BioC 3.2: CHECK report for Rcpi on oaxaca

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 03:09:40 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:13:17 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 217.4 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 (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 ‘1.5.0’
* 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 ... [17s/27s] 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 ... [18s/18s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [9s/9s]
 [9s/10s] 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	0.000	0.003
AA3DMoRSE	0.002	0.001	0.002
AAACF	0.001	0.000	0.002
AABLOSUM100	0.001	0.001	0.002
AABLOSUM45	0.001	0.000	0.002
AABLOSUM50	0.001	0.001	0.003
AABLOSUM62	0.002	0.000	0.002
AABLOSUM80	0.002	0.001	0.002
AABurden	0.002	0.000	0.003
AACPSA	0.002	0.001	0.003
AAConn	0.001	0.000	0.002
AAConst	0.002	0.000	0.002
AADescAll	0.002	0.000	0.002
AAEdgeAdj	0.001	0.000	0.002
AAEigIdx	0.002	0.001	0.002
AAFGC	0.001	0.000	0.002
AAGETAWAY	0.002	0.001	0.003
AAGeom	0.002	0.000	0.002
AAInfo	0.002	0.001	0.003
AAMOE2D	0.002	0.000	0.002
AAMOE3D	0.001	0.000	0.002
AAMetaInfo	0.001	0.000	0.002
AAMolProp	0.002	0.000	0.002
AAPAM120	0.002	0.000	0.002
AAPAM250	0.002	0.000	0.002
AAPAM30	0.002	0.001	0.002
AAPAM40	0.002	0.000	0.002
AAPAM70	0.001	0.001	0.002
AARDF	0.002	0.000	0.002
AARandic	0.002	0.001	0.002
AATopo	0.002	0.000	0.002
AATopoChg	0.002	0.001	0.002
AAWHIM	0.002	0.000	0.002
AAWalk	0.002	0.001	0.002
AAindex	0.002	0.000	0.002
OptAA3d	0.001	0.001	0.001
Rcpi-package	0.001	0.000	0.000
acc	0.017	0.004	0.021
calcDrugFPSim	0	0	0
calcDrugMCSSim	0	0	0
calcParProtGOSim	0	0	0
calcParProtSeqSim	0.000	0.000	0.001
calcTwoProtGOSim	0.000	0.000	0.001
calcTwoProtSeqSim	0.001	0.000	0.000
checkProt	0.004	0.000	0.003
convMolFormat	0.000	0.000	0.001
extractDrugAIO	0.000	0.000	0.001
extractDrugALOGP	0.000	0.000	0.001
extractDrugAminoAcidCount	0.000	0.000	0.001
extractDrugApol	0.001	0.000	0.000
extractDrugAromaticAtomsCount	0.001	0.000	0.000
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	0.001	0.000	0.000
extractDrugBPol	0.001	0.000	0.000
extractDrugBondCount	0.001	0.000	0.001
extractDrugCPSA	0.001	0.001	0.001
extractDrugCarbonTypes	0.001	0.000	0.000
extractDrugChiChain	0	0	0
extractDrugChiCluster	0	0	0
extractDrugChiPath	0.000	0.000	0.001
extractDrugChiPathCluster	0.000	0.000	0.001
extractDrugDescOB	0	0	0
extractDrugECI	0	0	0
extractDrugEstate	0.001	0.000	0.001
extractDrugEstateComplete	0.001	0.000	0.001
extractDrugExtended	0.001	0.000	0.001
extractDrugExtendedComplete	0.001	0.001	0.000
extractDrugFMF	0.001	0.000	0.000
extractDrugFragmentComplexity	0.000	0.000	0.001
extractDrugGraph	0.000	0.000	0.001
extractDrugGraphComplete	0.000	0.000	0.001
extractDrugGravitationalIndex	0.000	0.000	0.001
extractDrugHBondAcceptorCount	0	0	0
extractDrugHBondDonorCount	0.000	0.001	0.001
extractDrugHybridization	0.000	0.000	0.001
