BioC 3.2: CHECK report for Rcpi on perceval

Package: Rcpi

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.6.0.tar.gz

StartedAt: 2015-11-10 08:42:02 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 08:45:16 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 193.3 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_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Rcpi.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.6.0’
* 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 ... [18s/18s] 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 ... [17s/17s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [9s/9s]
 [10s/9s] 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	0.001	0.004
AA3DMoRSE	0.001	0.000	0.002
AAACF	0.001	0.000	0.002
AABLOSUM100	0.002	0.000	0.002
AABLOSUM45	0.001	0.000	0.002
AABLOSUM50	0.001	0.000	0.002
AABLOSUM62	0.002	0.000	0.002
AABLOSUM80	0.001	0.000	0.002
AABurden	0.002	0.001	0.001
AACPSA	0.002	0.000	0.001
AAConn	0.001	0.001	0.002
AAConst	0.002	0.000	0.002
AADescAll	0.002	0.001	0.002
AAEdgeAdj	0.001	0.000	0.002
AAEigIdx	0.002	0.001	0.002
AAFGC	0.002	0.000	0.001
AAGETAWAY	0.001	0.001	0.002
AAGeom	0.002	0.000	0.002
AAInfo	0.002	0.001	0.002
AAMOE2D	0.001	0.000	0.002
AAMOE3D	0.002	0.001	0.002
AAMetaInfo	0.002	0.000	0.001
AAMolProp	0.001	0.001	0.001
AAPAM120	0.001	0.000	0.002
AAPAM250	0.002	0.001	0.002
AAPAM30	0.001	0.000	0.002
AAPAM40	0.001	0.001	0.002
AAPAM70	0.002	0.000	0.002
AARDF	0.001	0.001	0.002
AARandic	0.001	0.000	0.001
AATopo	0.002	0.001	0.001
AATopoChg	0.001	0.000	0.002
AAWHIM	0.001	0.001	0.002
AAWalk	0.002	0.000	0.002
AAindex	0.002	0.001	0.002
OptAA3d	0	0	0
Rcpi-package	0	0	0
acc	0.020	0.007	0.027
calcDrugFPSim	0.000	0.000	0.001
calcDrugMCSSim	0.001	0.000	0.001
calcParProtGOSim	0.001	0.000	0.001
calcParProtSeqSim	0.001	0.001	0.001
calcTwoProtGOSim	0.000	0.000	0.001
calcTwoProtSeqSim	0.001	0.000	0.001
checkProt	0.003	0.001	0.004
convMolFormat	0.000	0.000	0.001
extractDrugAIO	0.001	0.000	0.000
extractDrugALOGP	0.001	0.001	0.000
extractDrugAminoAcidCount	0	0	0
extractDrugApol	0	0	0
extractDrugAromaticAtomsCount	0.001	0.000	0.000
extractDrugAromaticBondsCount	0.001	0.000	0.000
extractDrugAtomCount	0	0	0
extractDrugAutocorrelationCharge	0	0	0
extractDrugAutocorrelationMass	0.001	0.000	0.001
extractDrugAutocorrelationPolarizability	0.001	0.000	0.001
extractDrugBCUT	0.000	0.000	0.001
extractDrugBPol	0.001	0.000	0.001
extractDrugBondCount	0.001	0.001	0.000
extractDrugCPSA	0	0	0
extractDrugCarbonTypes	0	0	0
extractDrugChiChain	0.001	0.000	0.000
extractDrugChiCluster	0.001	0.001	0.000
extractDrugChiPath	0	0	0
extractDrugChiPathCluster	0.001	0.000	0.000
extractDrugDescOB	0.001	0.000	0.000
extractDrugECI	0.000	0.000	0.001
extractDrugEstate	0.000	0.000	0.001
extractDrugEstateComplete	0.001	0.000	0.001
extractDrugExtended	0.000	0.000	0.001
extractDrugExtendedComplete	0	0	0
extractDrugFMF	0.001	0.000	0.000
extractDrugFragmentComplexity	0.000	0.000	0.001
extractDrugGraph	0.000	0.000	0.001
extractDrugGraphComplete	0.001	0.000	0.000
extractDrugGravitationalIndex	0.001	0.000	0.000
extractDrugHBondAcceptorCount	0	0	0
extractDrugHBondDonorCount	0.001	0.000	0.000
