document() recompiles package source code, which requires a NAMESPACE #1016

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1. hadley commented on Jan 13, 2016

   

   hadley

   on Jan 13, 2016

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   Roxygen is a run-time documentation system - it inspects the objects in the package environment, not just the source code. That means it needs to load_all() the package, which obviously it can't do without compiling any C code.

   Would you mind briefly outlining a series of steps that gets you to this point? Normally the NAMESPACE doesn't matter when compiling code.
2. cboettig commented on Jan 13, 2016

   

   cboettig

   on Jan 13, 2016

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   Apologies for not having a good minimal example, this could be user error from a naive attempt to wrap a C program. Anyway, if you clone https://github.com/cboettig/rappl/tree/testing and run devtools::document() you should see the error about not having a NAMESPACE.

   Here's the run log I see:

   devtools::document()
   Updating rappl documentation
   Loading rappl
   Re-compiling rappl
   '/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore CMD  \
     INSTALL '/home/rstudio/rappl'  \
     --library='/tmp/RtmpDrJUwI/devtools_install_17fbdfe81' --no-R --no-data  \
     --no-help --no-demo --no-inst --no-docs --no-exec --no-multiarch  \
     --no-test-load --preclean 
   
   * installing *source* package ‘rappl’ ...
   rm -f ./PolicyGraph/PolicyGraph.o ./PolicyGraph/PolicyGraphGenerator.o ./Evaluator/EvaluationEngine.o ./Evaluator/EvaluatorSampleEngine.o ./Simulator/SimulationEngine.o ./MathLib/DenseVector.o ./MathLib/MathLib.o ./MathLib/SparseMatrix.o ./MathLib/SparseVector.o ./Algorithms/SARSOP/BinManager.o ./Algorithms/SARSOP/BinManagerSet.o ./Algorithms/SARSOP/Sample.o ./Algorithms/SARSOP/SampleBP.o ./Algorithms/SARSOP/SARSOP.o ./Algorithms/SARSOP/SARSOPPrune.o ./Models/MOMDP/BeliefTransitionMOMDP.o ./Models/MOMDP/ObservationProbabilities.o ./Models/MOMDP/VariableRelation.o ./Models/MOMDP/BooleanVariable.o ./Models/MOMDP/StateTransitionXY.o ./Models/MOMDP/StateTransitionY.o ./Models/MOMDP/MOMDPLite.o ./Models/MOMDP/MOMDP.o ./Models/MOMDP/VariableValue.o ./Models/MOMDP/Variable.o ./Models/MOMDP/StateTransitionXXpY.o ./Models/MOMDP/IVariable.o ./Models/MOMDP/VariableCombined.o ./Models/MOMDP/Rewards.o ./Models/MOMDP/StateTransitionX.o ./Models/MOMDP/BeliefTransitionMOMDPLite.o ./Models/MOMDP/IVariableValue.o ./OfflineSolver/GlobalResource.o ./OfflineSolver/solverUtils.o ./Bounds/AlphaPlane.o ./Bounds/AlphaPlanePool.o ./Bounds/AlphaPlanePoolSet.o ./Bounds/AlphaVectorPolicy.o ./Bounds/BackupAlphaPlaneMOMDP.o ./Bounds/BackupAlphaPlaneMOMDPLite.o ./Bounds/BackupBeliefValuePairMOMDP.o ./Bounds/BackupBeliefValuePairMOMDPLite.o ./Bounds/BeliefValuePair.o ./Bounds/BeliefValuePairPool.o ./Bounds/BeliefValuePairPoolSet.o ./Bounds/BlindLBInitializer.o ./Bounds/FastInfUBInitializer.o ./Bounds/FullObsUBInitializer.o ./Bounds/PruneAlphaPlane.o ./Bounds/PruneBeliefValuePair.o ./Bounds/xml_parse_lib.o ./Core/Actions.o ./Core/VariableContainer.o ./Core/Belief.o ./Core/BeliefCache.o ./Core/BeliefException.o ./Core/BeliefForest.o ./Core/BeliefTreeNode.o ./Core/BeliefWithState.o ./Core/MObject.o ./Core/Observations.o ./Core/States.o ./Core/UniqueBeliefHeap.o ./Parser/Cassandra/Parser.o ./Parser/Cassandra/POMDP.o ./Parser/Cassandra/pomdpCassandraWrapper.o ./Parser/ParserSelector.o ./Parser/POMDPX/FactoredPomdp.o ./Parser/POMDPX/Function.o ./Parser/POMDPX/ObsAct.o ./Parser/POMDPX/PreCEntry.o ./Parser/POMDPX/PreCMatrix.o ./Parser/POMDPX/SparseEntry.o ./Parser/POMDPX/SparseTable.o ./Parser/POMDPX/State.o ./Parser/POMDPX/StateObsAct.o ./Parser/POMDPX/tinystr.o ./Parser/POMDPX/tinyxml.o ./Parser/POMDPX/tinyxmlerror.o ./Parser/POMDPX/tinyxmlparser.o ./Utils/InfoLog.o ./Utils/md5.o ./Utils/md5wrapper.o ./Utils/CPMemUtils.o ./Utils/StatsCollector.o ./Utils/SimulationRewardCollector.o ./Parser/Cassandra/include/pomdp_spec.tab.o ./Parser/Cassandra/include/pomdp_spec.yy.o ./miniposix/getopt.o ./miniposix/getopt1.o ./miniposix/getopt_init.o ./Parser/Cassandra/decision-tree.o ./Parser/Cassandra/imm-reward.o ./Parser/Cassandra/mdpCassandra.o ./Parser/Cassandra/parse_err.o ./Parser/Cassandra/parse_hash.o ./Parser/Cassandra/sparse-matrix.o ./Controller/Controller.o   ./OfflineSolver/solver.o  ./Simulator/Simulator.o  ./Evaluator/Evaluator.o  ./PolicyGraph/PolicyGraph.o  ./PomdpConvertor/convertor.o  ./Controller/testControllerTiger.o 
   rm -f libappl.a pomdpsol pomdpsim pomdpeval polgraph pomdpconvert testControllerTiger
   ERROR: a 'NAMESPACE' file is required
   * removing ‘/tmp/RtmpDrJUwI/devtools_install_17fbdfe81/rappl’
   Error: Command failed (1)
   > 
   

   This seems to be related to the fact that I am using the Makefile from the original C program, which I understand isn't the right thing to do, so perhaps this isn't a problem once I figure out how to write the proper Makevars file in place of it, so perhaps this isn't a real issue. (I have a deal to learn still on that front). I was just surprised by the error.
3. hadley commented on Jan 13, 2016

   

   hadley

   on Jan 13, 2016

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   How did you create the original package? Most ways should give you a dummy/empty NAMESPACE.
4. cboettig commented on Jan 13, 2016

   

   cboettig

   on Jan 13, 2016

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   I created it with devtools::setup() (actually copied a template created with setup()). This created a dummy NAMESPACE (that does not have the #Generated by roxygen2: header), and so Roxygen was refusing to overwrite that. So I deleted the NAMESPACE and wound up with the above error.
5. hadley

   closed this as completedin 15ca9dfon Jan 20, 2016
6. lock commented on Sep 18, 2018

   

   lockbot

   on Sep 18, 2018

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   This old issue has been automatically locked. If you believe you have found a related problem, please file a new issue (with reprex) and link to this issue. https://reprex.tidyverse.org/
7. lock

   locked and limited conversation to collaborators on Sep 18, 2018