BioC 3.3: CHECK report for Rcpi on morelia

Package: Rcpi

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.7.0.tar.gz

StartedAt: 2015-10-22 10:14:51 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 10:16:58 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 126.8 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_1.7.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/Rcpi.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* 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 ‘1.7.0’
* 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 ... [12s/12s] 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 ... [10s/10s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [6s/6s]
 [6s/6s] 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	0.002	0.001	0.002
AA3DMoRSE	0.001	0.000	0.001
AAACF	0.001	0.000	0.001
AABLOSUM100	0.001	0.000	0.001
AABLOSUM45	0.001	0.000	0.001
AABLOSUM50	0.000	0.000	0.001
AABLOSUM62	0.001	0.001	0.001
AABLOSUM80	0.001	0.000	0.001
AABurden	0.001	0.000	0.002
AACPSA	0.001	0.000	0.001
AAConn	0.001	0.000	0.001
AAConst	0.001	0.000	0.001
AADescAll	0.001	0.000	0.001
AAEdgeAdj	0.001	0.000	0.001
AAEigIdx	0.001	0.000	0.001
AAFGC	0.001	0.000	0.001
AAGETAWAY	0.001	0.001	0.001
AAGeom	0.001	0.000	0.002
AAInfo	0.001	0.001	0.002
AAMOE2D	0.001	0.000	0.001
AAMOE3D	0.001	0.000	0.002
AAMetaInfo	0.002	0.000	0.002
AAMolProp	0.001	0.000	0.001
AAPAM120	0.001	0.000	0.001
AAPAM250	0.001	0.000	0.002
AAPAM30	0.001	0.000	0.001
AAPAM40	0.001	0.000	0.001
AAPAM70	0.001	0.001	0.001
AARDF	0.001	0.000	0.001
AARandic	0.001	0.000	0.002
AATopo	0.001	0.000	0.001
AATopoChg	0.001	0.000	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	0	0
Rcpi-package	0.000	0.000	0.001
acc	0.010	0.003	0.013
calcDrugFPSim	0	0	0
calcDrugMCSSim	0.000	0.000	0.001
calcParProtGOSim	0	0	0
calcParProtSeqSim	0.000	0.001	0.000
calcTwoProtGOSim	0.001	0.000	0.000
calcTwoProtSeqSim	0.001	0.000	0.001
checkProt	0.003	0.000	0.002
convMolFormat	0.001	0.000	0.000
extractDrugAIO	0.001	0.001	0.000
extractDrugALOGP	0.000	0.000	0.001
extractDrugAminoAcidCount	0	0	0
extractDrugApol	0	0	0
extractDrugAromaticAtomsCount	0	0	0
extractDrugAromaticBondsCount	0	0	0
extractDrugAtomCount	0.000	0.000	0.001
extractDrugAutocorrelationCharge	0.000	0.000	0.001
extractDrugAutocorrelationMass	0	0	0
extractDrugAutocorrelationPolarizability	0	0	0
extractDrugBCUT	0	0	0
extractDrugBPol	0.000	0.000	0.001
extractDrugBondCount	0.000	0.000	0.001
extractDrugCPSA	0.000	0.001	0.000
extractDrugCarbonTypes	0	0	0
extractDrugChiChain	0	0	0
extractDrugChiCluster	0	0	0
extractDrugChiPath	0.000	0.000	0.001
extractDrugChiPathCluster	0.001	0.000	0.000
extractDrugDescOB	0.000	0.001	0.001
extractDrugECI	0.000	0.000	0.001
extractDrugEstate	0	0	0
extractDrugEstateComplete	0	0	0
extractDrugExtended	0	0	0
extractDrugExtendedComplete	0.000	0.000	0.001
extractDrugFMF	0.000	0.000	0.001
extractDrugFragmentComplexity	0	0	0
extractDrugGraph	0	0	0
extractDrugGraphComplete	0	0	0
extractDrugGravitationalIndex	0	0	0
