BioC 3.5: CHECK report for Rcpi on veracruz2

Package: Rcpi

Version: 1.12.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.12.6.tar.gz

StartedAt: 2017-10-18 07:59:17 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 08:02:00 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 163.1 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 --no-vignettes --timings Rcpi_1.12.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Rcpi.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.12.6’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... 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

* installing *source* package ‘Rcpi’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rcpi)

name	user	system	elapsed
AA2DACOR	0.016	0.005	0.021
AA3DMoRSE	0.002	0.001	0.003
AAACF	0.002	0.001	0.002
AABLOSUM100	0.001	0.001	0.002
AABLOSUM45	0.002	0.001	0.002
AABLOSUM50	0.001	0.000	0.002
AABLOSUM62	0.002	0.000	0.002
AABLOSUM80	0.001	0.001	0.002
AABurden	0.001	0.001	0.002
AACPSA	0.002	0.001	0.003
AAConn	0.002	0.001	0.003
AAConst	0.001	0.001	0.002
AADescAll	0.001	0.001	0.001
AAEdgeAdj	0.001	0.000	0.001
AAEigIdx	0.001	0.000	0.002
AAFGC	0.002	0.000	0.002
AAGETAWAY	0.001	0.001	0.002
AAGeom	0.002	0.001	0.002
AAInfo	0.002	0.001	0.002
AAMOE2D	0.007	0.001	0.008
AAMOE3D	0.001	0.001	0.003
AAMetaInfo	0.001	0.000	0.002
AAMolProp	0.002	0.000	0.001
AAPAM120	0.001	0.001	0.002
AAPAM250	0.001	0.001	0.002
AAPAM30	0.001	0.001	0.003
AAPAM40	0.000	0.000	0.002
AAPAM70	0.002	0.001	0.002
AARDF	0.001	0.001	0.003
AARandic	0.001	0.000	0.002
AATopo	0.002	0.000	0.002
AATopoChg	0.001	0.001	0.001
AAWHIM	0.001	0.000	0.001
AAWalk	0.001	0.000	0.002
AAindex	0.001	0.000	0.001
OptAA3d	0.000	0.000	0.001
acc	0.012	0.004	0.015
calcDrugFPSim	1.833	0.124	0.991
calcDrugMCSSim	0.004	0.003	0.008
calcParProtGOSim	0.001	0.001	0.001
calcParProtSeqSim	0.034	0.001	0.035
calcTwoProtGOSim	0.001	0.000	0.001
calcTwoProtSeqSim	0.002	0.000	0.003
checkProt	0.002	0.000	0.002
convMolFormat	0.001	0.000	0.002
extractDrugAIO	0.001	0.001	0.001
extractDrugALOGP	0.001	0.000	0.001
extractDrugAminoAcidCount	0.001	0.000	0.001
extractDrugApol	0.001	0.000	0.001
extractDrugAromaticAtomsCount	0.002	0.000	0.002
extractDrugAromaticBondsCount	0.001	0.001	0.002
extractDrugAtomCount	0.001	0.000	0.001
extractDrugAutocorrelationCharge	0.002	0.000	0.002
extractDrugAutocorrelationMass	0.001	0.000	0.002
extractDrugAutocorrelationPolarizability	0.002	0.000	0.001
extractDrugBCUT	0.001	0.000	0.002
extractDrugBPol	0.001	0.000	0.001
extractDrugBondCount	0.001	0.000	0.001
extractDrugCPSA	0.001	0.001	0.001
extractDrugCarbonTypes	0.001	0.000	0.001
extractDrugChiChain	0.002	0.000	0.002
extractDrugChiCluster	0.001	0.000	0.002
extractDrugChiPath	0.002	0.000	0.001
extractDrugChiPathCluster	0.001	0.000	0.001
extractDrugDescOB	0.006	0.000	0.006
extractDrugECI	0.000	0.000	0.001
extractDrugEstate	0.001	0.000	0.001
extractDrugEstateComplete	0.001	0.000	0.001
extractDrugExtended	0.001	0.000	0.002
extractDrugExtendedComplete	0.001	0.001	0.001
extractDrugFMF	0.001	0.000	0.001
extractDrugFragmentComplexity	0.001	0.000	0.001
extractDrugGraph	0.001	0.001	0.001
extractDrugGraphComplete	0.001	0.000	0.002
extractDrugGravitationalIndex	0.001	0.000	0.001
