BioC 3.2: CHECK report for Rcpi on oaxaca

Package: Rcpi

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.6.0.tar.gz

StartedAt: 2015-10-27 07:03:49 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:07:04 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 195.5 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_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Rcpi.Rcheck’
* using R version 3.2.2 (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 ‘1.6.0’
* 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 ... [18s/19s] 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’ [9s/9s]
 [9s/9s] 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	0.003
AA3DMoRSE	0.001	0.000	0.002
AAACF	0.002	0.001	0.002
AABLOSUM100	0.002	0.000	0.002
AABLOSUM45	0.001	0.001	0.001
AABLOSUM50	0.001	0.000	0.002
AABLOSUM62	0.001	0.001	0.002
AABLOSUM80	0.002	0.000	0.002
AABurden	0.001	0.000	0.001
AACPSA	0.001	0.000	0.002
AAConn	0.001	0.000	0.001
AAConst	0.001	0.000	0.001
AADescAll	0.001	0.000	0.002
AAEdgeAdj	0.002	0.000	0.002
AAEigIdx	0.002	0.001	0.002
AAFGC	0.002	0.000	0.002
AAGETAWAY	0.001	0.001	0.002
AAGeom	0.001	0.000	0.001
AAInfo	0.001	0.000	0.001
AAMOE2D	0.001	0.001	0.002
AAMOE3D	0.001	0.000	0.001
AAMetaInfo	0.001	0.000	0.001
AAMolProp	0.001	0.000	0.001
AAPAM120	0.001	0.000	0.001
AAPAM250	0.002	0.000	0.002
AAPAM30	0.001	0.001	0.001
AAPAM40	0.001	0.000	0.001
AAPAM70	0.001	0.000	0.001
AARDF	0.001	0.000	0.001
AARandic	0.002	0.000	0.001
AATopo	0.002	0.000	0.001
AATopoChg	0.001	0.000	0.001
AAWHIM	0.002	0.000	0.002
AAWalk	0.002	0.000	0.002
AAindex	0.001	0.001	0.002
OptAA3d	0.000	0.000	0.001
Rcpi-package	0.001	0.000	0.001
acc	0.014	0.003	0.017
calcDrugFPSim	0.000	0.000	0.001
calcDrugMCSSim	0.001	0.000	0.001
calcParProtGOSim	0	0	0
calcParProtSeqSim	0.000	0.000	0.001
calcTwoProtGOSim	0	0	0
calcTwoProtSeqSim	0.001	0.000	0.000
checkProt	0.003	0.000	0.003
convMolFormat	0	0	0
extractDrugAIO	0	0	0
extractDrugALOGP	0	0	0
extractDrugAminoAcidCount	0.000	0.000	0.001
extractDrugApol	0.001	0.000	0.000
extractDrugAromaticAtomsCount	0.000	0.000	0.001
extractDrugAromaticBondsCount	0	0	0
extractDrugAtomCount	0	0	0
extractDrugAutocorrelationCharge	0.000	0.000	0.001
extractDrugAutocorrelationMass	0.000	0.000	0.001
extractDrugAutocorrelationPolarizability	0.000	0.000	0.001
extractDrugBCUT	0	0	0
extractDrugBPol	0	0	0
extractDrugBondCount	0.001	0.000	0.000
extractDrugCPSA	0.001	0.000	0.000
extractDrugCarbonTypes	0.001	0.000	0.000
extractDrugChiChain	0.001	0.000	0.001
extractDrugChiCluster	0	0	0
extractDrugChiPath	0.000	0.000	0.001
extractDrugChiPathCluster	0	0	0
extractDrugDescOB	0.001	0.000	0.000
extractDrugECI	0.001	0.000	0.001
extractDrugEstate	0.001	0.000	0.001
extractDrugEstateComplete	0.000	0.001	0.000
extractDrugExtended	0	0	0
extractDrugExtendedComplete	0.000	0.000	0.001
extractDrugFMF	0	0	0
extractDrugFragmentComplexity	0.001	0.000	0.001
extractDrugGraph	0.001	0.000	0.001
extractDrugGraphComplete	0.000	0.000	0.001
extractDrugGravitationalIndex	0.000	0.000	0.001
extractDrugHBondAcceptorCount	0.000	0.000	0.001
extractDrugHBondDonorCount	0.000	0.000	0.001
