BioC 3.5: CHECK report for Rcpi on oaxaca

Package: Rcpi

Version: 1.11.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.11.6.tar.gz

StartedAt: 2017-03-04 07:50:20 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 07:53:01 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 160.7 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_1.11.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Rcpi.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.11.6’
* 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 ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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	0.003
AA3DMoRSE	0.002	0.001	0.002
AAACF	0.002	0.001	0.002
AABLOSUM100	0.001	0.000	0.002
AABLOSUM45	0.001	0.000	0.003
AABLOSUM50	0.001	0.000	0.002
AABLOSUM62	0.002	0.000	0.003
AABLOSUM80	0.002	0.000	0.002
AABurden	0.002	0.001	0.002
AACPSA	0.002	0.001	0.002
AAConn	0.002	0.001	0.002
AAConst	0.001	0.001	0.002
AADescAll	0.002	0.000	0.002
AAEdgeAdj	0.001	0.001	0.001
AAEigIdx	0.002	0.001	0.003
AAFGC	0.002	0.001	0.002
AAGETAWAY	0.002	0.001	0.002
AAGeom	0.002	0.001	0.003
AAInfo	0.001	0.000	0.002
AAMOE2D	0.001	0.001	0.003
AAMOE3D	0.001	0.001	0.001
AAMetaInfo	0.001	0.001	0.002
AAMolProp	0.001	0.000	0.001
AAPAM120	0.002	0.001	0.003
AAPAM250	0.002	0.001	0.003
AAPAM30	0.002	0.000	0.002
AAPAM40	0.002	0.001	0.003
AAPAM70	0.002	0.001	0.002
AARDF	0.001	0.000	0.002
AARandic	0.002	0.000	0.003
AATopo	0.002	0.000	0.003
AATopoChg	0.002	0.001	0.003
AAWHIM	0.001	0.001	0.002
AAWalk	0.002	0.001	0.002
AAindex	0.002	0.000	0.003
OptAA3d	0.001	0.000	0.001
acc	0.018	0.006	0.024
calcDrugFPSim	2.114	0.116	2.642
calcDrugMCSSim	0.010	0.001	0.012
calcParProtGOSim	0.001	0.000	0.001
calcParProtSeqSim	0.037	0.001	0.038
calcTwoProtGOSim	0.001	0.000	0.001
calcTwoProtSeqSim	0.003	0.001	0.003
checkProt	0.002	0.000	0.002
convMolFormat	0.001	0.001	0.001
extractDrugAIO	0.001	0.000	0.002
extractDrugALOGP	0.001	0.000	0.001
extractDrugAminoAcidCount	0.001	0.001	0.002
extractDrugApol	0.001	0.000	0.001
extractDrugAromaticAtomsCount	0.001	0.000	0.002
extractDrugAromaticBondsCount	0.001	0.000	0.001
extractDrugAtomCount	0.001	0.000	0.002
extractDrugAutocorrelationCharge	0.001	0.000	0.001
extractDrugAutocorrelationMass	0.001	0.000	0.001
extractDrugAutocorrelationPolarizability	0.001	0.000	0.001
extractDrugBCUT	0.001	0.000	0.001
extractDrugBPol	0.001	0.000	0.001
extractDrugBondCount	0.001	0.001	0.001
extractDrugCPSA	0.001	0.000	0.001
extractDrugCarbonTypes	0.001	0.000	0.001
extractDrugChiChain	0.001	0.000	0.001
extractDrugChiCluster	0.000	0.001	0.001
extractDrugChiPath	0.001	0.000	0.001
extractDrugChiPathCluster	0.001	0.000	0.001
extractDrugDescOB	0.012	0.002	0.014
extractDrugECI	0.001	0.000	0.001
extractDrugEstate	0.001	0.000	0.001
extractDrugEstateComplete	0.001	0.000	0.001
extractDrugExtended	0.002	0.000	0.002
extractDrugExtendedComplete	0.000	0.000	0.001
extractDrugFMF	0.001	0.000	0.000
extractDrugFragmentComplexity	0.000	0.000	0.001
extractDrugGraph	0.001	0.001	0.001
extractDrugGraphComplete	0	0	0
