+        out.write('to reproduce errors and warnings.<BR><BR>\n')
+        out.write('Note: If "R CMD check" recently failed on the Linux ')
+        out.write('builder over a missing dependency, add the missing ')
+        out.write('dependency to "Suggests" in your DESCRIPTION file. See ')
+        out.write('the <A href="../%s">Renviron.bioc</A> ' % 'Renviron.bioc')
+        out.write('for details.\n')
     out.write('</TD></TR></TABLE>\n')
     out.write('</DIV>\n')
     return