BioC 3.5: CHECK report for Rcpi on veracruz2

Package: Rcpi

Version: 1.12.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.12.4.tar.gz

StartedAt: 2017-08-16 07:12:33 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 07:15:05 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 151.1 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_1.12.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Rcpi.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.12.4’
* 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	0.017	0.004	0.021
AA3DMoRSE	0.001	0.001	0.002
AAACF	0.002	0.001	0.002
AABLOSUM100	0.001	0.001	0.002
AABLOSUM45	0.001	0.001	0.002
AABLOSUM50	0.001	0.000	0.003
AABLOSUM62	0.002	0.000	0.002
AABLOSUM80	0.001	0.001	0.001
AABurden	0.002	0.001	0.002
AACPSA	0.001	0.001	0.002
AAConn	0.002	0.000	0.002
AAConst	0.001	0.000	0.002
AADescAll	0.002	0.001	0.002
AAEdgeAdj	0.002	0.001	0.002
AAEigIdx	0.001	0.001	0.002
AAFGC	0.001	0.000	0.002
AAGETAWAY	0.002	0.000	0.002
AAGeom	0.001	0.000	0.003
AAInfo	0.001	0.001	0.002
AAMOE2D	0.001	0.000	0.001
AAMOE3D	0.001	0.001	0.001
AAMetaInfo	0.001	0.001	0.002
AAMolProp	0.002	0.001	0.002
AAPAM120	0.001	0.000	0.003
AAPAM250	0.001	0.000	0.003
AAPAM30	0.002	0.001	0.002
AAPAM40	0.002	0.001	0.003
AAPAM70	0.001	0.001	0.002
AARDF	0.002	0.000	0.002
AARandic	0.002	0.000	0.002
AATopo	0.001	0.000	0.002
AATopoChg	0.001	0.001	0.003
AAWHIM	0.002	0.001	0.002
AAWalk	0.002	0.001	0.002
AAindex	0.001	0.000	0.002
OptAA3d	0.001	0.000	0.001
acc	0.015	0.004	0.029
calcDrugFPSim	2.028	0.176	1.073
calcDrugMCSSim	0.007	0.002	0.015
calcParProtGOSim	0.001	0.000	0.001
calcParProtSeqSim	0.028	0.001	0.028
calcTwoProtGOSim	0.001	0.000	0.001
calcTwoProtSeqSim	0.002	0.000	0.003
checkProt	0.002	0.000	0.002
convMolFormat	0.001	0.001	0.000
extractDrugAIO	0.000	0.000	0.001
extractDrugALOGP	0.001	0.000	0.000
extractDrugAminoAcidCount	0.001	0.000	0.001
extractDrugApol	0	0	0
extractDrugAromaticAtomsCount	0.001	0.001	0.001
extractDrugAromaticBondsCount	0.001	0.000	0.000
extractDrugAtomCount	0.001	0.000	0.001
extractDrugAutocorrelationCharge	0.001	0.000	0.001
extractDrugAutocorrelationMass	0.001	0.001	0.001
extractDrugAutocorrelationPolarizability	0.001	0.000	0.004
extractDrugBCUT	0.001	0.000	0.001
extractDrugBPol	0.001	0.001	0.001
extractDrugBondCount	0.001	0.000	0.001
extractDrugCPSA	0.001	0.000	0.002
extractDrugCarbonTypes	0.001	0.000	0.001
extractDrugChiChain	0.001	0.000	0.001
extractDrugChiCluster	0.001	0.000	0.002
extractDrugChiPath	0.001	0.001	0.001
extractDrugChiPathCluster	0.001	0.000	0.002
extractDrugDescOB	0.009	0.002	0.012
extractDrugECI	0.001	0.001	0.002
extractDrugEstate	0.002	0.000	0.001
extractDrugEstateComplete	0.001	0.000	0.001
extractDrugExtended	0.001	0.000	0.001
extractDrugExtendedComplete	0.001	0.000	0.002
extractDrugFMF	0.001	0.000	0.001
extractDrugFragmentComplexity	0.001	0.001	0.002
extractDrugGraph	0.002	0.000	0.002
extractDrugGraphComplete	0.001	0.000	0.001
extractDrugGravitationalIndex	0.001	0.000	0.001
extractDrugHBondAcceptorCount	0.001	0.000	0.001
extractDrugHBondDonorCount	0.002	0.000	0.001
extractDrugHybridization	0.001	0.000	0.001
extractDrugHybridizationComplete	0.001	0.000	0.001
extractDrugHybridizationRatio	0.001	0.000	0.002
