BioC 3.2: CHECK report for Rcpi on perceval

Package: Rcpi

Version: 1.5.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.5.0.tar.gz

StartedAt: 2015-08-24 04:24:26 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 04:28:11 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 225.1 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_1.5.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Rcpi.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.5.0’
* 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 ... [20s/20s] 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 ... [20s/19s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [11s/11s]
 [12s/11s] 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	0.003	0.001	0.005
AA3DMoRSE	0.002	0.000	0.002
AAACF	0.002	0.001	0.002
AABLOSUM100	0.002	0.001	0.002
AABLOSUM45	0.001	0.001	0.003
AABLOSUM50	0.001	0.000	0.002
AABLOSUM62	0.001	0.000	0.002
AABLOSUM80	0.002	0.000	0.002
AABurden	0.002	0.000	0.002
AACPSA	0.002	0.001	0.002
AAConn	0.003	0.001	0.004
AAConst	0.002	0.001	0.004
AADescAll	0.002	0.000	0.003
AAEdgeAdj	0.004	0.001	0.004
AAEigIdx	0.002	0.001	0.003
AAFGC	0.002	0.000	0.002
AAGETAWAY	0.002	0.000	0.002
AAGeom	0.001	0.000	0.002
AAInfo	0.002	0.001	0.003
AAMOE2D	0.002	0.001	0.003
AAMOE3D	0.002	0.000	0.002
AAMetaInfo	0.002	0.000	0.002
AAMolProp	0.002	0.001	0.002
AAPAM120	0.001	0.000	0.002
AAPAM250	0.002	0.000	0.002
AAPAM30	0.002	0.001	0.001
AAPAM40	0.002	0.001	0.002
AAPAM70	0.001	0.000	0.002
AARDF	0.002	0.000	0.002
AARandic	0.002	0.000	0.001
AATopo	0.001	0.000	0.002
AATopoChg	0.002	0.001	0.002
AAWHIM	0.002	0.000	0.002
AAWalk	0.002	0.000	0.003
AAindex	0.002	0.000	0.001
OptAA3d	0.001	0.000	0.001
Rcpi-package	0.001	0.000	0.001
acc	0.021	0.009	0.031
calcDrugFPSim	0.000	0.000	0.001
calcDrugMCSSim	0.001	0.000	0.000
calcParProtGOSim	0.001	0.000	0.001
calcParProtSeqSim	0.001	0.000	0.000
calcTwoProtGOSim	0	0	0
calcTwoProtSeqSim	0.000	0.000	0.001
checkProt	0.003	0.001	0.004
convMolFormat	0	0	0
extractDrugAIO	0.001	0.000	0.000
extractDrugALOGP	0	0	0
extractDrugAminoAcidCount	0	0	0
extractDrugApol	0.001	0.001	0.000
extractDrugAromaticAtomsCount	0	0	0
extractDrugAromaticBondsCount	0	0	0
extractDrugAtomCount	0.001	0.000	0.000
extractDrugAutocorrelationCharge	0.001	0.001	0.000
extractDrugAutocorrelationMass	0.001	0.000	0.001
extractDrugAutocorrelationPolarizability	0.001	0.000	0.001
extractDrugBCUT	0.001	0.000	0.001
extractDrugBPol	0.000	0.000	0.001
extractDrugBondCount	0.000	0.000	0.001
extractDrugCPSA	0.000	0.000	0.001
extractDrugCarbonTypes	0.001	0.000	0.001
extractDrugChiChain	0.001	0.000	0.000
extractDrugChiCluster	0.000	0.000	0.001
extractDrugChiPath	0.001	0.000	0.001
extractDrugChiPathCluster	0.001	0.000	0.001
extractDrugDescOB	0.001	0.000	0.001
extractDrugECI	0.001	0.000	0.001
extractDrugEstate	0.001	0.000	0.001
extractDrugEstateComplete	0.001	0.000	0.001
extractDrugExtended	0.001	0.000	0.001
extractDrugExtendedComplete	0.001	0.000	0.001
extractDrugFMF	0	0	0
extractDrugFragmentComplexity	0.000	0.000	0.001
extractDrugGraph	0.001	0.000	0.000
extractDrugGraphComplete	0.001	0.000	0.000
extractDrugGravitationalIndex	0.001	0.000	0.000
extractDrugHBondAcceptorCount	0.001	0.000	0.001
