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: 2016-04-23 03:36:41 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 03:39:52 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 190.3 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 3.2.4 (2016-03-10)
* 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/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 ... [17s/17s] 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	0.020	0.002	0.023
AA3DMoRSE	0.001	0.001	0.001
AAACF	0.002	0.001	0.003
AABLOSUM100	0.002	0.001	0.003
AABLOSUM45	0.002	0.001	0.002
AABLOSUM50	0.001	0.000	0.001
AABLOSUM62	0.002	0.001	0.002
AABLOSUM80	0.001	0.001	0.002
AABurden	0.001	0.001	0.003
AACPSA	0.002	0.000	0.003
AAConn	0.002	0.000	0.003
AAConst	0.002	0.000	0.002
AADescAll	0.002	0.000	0.002
AAEdgeAdj	0.002	0.001	0.003
AAEigIdx	0.001	0.000	0.003
AAFGC	0.001	0.001	0.002
AAGETAWAY	0.002	0.002	0.003
AAGeom	0.002	0.001	0.003
AAInfo	0.002	0.001	0.002
AAMOE2D	0.001	0.001	0.001
AAMOE3D	0.002	0.000	0.002
AAMetaInfo	0.002	0.000	0.002
AAMolProp	0.002	0.001	0.002
AAPAM120	0.002	0.001	0.002
AAPAM250	0.002	0.001	0.003
AAPAM30	0.002	0.001	0.003
AAPAM40	0.002	0.000	0.002
AAPAM70	0.001	0.001	0.001
AARDF	0.002	0.001	0.002
AARandic	0.001	0.000	0.002
AATopo	0.002	0.001	0.002
AATopoChg	0.002	0.001	0.002
AAWHIM	0.002	0.001	0.002
AAWalk	0.001	0.000	0.002
AAindex	0.002	0.001	0.003
OptAA3d	0.000	0.001	0.000
Rcpi-package	0.001	0.000	0.000
acc	0.014	0.004	0.017
calcDrugFPSim	0.001	0.000	0.000
calcDrugMCSSim	0.001	0.000	0.000
calcParProtGOSim	0.000	0.000	0.001
calcParProtSeqSim	0.001	0.000	0.000
calcTwoProtGOSim	0.001	0.000	0.000
calcTwoProtSeqSim	0.000	0.000	0.001
checkProt	0.004	0.001	0.004
convMolFormat	0.001	0.000	0.000
extractDrugAIO	0.001	0.000	0.001
extractDrugALOGP	0.001	0.000	0.001
extractDrugAminoAcidCount	0.001	0.000	0.000
extractDrugApol	0.001	0.000	0.000
extractDrugAromaticAtomsCount	0.000	0.001	0.001
extractDrugAromaticBondsCount	0.000	0.000	0.001
extractDrugAtomCount	0.000	0.000	0.001
extractDrugAutocorrelationCharge	0	0	0
extractDrugAutocorrelationMass	0.000	0.000	0.001
extractDrugAutocorrelationPolarizability	0.001	0.000	0.000
extractDrugBCUT	0	0	0
extractDrugBPol	0.000	0.000	0.001
extractDrugBondCount	0.001	0.000	0.001
extractDrugCPSA	0.001	0.000	0.000
extractDrugCarbonTypes	0	0	0
extractDrugChiChain	0.001	0.000	0.000
extractDrugChiCluster	0.001	0.001	0.001
extractDrugChiPath	0.001	0.000	0.001
extractDrugChiPathCluster	0.001	0.000	0.000
extractDrugDescOB	0.001	0.000	0.001
extractDrugECI	0.000	0.000	0.001
extractDrugEstate	0.000	0.000	0.001
extractDrugEstateComplete	0	0	0
extractDrugExtended	0	0	0
extractDrugExtendedComplete	0	0	0
extractDrugFMF	0.001	0.000	0.000
extractDrugFragmentComplexity	0.001	0.000	0.001
extractDrugGraph	0.001	0.000	0.000
extractDrugGraphComplete	0.001	0.000	0.000
extractDrugGravitationalIndex	0	0	0
extractDrugHBondAcceptorCount	0	0	0
extractDrugHBondDonorCount	0.000	0.000	0.001
