BioC 3.5: CHECK report for Rcpi on malbec2

Package: Rcpi

Version: 1.12.4

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Rcpi_1.12.4.tar.gz

StartedAt: 2017-08-16 01:40:19 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:42:27 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 128.0 seconds

RetCode: 0

Status:  OK

CheckDir: Rcpi.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Rcpi_1.12.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/Rcpi.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.12.4’
* package encoding: UTF-8
* 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 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	0.004	0.008	0.014
AA3DMoRSE	0.000	0.000	0.001
AAACF	0.004	0.000	0.001
AABLOSUM100	0.000	0.000	0.001
AABLOSUM45	0.004	0.000	0.001
AABLOSUM50	0.000	0.000	0.001
AABLOSUM62	0.000	0.000	0.001
AABLOSUM80	0.000	0.000	0.001
AABurden	0.000	0.000	0.001
AACPSA	0.000	0.000	0.002
AAConn	0.000	0.000	0.001
AAConst	0.000	0.004	0.001
AADescAll	0.000	0.000	0.001
AAEdgeAdj	0.004	0.000	0.001
AAEigIdx	0.000	0.000	0.001
AAFGC	0.000	0.000	0.001
AAGETAWAY	0.000	0.000	0.001
AAGeom	0.000	0.000	0.001
AAInfo	0.000	0.000	0.001
AAMOE2D	0.000	0.000	0.001
AAMOE3D	0.000	0.000	0.001
AAMetaInfo	0.000	0.000	0.001
AAMolProp	0.004	0.000	0.001
AAPAM120	0.000	0.000	0.001
AAPAM250	0.004	0.000	0.001
AAPAM30	0.000	0.000	0.001
AAPAM40	0.004	0.000	0.001
AAPAM70	0.000	0.000	0.002
AARDF	0.004	0.000	0.001
AARandic	0.000	0.000	0.001
AATopo	0.000	0.000	0.001
AATopoChg	0.000	0.000	0.001
AAWHIM	0.000	0.000	0.001
AAWalk	0.000	0.000	0.001
AAindex	0.000	0.000	0.001
OptAA3d	0	0	0
acc	0.008	0.000	0.010
calcDrugFPSim	1.964	0.088	0.814
calcDrugMCSSim	0.024	0.000	0.021
calcParProtGOSim	0.000	0.000	0.001
calcParProtSeqSim	0.032	0.000	0.033
calcTwoProtGOSim	0.000	0.000	0.001
calcTwoProtSeqSim	0.000	0.000	0.002
checkProt	0.004	0.000	0.001
convMolFormat	0.000	0.000	0.001
extractDrugAIO	0.000	0.000	0.001
extractDrugALOGP	0	0	0
extractDrugAminoAcidCount	0.000	0.000	0.001
extractDrugApol	0	0	0
extractDrugAromaticAtomsCount	0	0	0
extractDrugAromaticBondsCount	0.000	0.000	0.001
extractDrugAtomCount	0.004	0.000	0.001
extractDrugAutocorrelationCharge	0	0	0
extractDrugAutocorrelationMass	0.000	0.000	0.001
extractDrugAutocorrelationPolarizability	0	0	0
extractDrugBCUT	0.000	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	0.004	0.000	0.001
extractDrugChiChain	0.000	0.000	0.001
extractDrugChiCluster	0.000	0.000	0.001
extractDrugChiPath	0	0	0
extractDrugChiPathCluster	0.000	0.000	0.001
extractDrugDescOB	0.216	0.004	0.221
extractDrugECI	0.000	0.000	0.001
extractDrugEstate	0.000	0.000	0.001
extractDrugEstateComplete	0.000	0.000	0.001
extractDrugExtended	0.004	0.000	0.000
extractDrugExtendedComplete	0.000	0.000	0.001
extractDrugFMF	0	0	0
extractDrugFragmentComplexity	0.000	0.000	0.001
extractDrugGraph	0.000	0.000	0.001
extractDrugGraphComplete	0.000	0.000	0.001
extractDrugGravitationalIndex	0	0	0
extractDrugHBondAcceptorCount	0.000	0.000	0.001