extractDrugHybridization	0.001	0.000	0.001
extractDrugHybridizationComplete	0.000	0.000	0.001
extractDrugHybridizationRatio	0.000	0.000	0.001
extractDrugIPMolecularLearning	0.001	0.001	0.000
extractDrugKR	0.001	0.000	0.000
extractDrugKRComplete	0	0	0
extractDrugKappaShapeIndices	0.001	0.000	0.001
extractDrugKierHallSmarts	0.001	0.000	0.001
extractDrugLargestChain	0.000	0.000	0.001
extractDrugLargestPiSystem	0.000	0.000	0.001
extractDrugLengthOverBreadth	0.001	0.000	0.001
extractDrugLongestAliphaticChain	0.001	0.000	0.001
extractDrugMACCS	0.000	0.000	0.001
extractDrugMACCSComplete	0.000	0.000	0.001
extractDrugMDE	0.001	0.001	0.000
extractDrugMannholdLogP	0	0	0
extractDrugMomentOfInertia	0.001	0.000	0.001
extractDrugOBFP2	0.000	0.000	0.001
extractDrugOBFP3	0.000	0.000	0.001
extractDrugOBFP4	0.001	0.000	0.001
extractDrugOBMACCS	0.000	0.000	0.001
extractDrugPetitjeanNumber	0.000	0.000	0.001
extractDrugPetitjeanShapeIndex	0.000	0.000	0.001
extractDrugPubChem	0.001	0.000	0.001
extractDrugPubChemComplete	0.000	0.000	0.001
extractDrugRotatableBondsCount	0	0	0
extractDrugRuleOfFive	0	0	0
extractDrugShortestPath	0.001	0.000	0.000
extractDrugShortestPathComplete	0.001	0.001	0.000
extractDrugStandard	0.000	0.000	0.001
extractDrugStandardComplete	0.001	0.000	0.001
extractDrugTPSA	0.001	0.000	0.001
extractDrugVABC	0.000	0.000	0.001
extractDrugVAdjMa	0.000	0.000	0.001
extractDrugWHIM	0.001	0.000	0.001
extractDrugWeight	0.001	0.001	0.001
extractDrugWeightedPath	0.000	0.000	0.001
extractDrugWienerNumbers	0.001	0.000	0.001
extractDrugXLogP	0.001	0.000	0.001
extractDrugZagrebIndex	0.000	0.000	0.001
extractPCMBLOSUM	0.021	0.002	0.024
extractPCMDescScales	0.016	0.000	0.017
extractPCMFAScales	0.023	0.003	0.026
extractPCMMDSScales	0.017	0.002	0.019
extractPCMPropScales	0.016	0.001	0.018
extractPCMScales	0.028	0.002	0.030
extractProtAAC	0.003	0.001	0.003
extractProtAPAAC	2.671	0.007	2.678
extractProtCTDC	0.007	0.000	0.007
extractProtCTDD	0.007	0.001	0.008
extractProtCTDT	0.012	0.001	0.012
extractProtCTriad	0.240	0.009	0.249
extractProtDC	0.005	0.003	0.008
extractProtGeary	0.215	0.008	0.223
extractProtMoran	0.209	0.005	0.215
extractProtMoreauBroto	0.206	0.004	0.210
extractProtPAAC	0.977	0.004	0.973
extractProtPSSM	0.000	0.000	0.001
extractProtPSSMAcc	0.001	0.000	0.000
extractProtPSSMFeature	0	0	0
extractProtQSO	1.736	0.046	1.782
extractProtSOCN	1.710	0.035	1.744
extractProtTC	0.065	0.049	0.114
getCPI	0.007	0.000	0.008
getDrug	0.001	0.000	0.000
getFASTAFromKEGG	0	0	0
getFASTAFromUniProt	0	0	0
getMolFromCAS	0.001	0.000	0.000
getMolFromChEMBL	0.001	0.000	0.000
getMolFromDrugBank	0.000	0.000	0.001
getMolFromKEGG	0.001	0.000	0.001
getMolFromPubChem	0.001	0.000	0.001
getPDBFromRCSBPDB	0.000	0.000	0.001
getPPI	0.004	0.001	0.006
getProt	0.001	0.000	0.001
getSeqFromKEGG	0	0	0
getSeqFromRCSBPDB	0.000	0.000	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	0.000	0.001
getSmiFromPubChem	0.000	0.000	0.001
readFASTA	0.001	0.001	0.001
readMolFromSDF	0.000	0.000	0.001
readMolFromSmi	0.001	0.000	0.000
readPDB	1.518	0.028	1.545
searchDrug	0	0	0
segProt	0.003	0.001	0.003

BioC 3.2: CHECK report for Rcpi on perceval

Summary

Command output