BioC 3.1: CHECK report for Rcpi on morelia

Package: Rcpi

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.4.0.tar.gz

StartedAt: 2015-10-09 05:26:44 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:29:39 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 174.1 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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/Rcpi.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.4.0’
* 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 ... [16s/16s] 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [15s/15s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [8s/8s]
 [8s/8s] 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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (Rcpi)

name	user	system	elapsed
AA2DACOR	0.003	0.000	0.004
AA3DMoRSE	0.002	0.001	0.002
AAACF	0.002	0.000	0.002
AABLOSUM100	0.001	0.000	0.001
AABLOSUM45	0.001	0.000	0.002
AABLOSUM50	0.001	0.001	0.002
AABLOSUM62	0.001	0.000	0.002
AABLOSUM80	0.001	0.000	0.002
AABurden	0.002	0.001	0.002
AACPSA	0.001	0.000	0.002
AAConn	0.001	0.000	0.002
AAConst	0.001	0.001	0.002
AADescAll	0.002	0.000	0.002
AAEdgeAdj	0.002	0.001	0.001
AAEigIdx	0.002	0.000	0.002
AAFGC	0.001	0.000	0.002
AAGETAWAY	0.001	0.000	0.002
AAGeom	0.001	0.000	0.001
AAInfo	0.001	0.001	0.001
AAMOE2D	0.001	0.000	0.001
AAMOE3D	0.001	0.000	0.002
AAMetaInfo	0.002	0.000	0.002
AAMolProp	0.002	0.000	0.002
AAPAM120	0.002	0.001	0.001
AAPAM250	0.001	0.000	0.002
AAPAM30	0.001	0.001	0.002
AAPAM40	0.002	0.000	0.002
AAPAM70	0.002	0.001	0.002
AARDF	0.001	0.000	0.002
AARandic	0.001	0.001	0.001
AATopo	0.001	0.000	0.001
AATopoChg	0.001	0.000	0.002
AAWHIM	0.001	0.001	0.002
AAWalk	0.001	0.000	0.001
AAindex	0.002	0.001	0.001
OptAA3d	0.000	0.000	0.001
Rcpi-package	0.000	0.000	0.001
acc	0.016	0.003	0.019
calcDrugFPSim	0.001	0.000	0.000
calcDrugMCSSim	0	0	0
calcParProtGOSim	0	0	0
calcParProtSeqSim	0.001	0.001	0.001
calcTwoProtGOSim	0.001	0.000	0.001
calcTwoProtSeqSim	0.001	0.000	0.001
checkProt	0.003	0.000	0.004
convMolFormat	0.001	0.000	0.001
extractDrugAIO	0	0	0
extractDrugALOGP	0.001	0.000	0.000
extractDrugAminoAcidCount	0.001	0.000	0.000
extractDrugApol	0	0	0
extractDrugAromaticAtomsCount	0.001	0.000	0.000
extractDrugAromaticBondsCount	0.001	0.000	0.000
extractDrugAtomCount	0	0	0
extractDrugAutocorrelationCharge	0	0	0
extractDrugAutocorrelationMass	0.001	0.000	0.000
extractDrugAutocorrelationPolarizability	0.001	0.001	0.000
extractDrugBCUT	0	0	0
extractDrugBPol	0.001	0.000	0.000
extractDrugBondCount	0.001	0.000	0.000
extractDrugCPSA	0	0	0
extractDrugCarbonTypes	0	0	0
extractDrugChiChain	0.001	0.000	0.000
extractDrugChiCluster	0.001	0.000	0.000
extractDrugChiPath	0	0	0
extractDrugChiPathCluster	0	0	0
extractDrugDescOB	0.001	0.000	0.000
extractDrugECI	0.000	0.001	0.000
extractDrugEstate	0	0	0
extractDrugEstateComplete	0	0	0
extractDrugExtended	0.001	0.000	0.000
extractDrugExtendedComplete	0.001	0.000	0.000
extractDrugFMF	0	0	0
extractDrugFragmentComplexity	0.001	0.000	0.000
extractDrugGraph	0.001	0.000	0.000
extractDrugGraphComplete	0	0	0
extractDrugGravitationalIndex	0.001	0.000	0.001
extractDrugHBondAcceptorCount	0.001	0.000	0.001