extractDrugHybridizationComplete	0.001	0.000	0.000
extractDrugHybridizationRatio	0.000	0.000	0.001
extractDrugIPMolecularLearning	0	0	0
extractDrugKR	0.000	0.000	0.001
extractDrugKRComplete	0.000	0.000	0.001
extractDrugKappaShapeIndices	0	0	0
extractDrugKierHallSmarts	0.000	0.000	0.001
extractDrugLargestChain	0.000	0.000	0.001
extractDrugLargestPiSystem	0.000	0.001	0.001
extractDrugLengthOverBreadth	0	0	0
extractDrugLongestAliphaticChain	0	0	0
extractDrugMACCS	0.000	0.000	0.001
extractDrugMACCSComplete	0	0	0
extractDrugMDE	0	0	0
extractDrugMannholdLogP	0.000	0.000	0.001
extractDrugMomentOfInertia	0.000	0.000	0.001
extractDrugOBFP2	0	0	0
extractDrugOBFP3	0	0	0
extractDrugOBFP4	0.001	0.000	0.001
extractDrugOBMACCS	0.001	0.001	0.001
extractDrugPetitjeanNumber	0.001	0.000	0.001
extractDrugPetitjeanShapeIndex	0.001	0.000	0.000
extractDrugPubChem	0.001	0.000	0.001
extractDrugPubChemComplete	0.001	0.000	0.001
extractDrugRotatableBondsCount	0.001	0.000	0.000
extractDrugRuleOfFive	0.001	0.000	0.000
extractDrugShortestPath	0.001	0.000	0.001
extractDrugShortestPathComplete	0.001	0.000	0.001
extractDrugStandard	0.000	0.000	0.001
extractDrugStandardComplete	0	0	0
extractDrugTPSA	0.000	0.001	0.000
extractDrugVABC	0	0	0
extractDrugVAdjMa	0.001	0.000	0.001
extractDrugWHIM	0.001	0.000	0.001
extractDrugWeight	0.001	0.000	0.001
extractDrugWeightedPath	0.000	0.000	0.001
extractDrugWienerNumbers	0.000	0.000	0.001
extractDrugXLogP	0	0	0
extractDrugZagrebIndex	0	0	0
extractPCMBLOSUM	0.016	0.002	0.019
extractPCMDescScales	0.023	0.002	0.025
extractPCMFAScales	0.024	0.001	0.026
extractPCMMDSScales	0.020	0.002	0.022
extractPCMPropScales	0.019	0.000	0.019
extractPCMScales	0.032	0.002	0.034
extractProtAAC	0.003	0.001	0.004
extractProtAPAAC	2.851	0.036	2.891
extractProtCTDC	0.011	0.001	0.011
extractProtCTDD	0.007	0.001	0.008
extractProtCTDT	0.009	0.000	0.009
extractProtCTriad	0.261	0.003	0.264
extractProtDC	0.006	0.003	0.008
extractProtGeary	0.227	0.005	0.231
extractProtMoran	0.218	0.004	0.222
extractProtMoreauBroto	0.227	0.004	0.244
extractProtPAAC	0.982	0.003	0.985
extractProtPSSM	0.001	0.000	0.000
extractProtPSSMAcc	0.001	0.000	0.000
extractProtPSSMFeature	0.001	0.000	0.000
extractProtQSO	1.760	0.008	1.769
extractProtSOCN	1.810	0.008	1.840
extractProtTC	0.070	0.049	0.119
getCPI	0.004	0.001	0.004
getDrug	0	0	0
getFASTAFromKEGG	0.001	0.000	0.000
getFASTAFromUniProt	0.001	0.000	0.000
getMolFromCAS	0	0	0
getMolFromChEMBL	0	0	0
getMolFromDrugBank	0.001	0.000	0.000
getMolFromKEGG	0.001	0.000	0.000
getMolFromPubChem	0	0	0
getPDBFromRCSBPDB	0.000	0.000	0.001
getPPI	0.004	0.002	0.005
getProt	0	0	0
getSeqFromKEGG	0	0	0
getSeqFromRCSBPDB	0	0	0
getSeqFromUniProt	0.001	0.000	0.001
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	0.000	0.002
readMolFromSDF	0.000	0.000	0.001
readMolFromSmi	0.000	0.000	0.001
readPDB	1.596	0.016	1.617
searchDrug	0.001	0.000	0.001
segProt	0.003	0.001	0.004