extractDrugHBondDonorCount	0.000	0.000	0.001
extractDrugHybridization	0	0	0
extractDrugHybridizationComplete	0.000	0.000	0.001
extractDrugHybridizationRatio	0.004	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	0	0
extractDrugLargestPiSystem	0.000	0.000	0.001
extractDrugLengthOverBreadth	0.004	0.000	0.002
extractDrugLongestAliphaticChain	0.000	0.000	0.001
extractDrugMACCS	0	0	0
extractDrugMACCSComplete	0.004	0.000	0.001
extractDrugMDE	0.000	0.000	0.001
extractDrugMannholdLogP	0	0	0
extractDrugMomentOfInertia	0.004	0.000	0.001
extractDrugOBFP2	0.008	0.000	0.008
extractDrugOBFP3	0.004	0.004	0.008
extractDrugOBFP4	0.004	0.004	0.005
extractDrugOBMACCS	0.004	0.004	0.009
extractDrugPetitjeanNumber	0.004	0.000	0.000
extractDrugPetitjeanShapeIndex	0.000	0.000	0.001
extractDrugPubChem	0.004	0.000	0.002
extractDrugPubChemComplete	0	0	0
extractDrugRotatableBondsCount	0.000	0.000	0.001
extractDrugRuleOfFive	0.004	0.000	0.000
extractDrugShortestPath	0.000	0.000	0.001
extractDrugShortestPathComplete	0.000	0.000	0.001
extractDrugStandard	0.004	0.000	0.000
extractDrugStandardComplete	0.000	0.000	0.001
extractDrugTPSA	0.004	0.000	0.002
extractDrugVABC	0.000	0.000	0.001
extractDrugVAdjMa	0.000	0.000	0.001
extractDrugWHIM	0.004	0.000	0.000
extractDrugWeight	0.000	0.000	0.001
extractDrugWeightedPath	0.000	0.000	0.001
extractDrugWienerNumbers	0.004	0.000	0.000
extractDrugXLogP	0.000	0.000	0.001
extractDrugZagrebIndex	0.004	0.000	0.002
extractPCMBLOSUM	0.04	0.00	0.04
extractPCMDescScales	0.012	0.000	0.013
extractPCMFAScales	0.012	0.004	0.014
extractPCMMDSScales	0.008	0.000	0.008
extractPCMPropScales	0.024	0.000	0.021
extractPCMScales	0.012	0.000	0.014
extractProtAAC	0.004	0.000	0.003
extractProtAPAAC	0.844	0.032	0.874
extractProtCTDC	0.004	0.000	0.003
extractProtCTDD	0.004	0.000	0.004
extractProtCTDT	0.004	0.000	0.005
extractProtCTriad	0.08	0.00	0.08
extractProtDC	0.004	0.000	0.004
extractProtGeary	0.156	0.004	0.158
extractProtMoran	0.156	0.000	0.158
extractProtMoreauBroto	0.136	0.004	0.144
extractProtPAAC	0.440	0.000	0.442
extractProtPSSM	0.004	0.000	0.001
extractProtPSSMAcc	0.000	0.000	0.001
extractProtPSSMFeature	0.004	0.000	0.001
extractProtQSO	0.800	0.000	0.799
extractProtSOCN	0.792	0.004	0.796
extractProtTC	0.024	0.016	0.041
getCPI	0.000	0.000	0.002
getDrug	0.004	0.000	0.000
getFASTAFromKEGG	0.000	0.000	0.001
getFASTAFromUniProt	0.000	0.000	0.001
getMolFromCAS	0.000	0.000	0.001
getMolFromChEMBL	0.004	0.000	0.001
getMolFromDrugBank	0.000	0.000	0.001
getMolFromKEGG	0.000	0.000	0.001
getMolFromPubChem	0.000	0.000	0.001
getPDBFromRCSBPDB	0	0	0
getPPI	0.004	0.000	0.002
getProt	0.000	0.000	0.001
getSeqFromKEGG	0.000	0.000	0.001
getSeqFromRCSBPDB	0.000	0.000	0.001
getSeqFromUniProt	0.000	0.000	0.001
getSmiFromChEMBL	0	0	0
getSmiFromDrugBank	0	0	0
getSmiFromKEGG	0	0	0
getSmiFromPubChem	0	0	0
readFASTA	0.000	0.000	0.001
readMolFromSDF	0.004	0.000	0.002
readMolFromSmi	0	0	0
readPDB	0.964	0.000	0.964
searchDrug	0.000	0.000	0.001
segProt	0.004	0.000	0.002