extractDrugHybridization	0.001	0.000	0.001
extractDrugHybridizationComplete	0.001	0.000	0.001
extractDrugHybridizationRatio	0.001	0.000	0.001
extractDrugIPMolecularLearning	0.000	0.000	0.001
extractDrugKR	0	0	0
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	0.000	0.000	0.001
extractDrugLongestAliphaticChain	0.000	0.000	0.001
extractDrugMACCS	0.000	0.001	0.000
extractDrugMACCSComplete	0.001	0.000	0.000
extractDrugMDE	0.001	0.000	0.000
extractDrugMannholdLogP	0.001	0.000	0.000
extractDrugMomentOfInertia	0.000	0.000	0.001
extractDrugOBFP2	0.000	0.000	0.001
extractDrugOBFP3	0.000	0.000	0.001
extractDrugOBFP4	0.001	0.000	0.001
extractDrugOBMACCS	0.001	0.000	0.001
extractDrugPetitjeanNumber	0.001	0.000	0.001
extractDrugPetitjeanShapeIndex	0	0	0
extractDrugPubChem	0	0	0
extractDrugPubChemComplete	0	0	0
extractDrugRotatableBondsCount	0.000	0.000	0.001
extractDrugRuleOfFive	0.001	0.000	0.000
extractDrugShortestPath	0	0	0
extractDrugShortestPathComplete	0.000	0.000	0.001
extractDrugStandard	0.001	0.000	0.001
extractDrugStandardComplete	0	0	0
extractDrugTPSA	0.001	0.000	0.001
extractDrugVABC	0.001	0.000	0.001
extractDrugVAdjMa	0.000	0.000	0.001
extractDrugWHIM	0.000	0.000	0.001
extractDrugWeight	0.001	0.000	0.001
extractDrugWeightedPath	0.001	0.000	0.001
extractDrugWienerNumbers	0.001	0.000	0.001
extractDrugXLogP	0.000	0.001	0.000
extractDrugZagrebIndex	0	0	0
extractPCMBLOSUM	0.016	0.001	0.017
extractPCMDescScales	0.018	0.001	0.020
extractPCMFAScales	0.030	0.002	0.033
extractPCMMDSScales	0.015	0.002	0.018
extractPCMPropScales	0.017	0.002	0.019
extractPCMScales	0.031	0.003	0.034
extractProtAAC	0.003	0.000	0.004
extractProtAPAAC	2.504	0.026	2.532
extractProtCTDC	0.010	0.001	0.011
extractProtCTDD	0.007	0.001	0.007
extractProtCTDT	0.01	0.00	0.01
extractProtCTriad	0.251	0.006	0.260
extractProtDC	0.005	0.003	0.008
extractProtGeary	0.243	0.005	0.251
extractProtMoran	0.241	0.005	0.245
extractProtMoreauBroto	0.237	0.007	0.244
extractProtPAAC	0.975	0.004	0.988
extractProtPSSM	0.001	0.000	0.001
extractProtPSSMAcc	0.001	0.000	0.001
extractProtPSSMFeature	0.001	0.000	0.001
extractProtQSO	1.691	0.009	1.709
extractProtSOCN	1.776	0.007	1.811
extractProtTC	0.061	0.050	0.118
getCPI	0.004	0.001	0.004
getDrug	0.001	0.000	0.000
getFASTAFromKEGG	0.000	0.001	0.001
getFASTAFromUniProt	0.000	0.000	0.001
getMolFromCAS	0.001	0.000	0.001
getMolFromChEMBL	0.001	0.000	0.001
getMolFromDrugBank	0.001	0.000	0.001
getMolFromKEGG	0	0	0
getMolFromPubChem	0	0	0
getPDBFromRCSBPDB	0.000	0.001	0.000
getPPI	0.005	0.001	0.006
getProt	0.000	0.000	0.001
getSeqFromKEGG	0.000	0.000	0.001
getSeqFromRCSBPDB	0.000	0.000	0.001
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	0.001
getSmiFromPubChem	0	0	0
readFASTA	0.001	0.001	0.002
readMolFromSDF	0.000	0.000	0.001
readMolFromSmi	0.001	0.000	0.001
readPDB	1.597	0.017	1.648
searchDrug	0.001	0.000	0.001
segProt	0.004	0.001	0.005

BioC 3.2: CHECK report for Rcpi on oaxaca

Summary

Command output