extractDrugHBondAcceptorCount	0.001	0.000	0.002
extractDrugHBondDonorCount	0.001	0.000	0.001
extractDrugHybridization	0.001	0.000	0.001
extractDrugHybridizationComplete	0.001	0.000	0.002
extractDrugHybridizationRatio	0.001	0.000	0.001
extractDrugIPMolecularLearning	0.001	0.000	0.001
extractDrugKR	0.001	0.001	0.002
extractDrugKRComplete	0.002	0.000	0.002
extractDrugKappaShapeIndices	0.001	0.000	0.001
extractDrugKierHallSmarts	0.001	0.001	0.001
extractDrugLargestChain	0.001	0.000	0.001
extractDrugLargestPiSystem	0.001	0.000	0.001
extractDrugLengthOverBreadth	0.001	0.000	0.001
extractDrugLongestAliphaticChain	0.001	0.000	0.001
extractDrugMACCS	0.002	0.000	0.002
extractDrugMACCSComplete	0.001	0.000	0.001
extractDrugMDE	0.001	0.001	0.001
extractDrugMannholdLogP	0.001	0.000	0.002
extractDrugMomentOfInertia	0.001	0.000	0.001
extractDrugOBFP2	0.010	0.001	0.011
extractDrugOBFP3	0.008	0.000	0.009
extractDrugOBFP4	0.01	0.00	0.01
extractDrugOBMACCS	0.009	0.001	0.009
extractDrugPetitjeanNumber	0.001	0.000	0.001
extractDrugPetitjeanShapeIndex	0.001	0.000	0.001
extractDrugPubChem	0.001	0.000	0.002
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	0.001	0.000	0.001
extractDrugStandard	0.001	0.000	0.002
extractDrugStandardComplete	0.001	0.000	0.002
extractDrugTPSA	0.001	0.000	0.001
extractDrugVABC	0.001	0.000	0.001
extractDrugVAdjMa	0.001	0.000	0.002
extractDrugWHIM	0.001	0.001	0.000
extractDrugWeight	0.001	0.000	0.001
extractDrugWeightedPath	0.001	0.000	0.002
extractDrugWienerNumbers	0.001	0.001	0.002
extractDrugXLogP	0.001	0.000	0.001
extractDrugZagrebIndex	0.001	0.000	0.001
extractPCMBLOSUM	0.267	0.003	0.281
extractPCMDescScales	0.013	0.001	0.015
extractPCMFAScales	0.020	0.002	0.026
extractPCMMDSScales	0.012	0.001	0.014
extractPCMPropScales	0.038	0.001	0.040
extractPCMScales	0.017	0.002	0.022
extractProtAAC	0.003	0.001	0.004
extractProtAPAAC	1.241	0.034	1.303
extractProtCTDC	0.003	0.001	0.004
extractProtCTDD	0.006	0.001	0.008
extractProtCTDT	0.006	0.001	0.007
extractProtCTriad	0.106	0.009	0.119
extractProtDC	0.004	0.003	0.008
extractProtGeary	0.237	0.008	0.258
extractProtMoran	0.210	0.005	0.221
extractProtMoreauBroto	0.219	0.006	0.230
extractProtPAAC	0.758	0.011	0.794
extractProtPSSM	0.001	0.000	0.002
extractProtPSSMAcc	0.001	0.001	0.002
extractProtPSSMFeature	0.001	0.000	0.002
extractProtQSO	1.242	0.016	1.290
extractProtSOCN	1.298	0.009	1.338
extractProtTC	0.051	0.050	0.111
getCPI	0.003	0.001	0.004
getDrug	0.000	0.000	0.001
getFASTAFromKEGG	0.000	0.001	0.000
getFASTAFromUniProt	0.001	0.000	0.001
getMolFromCAS	0.001	0.000	0.001
getMolFromChEMBL	0	0	0
getMolFromDrugBank	0.000	0.000	0.001
getMolFromKEGG	0	0	0
getMolFromPubChem	0.000	0.000	0.001
getPDBFromRCSBPDB	0.001	0.000	0.001
getPPI	0.003	0.001	0.004
getProt	0.001	0.000	0.001
getSeqFromKEGG	0.000	0.000	0.001
getSeqFromRCSBPDB	0.000	0.000	0.001
getSeqFromUniProt	0.001	0.000	0.001
getSmiFromChEMBL	0.001	0.000	0.001
getSmiFromDrugBank	0.001	0.000	0.000
getSmiFromKEGG	0	0	0
getSmiFromPubChem	0.001	0.000	0.000
readFASTA	0.002	0.000	0.002
readMolFromSDF	0.002	0.001	0.002
readMolFromSmi	0.001	0.000	0.001
readPDB	1.113	0.015	1.166
searchDrug	0.002	0.000	0.002
segProt	0.002	0.001	0.002