extractDrugIPMolecularLearning	0.001	0.001	0.001
extractDrugKR	0.001	0.000	0.001
extractDrugKRComplete	0.001	0.000	0.001
extractDrugKappaShapeIndices	0.001	0.000	0.001
extractDrugKierHallSmarts	0.001	0.000	0.000
extractDrugLargestChain	0.001	0.000	0.001
extractDrugLargestPiSystem	0.001	0.000	0.001
extractDrugLengthOverBreadth	0.001	0.001	0.001
extractDrugLongestAliphaticChain	0.001	0.000	0.002
extractDrugMACCS	0.001	0.000	0.001
extractDrugMACCSComplete	0.001	0.000	0.002
extractDrugMDE	0.001	0.000	0.001
extractDrugMannholdLogP	0.001	0.000	0.001
extractDrugMomentOfInertia	0.001	0.000	0.001
extractDrugOBFP2	0.008	0.001	0.009
extractDrugOBFP3	0.008	0.000	0.008
extractDrugOBFP4	0.009	0.000	0.009
extractDrugOBMACCS	0.207	0.001	0.210
extractDrugPetitjeanNumber	0.001	0.000	0.001
extractDrugPetitjeanShapeIndex	0.001	0.001	0.001
extractDrugPubChem	0.001	0.000	0.001
extractDrugPubChemComplete	0.002	0.000	0.002
extractDrugRotatableBondsCount	0.001	0.000	0.001
extractDrugRuleOfFive	0.001	0.000	0.001
extractDrugShortestPath	0.001	0.000	0.002
extractDrugShortestPathComplete	0.001	0.000	0.001
extractDrugStandard	0.001	0.000	0.001
extractDrugStandardComplete	0.001	0.000	0.001
extractDrugTPSA	0.001	0.000	0.001
extractDrugVABC	0.001	0.000	0.001
extractDrugVAdjMa	0.001	0.000	0.001
extractDrugWHIM	0.001	0.000	0.001
extractDrugWeight	0.001	0.000	0.002
extractDrugWeightedPath	0.001	0.000	0.001
extractDrugWienerNumbers	0.001	0.000	0.001
extractDrugXLogP	0.001	0.000	0.001
extractDrugZagrebIndex	0.001	0.000	0.001
extractPCMBLOSUM	0.051	0.002	0.053
extractPCMDescScales	0.010	0.002	0.012
extractPCMFAScales	0.019	0.002	0.025
extractPCMMDSScales	0.011	0.002	0.012
extractPCMPropScales	0.033	0.001	0.035
extractPCMScales	0.015	0.002	0.017
extractProtAAC	0.003	0.000	0.003
extractProtAPAAC	1.178	0.036	1.230
extractProtCTDC	0.004	0.000	0.004
extractProtCTDD	0.007	0.001	0.008
extractProtCTDT	0.007	0.001	0.007
extractProtCTriad	0.101	0.006	0.113
extractProtDC	0.004	0.002	0.007
extractProtGeary	0.193	0.005	0.210
extractProtMoran	0.223	0.008	0.253
extractProtMoreauBroto	0.224	0.006	0.239
extractProtPAAC	0.688	0.007	0.728
extractProtPSSM	0.002	0.000	0.002
extractProtPSSMAcc	0.001	0.001	0.001
extractProtPSSMFeature	0.001	0.000	0.001
extractProtQSO	1.259	0.010	1.297
extractProtSOCN	1.229	0.028	1.317
extractProtTC	0.051	0.042	0.096
getCPI	0.002	0.000	0.003
getDrug	0.000	0.000	0.001
getFASTAFromKEGG	0.001	0.001	0.000
getFASTAFromUniProt	0.001	0.000	0.000
getMolFromCAS	0.000	0.000	0.001
getMolFromChEMBL	0.000	0.000	0.001
getMolFromDrugBank	0.000	0.000	0.001
getMolFromKEGG	0	0	0
getMolFromPubChem	0.001	0.000	0.001
getPDBFromRCSBPDB	0.001	0.000	0.001
getPPI	0.003	0.000	0.005
getProt	0.000	0.000	0.001
getSeqFromKEGG	0.001	0.000	0.001
getSeqFromRCSBPDB	0.001	0.000	0.000
getSeqFromUniProt	0.001	0.001	0.000
getSmiFromChEMBL	0.001	0.000	0.001
getSmiFromDrugBank	0.001	0.000	0.001
getSmiFromKEGG	0.001	0.000	0.001
getSmiFromPubChem	0.000	0.000	0.001
readFASTA	0.002	0.000	0.002
readMolFromSDF	0.002	0.000	0.003
readMolFromSmi	0.001	0.000	0.002
readPDB	1.095	0.010	1.132
searchDrug	0.002	0.000	0.002
segProt	0.003	0.001	0.004

BioC 3.5: CHECK report for Rcpi on veracruz2

Summary

Command output