extractDrugGravitationalIndex	0.001	0.000	0.001
extractDrugHBondAcceptorCount	0.001	0.000	0.001
extractDrugHBondDonorCount	0.001	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	0.001	0.000	0.002
extractDrugKR	0.002	0.000	0.001
extractDrugKRComplete	0.001	0.000	0.001
extractDrugKappaShapeIndices	0.001	0.000	0.001
extractDrugKierHallSmarts	0.001	0.000	0.002
extractDrugLargestChain	0.001	0.000	0.001
extractDrugLargestPiSystem	0.002	0.000	0.001
extractDrugLengthOverBreadth	0.001	0.000	0.002
extractDrugLongestAliphaticChain	0.001	0.000	0.001
extractDrugMACCS	0.001	0.000	0.001
extractDrugMACCSComplete	0.001	0.000	0.001
extractDrugMDE	0.001	0.000	0.002
extractDrugMannholdLogP	0.001	0.000	0.001
extractDrugMomentOfInertia	0.001	0.000	0.001
extractDrugOBFP2	0.011	0.000	0.011
extractDrugOBFP3	0.012	0.001	0.012
extractDrugOBFP4	0.011	0.001	0.012
extractDrugOBMACCS	0.011	0.000	0.012
extractDrugPetitjeanNumber	0.002	0.001	0.002
extractDrugPetitjeanShapeIndex	0.001	0.000	0.002
extractDrugPubChem	0.002	0.000	0.001
extractDrugPubChemComplete	0.001	0.001	0.001
extractDrugRotatableBondsCount	0.002	0.000	0.001
extractDrugRuleOfFive	0.001	0.000	0.001
extractDrugShortestPath	0.001	0.000	0.001
extractDrugShortestPathComplete	0.001	0.000	0.002
extractDrugStandard	0.001	0.000	0.002
extractDrugStandardComplete	0.001	0.000	0.002
extractDrugTPSA	0.001	0.000	0.001
extractDrugVABC	0.001	0.001	0.001
extractDrugVAdjMa	0.001	0.000	0.001
extractDrugWHIM	0.001	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	0.002	0.000	0.001
extractDrugZagrebIndex	0.001	0.000	0.001
extractPCMBLOSUM	0.063	0.001	0.064
extractPCMDescScales	0.010	0.001	0.011
extractPCMFAScales	0.204	0.004	0.207
extractPCMMDSScales	0.016	0.003	0.018
extractPCMPropScales	0.044	0.002	0.047
extractPCMScales	0.016	0.002	0.018
extractProtAAC	0.002	0.000	0.002
extractProtAPAAC	0.895	0.020	0.914
extractProtCTDC	0.002	0.000	0.003
extractProtCTDD	0.005	0.001	0.005
extractProtCTDT	0.007	0.000	0.007
extractProtCTriad	0.118	0.009	0.127
extractProtDC	0.005	0.002	0.007
extractProtGeary	0.267	0.003	0.270
extractProtMoran	0.309	0.007	0.316
extractProtMoreauBroto	0.199	0.004	0.202
extractProtPAAC	0.893	0.021	0.914
extractProtPSSM	0.002	0.000	0.002
extractProtPSSMAcc	0.002	0.001	0.002
extractProtPSSMFeature	0.002	0.000	0.002
extractProtQSO	1.346	0.015	1.362
extractProtSOCN	1.376	0.010	1.385
extractProtTC	0.059	0.047	0.106
getCPI	0.002	0.000	0.003
getDrug	0	0	0
getFASTAFromKEGG	0	0	0
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	0.000	0.000	0.001
getPDBFromRCSBPDB	0.001	0.000	0.000
getPPI	0.003	0.001	0.004
getProt	0.000	0.000	0.001
getSeqFromKEGG	0.001	0.000	0.001
getSeqFromRCSBPDB	0.000	0.001	0.001
getSeqFromUniProt	0.000	0.000	0.001
getSmiFromChEMBL	0.001	0.000	0.001
getSmiFromDrugBank	0.001	0.000	0.001
getSmiFromKEGG	0.001	0.001	0.001
getSmiFromPubChem	0.001	0.000	0.000
readFASTA	0.002	0.000	0.001
readMolFromSDF	0.001	0.000	0.002
readMolFromSmi	0.001	0.000	0.001
readPDB	1.154	0.006	1.160
searchDrug	0.002	0.000	0.002
segProt	0.003	0.001	0.004