Package: Rcpi

Version: 1.16.2

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_1.16.2.tar.gz

StartedAt: 2018-10-16 23:33:30 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 23:36:11 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 161.1 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_1.16.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/Rcpi.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.16.2’
* 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 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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 Oct 16 23:36:00 2018 
*********************************************** 
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 
  7.789   0.552   7.183 

name	user	system	elapsed
AA2DACOR	0.023	0.004	0.026
AA3DMoRSE	0.003	0.001	0.004
AAACF	0.002	0.000	0.003
AABLOSUM100	0.001	0.000	0.003
AABLOSUM45	0.002	0.001	0.003
AABLOSUM50	0.002	0.001	0.004
AABLOSUM62	0.002	0.001	0.004
AABLOSUM80	0.002	0.000	0.003
AABurden	0.003	0.001	0.004
AACPSA	0.002	0.001	0.003
AAConn	0.002	0.001	0.003
AAConst	0.002	0.000	0.002
AADescAll	0.002	0.000	0.002
AAEdgeAdj	0.002	0.001	0.002
AAEigIdx	0.001	0.001	0.003
AAFGC	0.002	0.001	0.003
AAGETAWAY	0.003	0.001	0.004
AAGeom	0.003	0.001	0.004
AAInfo	0.003	0.001	0.004
AAMOE2D	0.003	0.001	0.003
AAMOE3D	0.002	0.001	0.002
AAMetaInfo	0.003	0.001	0.004
AAMolProp	0.003	0.001	0.004
AAPAM120	0.002	0.001	0.003
AAPAM250	0.001	0.001	0.003
AAPAM30	0.002	0.001	0.003
AAPAM40	0.002	0.000	0.003
AAPAM70	0.002	0.000	0.003
AARDF	0.001	0.001	0.003
AARandic	0.002	0.001	0.003
AATopo	0.002	0.001	0.004
AATopoChg	0.003	0.002	0.004
AAWHIM	0.001	0.000	0.003
AAWalk	0.002	0.000	0.003
AAindex	0.003	0.001	0.004
OptAA3d	0.001	0.000	0.001
acc	0.017	0.006	0.022
calcDrugFPSim	2.263	0.284	0.769
calcDrugMCSSim	0.007	0.005	0.011
calcParProtGOSim	0.002	0.000	0.003
calcParProtSeqSim	0.007	0.001	0.009
calcTwoProtGOSim	0.002	0.000	0.003
calcTwoProtSeqSim	0.004	0.001	0.005
checkProt	0.003	0.001	0.004
convMolFormat	0.002	0.000	0.002
extractDrugAIO	0.002	0.000	0.002
extractDrugALOGP	0.003	0.000	0.003
extractDrugAminoAcidCount	0.002	0.000	0.003
extractDrugApol	0.002	0.000	0.002
extractDrugAromaticAtomsCount	0.002	0.001	0.003
extractDrugAromaticBondsCount	0.003	0.000	0.003
extractDrugAtomCount	0.002	0.001	0.002
extractDrugAutocorrelationCharge	0.002	0.000	0.002
extractDrugAutocorrelationMass	0.003	0.001	0.002
extractDrugAutocorrelationPolarizability	0.002	0.000	0.003
extractDrugBCUT	0.001	0.000	0.002
extractDrugBPol	0.002	0.000	0.003
extractDrugBondCount	0.002	0.000	0.003
extractDrugCPSA	0.003	0.000	0.002
extractDrugCarbonTypes	0.002	0.000	0.002
extractDrugChiChain	0.003	0.001	0.002
extractDrugChiCluster	0.002	0.000	0.003
extractDrugChiPath	0.002	0.001	0.003
extractDrugChiPathCluster	0.002	0.000	0.003
extractDrugDescOB	0.009	0.004	0.014
extractDrugECI	0.001	0.000	0.002
extractDrugEstate	0.001	0.000	0.001
extractDrugEstateComplete	0.002	0.000	0.001
extractDrugExtended	0.002	0.000	0.002
extractDrugExtendedComplete	0.002	0.000	0.003
extractDrugFMF	0.002	0.001	0.002
extractDrugFragmentComplexity	0.002	0.000	0.002
extractDrugGraph	0.002	0.001	0.002
extractDrugGraphComplete	0.002	0.000	0.002
extractDrugGravitationalIndex	0.002	0.001	0.002
extractDrugHBondAcceptorCount	0.002	0.000	0.002
