Package: Rcpi

Version: 1.18.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rcpi_1.18.2.tar.gz

StartedAt: 2019-04-16 02:13:43 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 02:16:24 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 161.2 seconds

RetCode: 0

Status:  OK

CheckDir: Rcpi.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rcpi_1.18.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/Rcpi.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.18.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rcpi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rcpi
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘Rcpi’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rcpi)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage('Rcpi')



RUNIT TEST PROTOCOL -- Tue Apr 16 02:16:12 2019 
*********************************************** 
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Rcpi RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  7.551   0.544   6.967 

name	user	system	elapsed
AA2DACOR	0.013	0.003	0.016
AA3DMoRSE	0.001	0.001	0.003
AAACF	0.002	0.001	0.002
AABLOSUM100	0.001	0.001	0.003
AABLOSUM45	0.002	0.001	0.003
AABLOSUM50	0.002	0.001	0.003
AABLOSUM62	0.001	0.001	0.003
AABLOSUM80	0.002	0.001	0.002
AABurden	0.001	0.001	0.002
AACPSA	0.002	0.001	0.003
AAConn	0.001	0.001	0.002
AAConst	0.001	0.000	0.002
AADescAll	0.002	0.001	0.003
AAEdgeAdj	0.001	0.000	0.002
AAEigIdx	0.002	0.001	0.002
AAFGC	0.001	0.001	0.002
AAGETAWAY	0.002	0.001	0.003
AAGeom	0.002	0.001	0.002
AAInfo	0.002	0.001	0.002
AAMOE2D	0.001	0.001	0.003
AAMOE3D	0.001	0.001	0.002
AAMetaInfo	0.001	0.001	0.002
AAMolProp	0.002	0.001	0.003
AAPAM120	0.002	0.001	0.003
AAPAM250	0.002	0.001	0.002
AAPAM30	0.001	0.001	0.003
AAPAM40	0.002	0.001	0.003
AAPAM70	0.002	0.001	0.003
AARDF	0.001	0.001	0.002
AARandic	0.001	0.000	0.002
AATopo	0.001	0.000	0.001
AATopoChg	0.001	0.001	0.002
AAWHIM	0.001	0.001	0.002
AAWalk	0.001	0.000	0.001
AAindex	0.002	0.000	0.002
OptAA3d	0	0	0
acc	0.016	0.005	0.021
calcDrugFPSim	2.105	0.254	0.784
calcDrugMCSSim	0.004	0.003	0.008
calcParProtGOSim	0	0	0
calcParProtSeqSim	0.005	0.001	0.007
calcTwoProtGOSim	0	0	0
calcTwoProtSeqSim	0.002	0.000	0.003
checkProt	0.002	0.001	0.002
convMolFormat	0.001	0.000	0.001
extractDrugAIO	0.001	0.001	0.001
extractDrugALOGP	0.001	0.000	0.001
extractDrugAminoAcidCount	0	0	0
extractDrugApol	0.000	0.001	0.001
extractDrugAromaticAtomsCount	0	0	0
extractDrugAromaticBondsCount	0.001	0.000	0.001
extractDrugAtomCount	0.001	0.001	0.000
extractDrugAutocorrelationCharge	0.001	0.000	0.001
extractDrugAutocorrelationMass	0.001	0.000	0.001
extractDrugAutocorrelationPolarizability	0.000	0.000	0.001
extractDrugBCUT	0.000	0.000	0.001
extractDrugBPol	0	0	0
extractDrugBondCount	0.001	0.000	0.001
extractDrugCPSA	0.001	0.000	0.000
extractDrugCarbonTypes	0.001	0.000	0.001
extractDrugChiChain	0.001	0.000	0.000
extractDrugChiCluster	0.000	0.001	0.001
extractDrugChiPath	0	0	0
extractDrugChiPathCluster	0.000	0.000	0.001
extractDrugDescOB	0.008	0.004	0.013
extractDrugECI	0.001	0.000	0.001
extractDrugEstate	0.001	0.000	0.001
extractDrugEstateComplete	0.000	0.000	0.001
extractDrugExtended	0	0	0
extractDrugExtendedComplete	0.000	0.000	0.001
extractDrugFMF	0.000	0.001	0.000
extractDrugFragmentComplexity	0.001	0.000	0.001
extractDrugGraph	0.001	0.000	0.001