extractDrugHybridization	0.001	0.000	0.000
extractDrugHybridizationComplete	0.000	0.000	0.001
extractDrugHybridizationRatio	0	0	0
extractDrugIPMolecularLearning	0.001	0.000	0.000
extractDrugKR	0	0	0
extractDrugKRComplete	0	0	0
extractDrugKappaShapeIndices	0	0	0
extractDrugKierHallSmarts	0.001	0.000	0.001
extractDrugLargestChain	0.001	0.000	0.001
extractDrugLargestPiSystem	0.000	0.001	0.001
extractDrugLengthOverBreadth	0	0	0
extractDrugLongestAliphaticChain	0.001	0.000	0.000
extractDrugMACCS	0	0	0
extractDrugMACCSComplete	0.000	0.001	0.001
extractDrugMDE	0.000	0.000	0.001
extractDrugMannholdLogP	0.000	0.000	0.001
extractDrugMomentOfInertia	0.000	0.001	0.001
extractDrugOBFP2	0.001	0.000	0.000
extractDrugOBFP3	0.000	0.000	0.001
extractDrugOBFP4	0	0	0
extractDrugOBMACCS	0	0	0
extractDrugPetitjeanNumber	0.001	0.000	0.000
extractDrugPetitjeanShapeIndex	0.001	0.000	0.000
extractDrugPubChem	0.001	0.000	0.000
extractDrugPubChemComplete	0.000	0.000	0.001
extractDrugRotatableBondsCount	0.000	0.000	0.001
extractDrugRuleOfFive	0.001	0.000	0.000
extractDrugShortestPath	0.000	0.000	0.001
extractDrugShortestPathComplete	0	0	0
extractDrugStandard	0	0	0
extractDrugStandardComplete	0.001	0.000	0.000
extractDrugTPSA	0.001	0.000	0.001
extractDrugVABC	0.000	0.000	0.001
extractDrugVAdjMa	0	0	0
extractDrugWHIM	0.001	0.000	0.001
extractDrugWeight	0.001	0.000	0.000
extractDrugWeightedPath	0	0	0
extractDrugWienerNumbers	0	0	0
extractDrugXLogP	0.001	0.000	0.000
extractDrugZagrebIndex	0.001	0.000	0.001
extractPCMBLOSUM	0.023	0.003	0.025
extractPCMDescScales	0.018	0.000	0.019
extractPCMFAScales	0.026	0.002	0.028
extractPCMMDSScales	0.020	0.001	0.021
extractPCMPropScales	0.018	0.001	0.018
extractPCMScales	0.019	0.001	0.020
extractProtAAC	0.004	0.001	0.004
extractProtAPAAC	1.961	0.023	1.984
extractProtCTDC	0.004	0.000	0.005
extractProtCTDD	0.004	0.001	0.005
extractProtCTDT	0.006	0.001	0.005
extractProtCTriad	0.186	0.003	0.190
extractProtDC	0.005	0.003	0.008
extractProtGeary	0.179	0.003	0.182
extractProtMoran	0.158	0.004	0.162
extractProtMoreauBroto	0.152	0.003	0.155
extractProtPAAC	0.814	0.002	0.815
extractProtPSSM	0	0	0
extractProtPSSMAcc	0	0	0
extractProtPSSMFeature	0.000	0.000	0.001
extractProtQSO	1.321	0.008	1.322
extractProtSOCN	1.760	0.008	1.768
extractProtTC	0.057	0.045	0.104
getCPI	0.004	0.000	0.006
getDrug	0.001	0.000	0.001
getFASTAFromKEGG	0.001	0.000	0.001
getFASTAFromUniProt	0.001	0.000	0.000
getMolFromCAS	0.001	0.000	0.001
getMolFromChEMBL	0.001	0.000	0.000
getMolFromDrugBank	0.000	0.001	0.001
getMolFromKEGG	0	0	0
getMolFromPubChem	0.000	0.000	0.001
getPDBFromRCSBPDB	0.000	0.000	0.001
getPPI	0.005	0.001	0.006
getProt	0.000	0.000	0.001
getSeqFromKEGG	0	0	0
getSeqFromRCSBPDB	0	0	0
getSeqFromUniProt	0.001	0.000	0.000
getSmiFromChEMBL	0.001	0.000	0.001
getSmiFromDrugBank	0.001	0.000	0.001
getSmiFromKEGG	0.001	0.000	0.000
getSmiFromPubChem	0.001	0.000	0.000
readFASTA	0.002	0.000	0.002
readMolFromSDF	0.001	0.001	0.000
readMolFromSmi	0.001	0.000	0.001
readPDB	1.259	0.014	1.273
searchDrug	0.001	0.000	0.000
segProt	0.004	0.001	0.004