extractDrugHBondDonorCount	0.001	0.000	0.001
extractDrugHybridization	0.002	0.000	0.003
extractDrugHybridizationComplete	0.002	0.001	0.003
extractDrugHybridizationRatio	0.002	0.000	0.003
extractDrugIPMolecularLearning	0.002	0.000	0.002
extractDrugKR	0.002	0.000	0.003
extractDrugKRComplete	0.001	0.000	0.001
extractDrugKappaShapeIndices	0.002	0.000	0.002
extractDrugKierHallSmarts	0.002	0.001	0.002
extractDrugLargestChain	0.002	0.000	0.002
extractDrugLargestPiSystem	0.002	0.000	0.003
extractDrugLengthOverBreadth	0.002	0.000	0.003
extractDrugLongestAliphaticChain	0.002	0.000	0.003
extractDrugMACCS	0.002	0.000	0.003
extractDrugMACCSComplete	0.002	0.000	0.003
extractDrugMDE	0.003	0.001	0.003
extractDrugMannholdLogP	0.002	0.000	0.003
extractDrugMomentOfInertia	0.002	0.001	0.003
extractDrugOBFP2	0.020	0.001	0.020
extractDrugOBFP3	0.010	0.001	0.010
extractDrugOBFP4	0.012	0.005	0.018
extractDrugOBMACCS	0.096	0.000	0.097
extractDrugPetitjeanNumber	0.002	0.001	0.002
extractDrugPetitjeanShapeIndex	0.002	0.000	0.003
extractDrugPubChem	0.002	0.001	0.002
extractDrugPubChemComplete	0.002	0.000	0.003
extractDrugRotatableBondsCount	0.002	0.000	0.003
extractDrugRuleOfFive	0.001	0.000	0.002
extractDrugShortestPath	0.001	0.001	0.002
extractDrugShortestPathComplete	0.002	0.000	0.002
extractDrugStandard	0.001	0.000	0.002
extractDrugStandardComplete	0.001	0.000	0.002
extractDrugTPSA	0.002	0.000	0.001
extractDrugVABC	0.001	0.000	0.001
extractDrugVAdjMa	0.001	0.001	0.001
extractDrugWHIM	0.001	0.001	0.002
extractDrugWeight	0.002	0.000	0.002
extractDrugWeightedPath	0.002	0.001	0.002
extractDrugWienerNumbers	0.002	0.000	0.003
extractDrugXLogP	0.003	0.001	0.003
extractDrugZagrebIndex	0.001	0.000	0.002
extractPCMBLOSUM	0.014	0.001	0.015
extractPCMDescScales	0.020	0.003	0.022
extractPCMFAScales	0.029	0.004	0.032
extractPCMMDSScales	0.016	0.002	0.017
extractPCMPropScales	0.020	0.002	0.022
extractPCMScales	0.037	0.003	0.042
extractProtAAC	0.004	0.001	0.006
extractProtAPAAC	1.114	0.025	1.143
extractProtCTDC	0.006	0.001	0.006
extractProtCTDD	0.007	0.001	0.008
extractProtCTDT	0.007	0.001	0.008
extractProtCTriad	0.157	0.015	0.172
extractProtDC	0.006	0.002	0.009
extractProtGeary	0.219	0.009	0.228
extractProtMoran	0.209	0.009	0.223
extractProtMoreauBroto	0.200	0.008	0.212
extractProtPAAC	0.742	0.005	0.757
extractProtPSSM	0.011	0.000	0.011
extractProtPSSMAcc	0.003	0.000	0.003
extractProtPSSMFeature	0.003	0.000	0.002
extractProtQSO	1.465	0.013	1.500
extractProtSOCN	1.394	0.019	1.427
extractProtTC	0.082	0.065	0.149
getCPI	0.007	0.002	0.008
getDrug	0.002	0.000	0.001
getFASTAFromKEGG	0.001	0.000	0.001
getFASTAFromUniProt	0.001	0.000	0.001
getMolFromCAS	0.001	0.000	0.002
getMolFromChEMBL	0.001	0.000	0.002
getMolFromDrugBank	0.001	0.000	0.002
getMolFromKEGG	0.001	0.000	0.002
getMolFromPubChem	0.002	0.000	0.002
getPDBFromRCSBPDB	0.001	0.000	0.002
getPPI	0.007	0.002	0.009
getProt	0.001	0.000	0.001
getSeqFromKEGG	0.002	0.000	0.001
getSeqFromRCSBPDB	0.001	0.000	0.001
getSeqFromUniProt	0.002	0.000	0.001
getSmiFromChEMBL	0.001	0.000	0.001
getSmiFromDrugBank	0.002	0.000	0.002
getSmiFromKEGG	0.001	0.000	0.001
getSmiFromPubChem	0.002	0.000	0.001
readFASTA	0.003	0.000	0.004
readMolFromSDF	0.002	0.001	0.003
readMolFromSmi	0.002	0.000	0.003
readPDB	1.145	0.005	1.162
searchDrug	0.003	0.000	0.003
segProt	0.003	0.001	0.003