extractDrugHBondDonorCount	0.001	0.000	0.000
extractDrugHybridization	0	0	0
extractDrugHybridizationComplete	0.001	0.000	0.000
extractDrugHybridizationRatio	0.000	0.000	0.001
extractDrugIPMolecularLearning	0.000	0.000	0.001
extractDrugKR	0.000	0.001	0.000
extractDrugKRComplete	0.001	0.000	0.001
extractDrugKappaShapeIndices	0.001	0.000	0.001
extractDrugKierHallSmarts	0.001	0.000	0.001
extractDrugLargestChain	0.000	0.000	0.001
extractDrugLargestPiSystem	0.000	0.001	0.000
extractDrugLengthOverBreadth	0.001	0.000	0.000
extractDrugLongestAliphaticChain	0.001	0.000	0.000
extractDrugMACCS	0	0	0
extractDrugMACCSComplete	0.001	0.000	0.000
extractDrugMDE	0.001	0.000	0.001
extractDrugMannholdLogP	0.000	0.000	0.001
extractDrugMomentOfInertia	0	0	0
extractDrugOBFP2	0.001	0.000	0.000
extractDrugOBFP3	0	0	0
extractDrugOBFP4	0.000	0.001	0.001
extractDrugOBMACCS	0.001	0.000	0.000
extractDrugPetitjeanNumber	0.001	0.000	0.001
extractDrugPetitjeanShapeIndex	0.000	0.000	0.001
extractDrugPubChem	0.000	0.001	0.001
extractDrugPubChemComplete	0.001	0.000	0.001
extractDrugRotatableBondsCount	0.001	0.000	0.001
extractDrugRuleOfFive	0.001	0.000	0.000
extractDrugShortestPath	0.001	0.000	0.001
extractDrugShortestPathComplete	0.001	0.000	0.000
extractDrugStandard	0	0	0
extractDrugStandardComplete	0	0	0
extractDrugTPSA	0.000	0.000	0.001
extractDrugVABC	0	0	0
extractDrugVAdjMa	0.000	0.001	0.001
extractDrugWHIM	0.001	0.000	0.001
extractDrugWeight	0.001	0.000	0.000
extractDrugWeightedPath	0.001	0.000	0.001
extractDrugWienerNumbers	0.001	0.001	0.001
extractDrugXLogP	0.001	0.000	0.001
extractDrugZagrebIndex	0	0	0
extractPCMBLOSUM	0.024	0.005	0.030
extractPCMDescScales	0.018	0.001	0.018
extractPCMFAScales	0.025	0.006	0.031
extractPCMMDSScales	0.021	0.003	0.024
extractPCMPropScales	0.018	0.001	0.020
extractPCMScales	0.033	0.003	0.036
extractProtAAC	0.003	0.000	0.004
extractProtAPAAC	3.465	0.075	3.544
extractProtCTDC	0.007	0.000	0.007
extractProtCTDD	0.008	0.001	0.008
extractProtCTDT	0.009	0.001	0.010
extractProtCTriad	0.239	0.006	0.244
extractProtDC	0.005	0.003	0.008
extractProtGeary	0.228	0.006	0.233
extractProtMoran	0.235	0.008	0.235
extractProtMoreauBroto	0.207	0.005	0.214
extractProtPAAC	1.065	0.004	1.071
extractProtPSSM	0.001	0.000	0.001
extractProtPSSMAcc	0.001	0.000	0.001
extractProtPSSMFeature	0.000	0.000	0.001
extractProtQSO	1.781	0.022	1.804
extractProtSOCN	1.728	0.016	1.747
extractProtTC	0.067	0.059	0.126
getCPI	0.003	0.000	0.004
getDrug	0	0	0
getFASTAFromKEGG	0.001	0.000	0.001
getFASTAFromUniProt	0.000	0.000	0.001
getMolFromCAS	0	0	0
getMolFromChEMBL	0.001	0.000	0.000
getMolFromDrugBank	0.001	0.000	0.000
getMolFromKEGG	0.000	0.001	0.000
getMolFromPubChem	0.001	0.000	0.001
getPDBFromRCSBPDB	0.000	0.000	0.001
getPPI	0.003	0.001	0.005
getProt	0	0	0
getSeqFromKEGG	0.001	0.000	0.000
getSeqFromRCSBPDB	0.000	0.000	0.001
getSeqFromUniProt	0.001	0.001	0.001
getSmiFromChEMBL	0.001	0.000	0.001
getSmiFromDrugBank	0.000	0.000	0.001
getSmiFromKEGG	0.000	0.001	0.001
getSmiFromPubChem	0.001	0.000	0.001
readFASTA	0.002	0.000	0.001
readMolFromSDF	0	0	0
readMolFromSmi	0.001	0.000	0.000
readPDB	1.700	0.047	1.755
searchDrug	0.000	0.000	0.001
segProt	0.004	0.001	0.005