3 errors during MetFragR installation

[ChangLiuuczlcl8]

Hi,

I am trying to install the MetFragR package running
R CMD check metfRag
in command line and I got 3 errors.

The log file shows as following:

• checking examples ... ERROR
  Running examples in ‘metfRag-Ex.R’ failed
  The error most likely occurred in:

Name: create.settings.sample

Title: Create a settings object used by run.metfrag function

Aliases: create.settings.sample

** Examples

#create settings sample object
settingsObject<-create.settings.sample()
#run MetFrag
scored.candidates<-run.metfrag(settingsObject)
13:10:27.045 INFO de.ipbhalle.metfraglib.database.OnlinePubChemDatabase - Fetching candidates from PubChem
13:10:28.667 INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - Got 5 candidate(s)
13:10:29.402 INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 20 %
13:10:29.413 INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 40 %
13:10:29.424 INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 60 %
13:10:29.431 INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 80 %
13:10:29.459 INFO de.ipbhalle.metfraglib.process.ProcessingStatus - 100 %
13:10:29.679 INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - 0 candidate(s) were discarded before processing due to pre-filtering
13:10:29.679 INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - 0 candidate(s) discarded during processing due to errors
13:10:29.680 INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - 0 candidate(s) discarded after processing due to post-filtering
13:10:29.680 INFO de.ipbhalle.metfraglib.process.CombinedMetFragProcess - Stored 5 candidate(s)
Error in .jcall(obj, "Lde/ipbhalle/metfraglib/list/CandidateList;", "runMetFrag", :
java.lang.NullPointerException: Cannot invoke "org.openscience.cdk.interfaces.IAtomContainer.getAtomCount()" because the return value of "de.ipbhalle.metfraglib.interfaces.IMolecularStructure.getStructureAsIAtomContainer()" is null
Calls: run.metfrag -> .jcall -> .jcheck
Execution halted

• checking re-building of vignette outputs ... ERROR
  Error(s) in re-building vignettes:
  ...
  --- re-building ‘metfRag.Rnw’ using Sweave
  Loading required package: rJava
  Loading required package: rcdk
  Loading required package: rcdklibs
  Loading required package: rjson
  Error retrieving candidates
  java.lang.NullPointerException: Cannot invoke "de.ipbhalle.metfraglib.list.CandidateList.getNumberElements()" because "this.sortedScoredCandidateList" is null
  at de.ipbhalle.metfraglib.process.CombinedMetFragProcess.run(CombinedMetFragProcess.java:138)
  at de.ipbhalle.metfrag.r.MetfRag.scoreMoleculesAgainstSpectrum(MetfRag.java:231)
  Error running MetFrag process.

Error: processing vignette 'metfRag.Rnw' failed with diagnostics:
chunk 3 (label = scoreMetfrag)
Error in .jcall(obj, "[Lorg/openscience/cdk/interfaces/IAtomContainer;", :
java.lang.NullPointerException: Cannot invoke "de.ipbhalle.metfraglib.list.SortedScoredCandidateList.getNumberElements()" because "scoredCandidateList" is null

--- failed re-building ‘metfRag.Rnw’

SUMMARY: processing the following file failed:
‘metfRag.Rnw’

Error: Vignette re-building failed.
Execution halted

• checking PDF version of manual without index ... ERROR
  Re-running with no redirection of stdout/stderr.