extractDrugGraphComplete	0.001	0.001	0.001
extractDrugGravitationalIndex	0.000	0.000	0.001
extractDrugHBondAcceptorCount	0	0	0
extractDrugHBondDonorCount	0.000	0.000	0.001
extractDrugHybridization	0	0	0
extractDrugHybridizationComplete	0.001	0.000	0.001
extractDrugHybridizationRatio	0.001	0.000	0.001
extractDrugIPMolecularLearning	0.001	0.001	0.001
extractDrugKR	0.001	0.000	0.001
extractDrugKRComplete	0.001	0.000	0.000
extractDrugKappaShapeIndices	0.000	0.001	0.001
extractDrugKierHallSmarts	0	0	0
extractDrugLargestChain	0.000	0.000	0.001
extractDrugLargestPiSystem	0.000	0.001	0.001
extractDrugLengthOverBreadth	0.001	0.000	0.001
extractDrugLongestAliphaticChain	0.001	0.000	0.001
extractDrugMACCS	0.001	0.001	0.000
extractDrugMACCSComplete	0.001	0.000	0.001
extractDrugMDE	0.001	0.000	0.000
extractDrugMannholdLogP	0.000	0.001	0.001
extractDrugMomentOfInertia	0	0	0
extractDrugOBFP2	0.012	0.001	0.013
extractDrugOBFP3	0.005	0.000	0.005
extractDrugOBFP4	0.007	0.004	0.010
extractDrugOBMACCS	0.095	0.001	0.096
extractDrugPetitjeanNumber	0.001	0.000	0.001
extractDrugPetitjeanShapeIndex	0.001	0.000	0.001
extractDrugPubChem	0.000	0.000	0.001
extractDrugPubChemComplete	0.001	0.000	0.001
extractDrugRotatableBondsCount	0.001	0.000	0.002
extractDrugRuleOfFive	0.001	0.000	0.001
extractDrugShortestPath	0.001	0.000	0.001
extractDrugShortestPathComplete	0.000	0.000	0.001
extractDrugStandard	0.001	0.000	0.002
extractDrugStandardComplete	0.001	0.000	0.001
extractDrugTPSA	0.001	0.000	0.001
extractDrugVABC	0.001	0.000	0.000
extractDrugVAdjMa	0.001	0.000	0.001
extractDrugWHIM	0.001	0.000	0.001
extractDrugWeight	0.000	0.000	0.001
extractDrugWeightedPath	0.000	0.000	0.001
extractDrugWienerNumbers	0	0	0
extractDrugXLogP	0.000	0.000	0.001
extractDrugZagrebIndex	0.001	0.001	0.000
extractPCMBLOSUM	0.010	0.002	0.012
extractPCMDescScales	0.013	0.001	0.015
extractPCMFAScales	0.026	0.003	0.029
extractPCMMDSScales	0.013	0.003	0.016
extractPCMPropScales	0.013	0.002	0.015
extractPCMScales	0.031	0.002	0.033
extractProtAAC	0.002	0.000	0.002
extractProtAPAAC	1.241	0.031	1.281
extractProtCTDC	0.003	0.000	0.004
extractProtCTDD	0.008	0.002	0.010
extractProtCTDT	0.009	0.001	0.011
extractProtCTriad	0.153	0.017	0.171
extractProtDC	0.006	0.004	0.011
extractProtGeary	0.193	0.010	0.203
extractProtMoran	0.185	0.013	0.198
extractProtMoreauBroto	0.213	0.011	0.229
extractProtPAAC	0.719	0.005	0.739
extractProtPSSM	0.001	0.001	0.001
extractProtPSSMAcc	0.002	0.000	0.002
extractProtPSSMFeature	0.001	0.000	0.002
extractProtQSO	1.405	0.014	1.440
extractProtSOCN	1.558	0.015	1.579
extractProtTC	0.070	0.054	0.125
getCPI	0.003	0.001	0.003
getDrug	0	0	0
getFASTAFromKEGG	0.000	0.001	0.000
getFASTAFromUniProt	0.000	0.000	0.001
getMolFromCAS	0.000	0.000	0.001
getMolFromChEMBL	0.000	0.000	0.001
getMolFromDrugBank	0	0	0
getMolFromKEGG	0	0	0
getMolFromPubChem	0.001	0.000	0.000
getPDBFromRCSBPDB	0	0	0
getPPI	0.004	0.002	0.006
getProt	0	0	0
getSeqFromKEGG	0.000	0.000	0.001
getSeqFromRCSBPDB	0	0	0
getSeqFromUniProt	0.000	0.000	0.001
getSmiFromChEMBL	0	0	0
getSmiFromDrugBank	0	0	0
getSmiFromKEGG	0.000	0.000	0.001
getSmiFromPubChem	0.001	0.000	0.000
readFASTA	0.002	0.000	0.002
readMolFromSDF	0.002	0.000	0.002
readMolFromSmi	0.001	0.001	0.001
readPDB	1.261	0.008	1.279
searchDrug	0.001	0.001	0.003
segProt	0.004	0.001	0.005