extractDrugHBondDonorCount	0.000	0.000	0.001
extractDrugHybridization	0.000	0.000	0.001
extractDrugHybridizationComplete	0.000	0.001	0.001
extractDrugHybridizationRatio	0.000	0.000	0.001
extractDrugIPMolecularLearning	0.000	0.001	0.001
extractDrugKR	0.001	0.000	0.001
extractDrugKRComplete	0.001	0.000	0.000
extractDrugKappaShapeIndices	0.001	0.000	0.000
extractDrugKierHallSmarts	0	0	0
extractDrugLargestChain	0.000	0.000	0.001
extractDrugLargestPiSystem	0.000	0.000	0.001
extractDrugLengthOverBreadth	0	0	0
extractDrugLongestAliphaticChain	0	0	0
extractDrugMACCS	0.001	0.000	0.000
extractDrugMACCSComplete	0.001	0.000	0.001
extractDrugMDE	0.001	0.000	0.001
extractDrugMannholdLogP	0.001	0.000	0.000
extractDrugMomentOfInertia	0	0	0
extractDrugOBFP2	0	0	0
extractDrugOBFP3	0.001	0.000	0.000
extractDrugOBFP4	0.001	0.001	0.000
extractDrugOBMACCS	0	0	0
extractDrugPetitjeanNumber	0.000	0.000	0.001
extractDrugPetitjeanShapeIndex	0.000	0.000	0.001
extractDrugPubChem	0.001	0.000	0.001
extractDrugPubChemComplete	0.001	0.001	0.001
extractDrugRotatableBondsCount	0.001	0.000	0.000
extractDrugRuleOfFive	0.001	0.000	0.001
extractDrugShortestPath	0.001	0.000	0.000
extractDrugShortestPathComplete	0	0	0
extractDrugStandard	0	0	0
extractDrugStandardComplete	0	0	0
extractDrugTPSA	0.000	0.000	0.001
extractDrugVABC	0.001	0.000	0.001
extractDrugVAdjMa	0.001	0.000	0.001
extractDrugWHIM	0.001	0.000	0.000
extractDrugWeight	0	0	0
extractDrugWeightedPath	0	0	0
extractDrugWienerNumbers	0.001	0.000	0.000
extractDrugXLogP	0.001	0.001	0.001
extractDrugZagrebIndex	0.001	0.000	0.001
extractPCMBLOSUM	0.012	0.002	0.014
extractPCMDescScales	0.019	0.001	0.020
extractPCMFAScales	0.017	0.001	0.018
extractPCMMDSScales	0.009	0.001	0.010
extractPCMPropScales	0.013	0.001	0.013
extractPCMScales	0.018	0.002	0.020
extractProtAAC	0.002	0.001	0.002
extractProtAPAAC	2.361	0.106	2.467
extractProtCTDC	0.005	0.001	0.005
extractProtCTDD	0.004	0.001	0.006
extractProtCTDT	0.009	0.000	0.010
extractProtCTriad	0.236	0.018	0.254
extractProtDC	0.003	0.003	0.007
extractProtGeary	0.195	0.006	0.201
extractProtMoran	0.164	0.005	0.170
extractProtMoreauBroto	0.216	0.007	0.223
extractProtPAAC	0.787	0.050	0.838
extractProtPSSM	0	0	0
extractProtPSSMAcc	0.000	0.000	0.001
extractProtPSSMFeature	0.000	0.000	0.001
extractProtQSO	1.504	0.045	1.546
extractProtSOCN	1.551	0.077	1.628
extractProtTC	0.057	0.045	0.102
getCPI	0.003	0.001	0.005
getDrug	0.001	0.001	0.001
getFASTAFromKEGG	0.001	0.000	0.000
getFASTAFromUniProt	0.001	0.001	0.001
getMolFromCAS	0.000	0.000	0.001
getMolFromChEMBL	0.000	0.000	0.001
getMolFromDrugBank	0.001	0.000	0.001
getMolFromKEGG	0.001	0.001	0.001
getMolFromPubChem	0	0	0
getPDBFromRCSBPDB	0.001	0.000	0.000
getPPI	0.004	0.001	0.005
getProt	0.000	0.000	0.001
getSeqFromKEGG	0.001	0.000	0.001
getSeqFromRCSBPDB	0.000	0.000	0.001
getSeqFromUniProt	0.000	0.000	0.001
getSmiFromChEMBL	0.001	0.000	0.001
getSmiFromDrugBank	0.001	0.000	0.001
getSmiFromKEGG	0.000	0.000	0.001
getSmiFromPubChem	0.001	0.000	0.001
readFASTA	0.002	0.000	0.002
readMolFromSDF	0.000	0.000	0.001
readMolFromSmi	0.000	0.000	0.001
readPDB	1.291	0.046	1.337
searchDrug	0.001	0.000	0.000
segProt	0.003	0.001	0.004