BioC 3.6: CHECK report for Rcpi on veracruz1

Package: Rcpi

Version: 1.13.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.13.4.tar.gz

StartedAt: 2017-08-16 07:28:10 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 07:30:40 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 150.7 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_1.13.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.13.4’
* 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	0.012	0.002	0.016
AA3DMoRSE	0.001	0.000	0.001
AAACF	0.001	0.001	0.001
AABLOSUM100	0.001	0.000	0.002
AABLOSUM45	0.001	0.001	0.001
AABLOSUM50	0.001	0.000	0.002
AABLOSUM62	0.002	0.001	0.002
AABLOSUM80	0.001	0.001	0.001
AABurden	0.001	0.000	0.001
AACPSA	0.001	0.001	0.001
AAConn	0.001	0.000	0.001
AAConst	0.001	0.001	0.002
AADescAll	0.001	0.000	0.002
AAEdgeAdj	0.001	0.001	0.001
AAEigIdx	0.001	0.000	0.001
AAFGC	0.001	0.001	0.002
AAGETAWAY	0.001	0.000	0.001
AAGeom	0.001	0.000	0.002
AAInfo	0.001	0.001	0.002
AAMOE2D	0.001	0.000	0.002
AAMOE3D	0.001	0.001	0.001
AAMetaInfo	0.001	0.000	0.002
AAMolProp	0.002	0.000	0.002
AAPAM120	0.001	0.001	0.002
AAPAM250	0.001	0.000	0.001
AAPAM30	0.001	0.001	0.002
AAPAM40	0.002	0.001	0.002
AAPAM70	0.001	0.000	0.002
AARDF	0.002	0.001	0.001
AARandic	0.002	0.001	0.003
AATopo	0.002	0.000	0.003
AATopoChg	0.001	0.000	0.001
AAWHIM	0.001	0.001	0.002
AAWalk	0.001	0.000	0.002
AAindex	0.001	0.001	0.002
OptAA3d	0.000	0.000	0.001
acc	0.012	0.004	0.016
calcDrugFPSim	1.762	0.110	0.880
calcDrugMCSSim	0.010	0.002	0.011
calcParProtGOSim	0.001	0.000	0.001
calcParProtSeqSim	0.033	0.001	0.034
calcTwoProtGOSim	0.000	0.000	0.001
calcTwoProtSeqSim	0.002	0.000	0.002
checkProt	0.002	0.000	0.002
convMolFormat	0.002	0.001	0.002
extractDrugAIO	0.000	0.000	0.001
extractDrugALOGP	0.001	0.000	0.001
extractDrugAminoAcidCount	0.001	0.001	0.001
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	0.001
extractDrugAutocorrelationCharge	0.001	0.000	0.002
extractDrugAutocorrelationMass	0.001	0.000	0.001
extractDrugAutocorrelationPolarizability	0.002	0.000	0.001
extractDrugBCUT	0.001	0.000	0.002
extractDrugBPol	0.001	0.000	0.001
extractDrugBondCount	0.001	0.000	0.001
extractDrugCPSA	0.001	0.000	0.001
extractDrugCarbonTypes	0.001	0.000	0.002
extractDrugChiChain	0.001	0.000	0.002
extractDrugChiCluster	0.001	0.000	0.001
extractDrugChiPath	0.001	0.000	0.000
extractDrugChiPathCluster	0.000	0.001	0.001
extractDrugDescOB	0.010	0.002	0.012
extractDrugECI	0.001	0.000	0.001
extractDrugEstate	0.001	0.000	0.001
extractDrugEstateComplete	0.001	0.001	0.001
extractDrugExtended	0.001	0.000	0.001
extractDrugExtendedComplete	0.001	0.000	0.000
extractDrugFMF	0.001	0.001	0.001
extractDrugFragmentComplexity	0.001	0.000	0.001
extractDrugGraph	0.001	0.000	0.002
extractDrugGraphComplete	0.001	0.001	0.001
extractDrugGravitationalIndex	0.001	0.000	0.001
extractDrugHBondAcceptorCount	0.001	0.000	0.002
extractDrugHBondDonorCount	0.001	0.001	0.001
extractDrugHybridization	0.001	0.000	0.002
extractDrugHybridizationComplete	0.000	0.000	0.001
extractDrugHybridizationRatio	0.001	0.000	0.001