extractDrugHBondAcceptorCount	0.000	0.000	0.001
extractDrugHBondDonorCount	0.000	0.000	0.001
extractDrugHybridization	0	0	0
extractDrugHybridizationComplete	0	0	0
extractDrugHybridizationRatio	0	0	0
extractDrugIPMolecularLearning	0.000	0.000	0.001
extractDrugKR	0.000	0.000	0.001
extractDrugKRComplete	0	0	0
extractDrugKappaShapeIndices	0.001	0.000	0.000
extractDrugKierHallSmarts	0.001	0.000	0.000
extractDrugLargestChain	0.001	0.000	0.001
extractDrugLargestPiSystem	0.001	0.000	0.001
extractDrugLengthOverBreadth	0.001	0.000	0.000
extractDrugLongestAliphaticChain	0	0	0
extractDrugMACCS	0	0	0
extractDrugMACCSComplete	0.000	0.000	0.001
extractDrugMDE	0.000	0.000	0.001
extractDrugMannholdLogP	0	0	0
extractDrugMomentOfInertia	0	0	0
extractDrugOBFP2	0	0	0
extractDrugOBFP3	0.000	0.000	0.001
extractDrugOBFP4	0	0	0
extractDrugOBMACCS	0	0	0
extractDrugPetitjeanNumber	0.001	0.000	0.001
extractDrugPetitjeanShapeIndex	0	0	0
extractDrugPubChem	0	0	0
extractDrugPubChemComplete	0.000	0.000	0.001
extractDrugRotatableBondsCount	0	0	0
extractDrugRuleOfFive	0	0	0
extractDrugShortestPath	0.001	0.000	0.000
extractDrugShortestPathComplete	0.001	0.000	0.001
extractDrugStandard	0.001	0.000	0.000
extractDrugStandardComplete	0.001	0.000	0.000
extractDrugTPSA	0.001	0.000	0.000
extractDrugVABC	0.001	0.000	0.000
extractDrugVAdjMa	0.001	0.000	0.001
extractDrugWHIM	0.000	0.000	0.001
extractDrugWeight	0	0	0
extractDrugWeightedPath	0	0	0
extractDrugWienerNumbers	0	0	0
extractDrugXLogP	0	0	0
extractDrugZagrebIndex	0.000	0.001	0.001
extractPCMBLOSUM	0.009	0.001	0.010
extractPCMDescScales	0.010	0.001	0.012
extractPCMFAScales	0.018	0.002	0.020
extractPCMMDSScales	0.013	0.001	0.015
extractPCMPropScales	0.011	0.001	0.012
extractPCMScales	0.015	0.001	0.015
extractProtAAC	0.002	0.000	0.002
extractProtAPAAC	1.579	0.016	1.595
extractProtCTDC	0.007	0.000	0.007
extractProtCTDD	0.004	0.000	0.005
extractProtCTDT	0.006	0.001	0.006
extractProtCTriad	0.096	0.004	0.100
extractProtDC	0.003	0.001	0.005
extractProtGeary	0.129	0.002	0.131
extractProtMoran	0.141	0.003	0.144
extractProtMoreauBroto	0.129	0.002	0.132
extractProtPAAC	0.566	0.003	0.568
extractProtPSSM	0.000	0.000	0.001
extractProtPSSMAcc	0	0	0
extractProtPSSMFeature	0	0	0
extractProtQSO	1.019	0.005	1.024
extractProtSOCN	1.042	0.006	1.047
extractProtTC	0.042	0.030	0.067
getCPI	0.002	0.000	0.002
getDrug	0	0	0
getFASTAFromKEGG	0.001	0.000	0.000
getFASTAFromUniProt	0	0	0
getMolFromCAS	0	0	0
getMolFromChEMBL	0	0	0
getMolFromDrugBank	0.001	0.000	0.000
getMolFromKEGG	0.001	0.000	0.000
getMolFromPubChem	0.001	0.000	0.001
getPDBFromRCSBPDB	0.001	0.000	0.001
getPPI	0.003	0.001	0.003
getProt	0	0	0
getSeqFromKEGG	0	0	0
getSeqFromRCSBPDB	0	0	0
getSeqFromUniProt	0	0	0
getSmiFromChEMBL	0.000	0.000	0.001
getSmiFromDrugBank	0.000	0.000	0.001
getSmiFromKEGG	0	0	0
getSmiFromPubChem	0	0	0
readFASTA	0.001	0.000	0.001
readMolFromSDF	0	0	0
readMolFromSmi	0.000	0.000	0.001
readPDB	1.058	0.011	1.073
searchDrug	0	0	0
segProt	0.002	0.001	0.003