extractDrugIPMolecularLearning	0.001	0.000	0.002
extractDrugKR	0.001	0.000	0.001
extractDrugKRComplete	0.001	0.000	0.001
extractDrugKappaShapeIndices	0.000	0.000	0.001
extractDrugKierHallSmarts	0.001	0.000	0.001
extractDrugLargestChain	0.001	0.000	0.001
extractDrugLargestPiSystem	0.001	0.001	0.001
extractDrugLengthOverBreadth	0.002	0.000	0.002
extractDrugLongestAliphaticChain	0.001	0.000	0.001
extractDrugMACCS	0.001	0.000	0.001
extractDrugMACCSComplete	0.002	0.000	0.002
extractDrugMDE	0.001	0.000	0.001
extractDrugMannholdLogP	0.001	0.000	0.001
extractDrugMomentOfInertia	0.002	0.000	0.002
extractDrugOBFP2	0.009	0.000	0.009
extractDrugOBFP3	0.009	0.000	0.010
extractDrugOBFP4	0.009	0.000	0.010
extractDrugOBMACCS	0.009	0.000	0.010
extractDrugPetitjeanNumber	0.001	0.000	0.001
extractDrugPetitjeanShapeIndex	0.002	0.000	0.001
extractDrugPubChem	0.001	0.000	0.002
extractDrugPubChemComplete	0.001	0.000	0.001
extractDrugRotatableBondsCount	0.001	0.000	0.001
extractDrugRuleOfFive	0.000	0.000	0.001
extractDrugShortestPath	0.001	0.000	0.000
extractDrugShortestPathComplete	0.001	0.000	0.001
extractDrugStandard	0.000	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	0.001	0.001
extractDrugWHIM	0.001	0.000	0.002
extractDrugWeight	0.001	0.000	0.001
extractDrugWeightedPath	0.001	0.000	0.001
extractDrugWienerNumbers	0.001	0.000	0.002
extractDrugXLogP	0.000	0.000	0.001
extractDrugZagrebIndex	0.001	0.000	0.001
extractPCMBLOSUM	0.039	0.002	0.042
extractPCMDescScales	0.010	0.001	0.011
extractPCMFAScales	0.190	0.002	0.198
extractPCMMDSScales	0.009	0.002	0.011
extractPCMPropScales	0.029	0.001	0.032
extractPCMScales	0.021	0.002	0.022
extractProtAAC	0.002	0.000	0.002
extractProtAPAAC	0.988	0.022	1.031
extractProtCTDC	0.002	0.000	0.002
extractProtCTDD	0.005	0.001	0.008
extractProtCTDT	0.006	0.000	0.007
extractProtCTriad	0.121	0.010	0.131
extractProtDC	0.004	0.001	0.006
extractProtGeary	0.210	0.005	0.232
extractProtMoran	0.219	0.007	0.228
extractProtMoreauBroto	0.199	0.004	0.205
extractProtPAAC	0.720	0.015	0.763
extractProtPSSM	0.002	0.000	0.001
extractProtPSSMAcc	0.002	0.000	0.001
extractProtPSSMFeature	0.001	0.000	0.001
extractProtQSO	1.220	0.012	1.270
extractProtSOCN	1.174	0.006	1.211
extractProtTC	0.042	0.038	0.079
getCPI	0.003	0.001	0.003
getDrug	0.001	0.000	0.001
getFASTAFromKEGG	0.000	0.000	0.001
getFASTAFromUniProt	0.001	0.000	0.000
getMolFromCAS	0.001	0.000	0.000
getMolFromChEMBL	0	0	0
getMolFromDrugBank	0.001	0.000	0.001
getMolFromKEGG	0.000	0.000	0.001
getMolFromPubChem	0.000	0.000	0.001
getPDBFromRCSBPDB	0.001	0.000	0.001
getPPI	0.002	0.001	0.003
getProt	0.001	0.000	0.001
getSeqFromKEGG	0.000	0.000	0.001
getSeqFromRCSBPDB	0.001	0.001	0.001
getSeqFromUniProt	0.001	0.000	0.001
getSmiFromChEMBL	0.000	0.000	0.001
getSmiFromDrugBank	0.000	0.000	0.001
getSmiFromKEGG	0.001	0.001	0.001
getSmiFromPubChem	0.001	0.000	0.001
readFASTA	0.002	0.000	0.002
readMolFromSDF	0.002	0.001	0.002
readMolFromSmi	0.001	0.000	0.001
readPDB	1.118	0.008	1.157
searchDrug	0.001	0.000	0.002
segProt	0.002	0.001	0.003

BioC 3.6: CHECK report for Rcpi on veracruz1

Summary

Command output