BioC 3.0: CHECK report for Rcpi on oaxaca

Package: Rcpi

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rcpi_1.2.0.tar.gz

StartedAt: 2015-04-10 02:39:10 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 02:43:42 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 271.8 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 --no-multiarch Rcpi_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/Rcpi.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.2.0’
* 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 ... [23s/24s] 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 ... [21s/26s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [12s/13s]
 [12s/13s] 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

* 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	0.013	0.001	0.013
AA3DMoRSE	0.002	0.000	0.002
AAACF	0.002	0.000	0.002
AABLOSUM100	0.002	0.001	0.002
AABLOSUM45	0.002	0.000	0.002
AABLOSUM50	0.002	0.000	0.002
AABLOSUM62	0.009	0.001	0.010
AABLOSUM80	0.002	0.000	0.002
AABurden	0.002	0.000	0.002
AACPSA	0.002	0.001	0.002
AAConn	0.002	0.000	0.003
AAConst	0.002	0.000	0.003
AADescAll	0.002	0.001	0.002
AAEdgeAdj	0.002	0.000	0.003
AAEigIdx	0.002	0.000	0.002
AAFGC	0.002	0.000	0.002
AAGETAWAY	0.002	0.001	0.002
AAGeom	0.002	0.000	0.002
AAInfo	0.002	0.001	0.002
AAMOE2D	0.002	0.000	0.003
AAMOE3D	0.002	0.000	0.002
AAMetaInfo	0.002	0.001	0.002
AAMolProp	0.002	0.000	0.003
AAPAM120	0.002	0.000	0.003
AAPAM250	0.002	0.001	0.003
AAPAM30	0.002	0.000	0.003
AAPAM40	0.001	0.000	0.003
AAPAM70	0.002	0.000	0.003
AARDF	0.002	0.000	0.003
AARandic	0.002	0.001	0.003
AATopo	0.003	0.000	0.002
AATopoChg	0.002	0.001	0.003
AAWHIM	0.002	0.001	0.003
AAWalk	0.002	0.000	0.003
AAindex	0.002	0.001	0.003
OptAA3d	0.001	0.000	0.001
Rcpi-package	0.000	0.000	0.001
acc	0.018	0.004	0.022
calcDrugFPSim	0	0	0
calcDrugMCSSim	0.000	0.000	0.001
calcParProtGOSim	0.000	0.001	0.001
calcParProtSeqSim	0	0	0
calcTwoProtGOSim	0	0	0
calcTwoProtSeqSim	0.000	0.000	0.001
checkProt	0.005	0.001	0.006
convMolFormat	0	0	0
extractDrugAIO	0.001	0.000	0.000
extractDrugALOGP	0	0	0
extractDrugAminoAcidCount	0.000	0.000	0.001
extractDrugApol	0.000	0.000	0.001
extractDrugAromaticAtomsCount	0.000	0.000	0.001
extractDrugAromaticBondsCount	0.001	0.000	0.000
extractDrugAtomCount	0.001	0.000	0.000
extractDrugAutocorrelationCharge	0.001	0.000	0.001
extractDrugAutocorrelationMass	0.001	0.000	0.000
extractDrugAutocorrelationPolarizability	0.001	0.000	0.000
extractDrugBCUT	0.001	0.000	0.001
extractDrugBPol	0.001	0.000	0.001
extractDrugBondCount	0.001	0.000	0.000
extractDrugCPSA	0.001	0.000	0.001
extractDrugCarbonTypes	0.001	0.000	0.001
extractDrugChiChain	0	0	0
extractDrugChiCluster	0.000	0.000	0.001
extractDrugChiPath	0.000	0.000	0.001
extractDrugChiPathCluster	0	0	0
extractDrugDescOB	0.000	0.000	0.001
extractDrugECI	0.000	0.000	0.001
extractDrugEstate	0.000	0.000	0.001
extractDrugEstateComplete	0	0	0
extractDrugExtended	0.000	0.001	0.001
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	0	0
extractDrugGravitationalIndex	0.000	0.000	0.001
extractDrugHBondAcceptorCount	0.000	0.000	0.001
extractDrugHBondDonorCount	0	0	0
extractDrugHybridization	0.000	0.000	0.001
extractDrugHybridizationComplete	0.000	0.000	0.001
extractDrugHybridizationRatio	0	0	0
extractDrugIPMolecularLearning	0.000	0.000	0.001
extractDrugKR	0.000	0.000	0.001
extractDrugKRComplete	0.001	0.000	0.000
extractDrugKappaShapeIndices	0.001	0.000	0.001
extractDrugKierHallSmarts	0.001	0.000	0.001
extractDrugLargestChain	0.001	0.000	0.000
extractDrugLargestPiSystem	0.001	0.001	0.001
extractDrugLengthOverBreadth	0.001	0.000	0.001
extractDrugLongestAliphaticChain	0.001	0.000	0.000
extractDrugMACCS	0.001	0.000	0.001
extractDrugMACCSComplete	0.001	0.000	0.001
extractDrugMDE	0.001	0.000	0.000
extractDrugMannholdLogP	0.001	0.000	0.001
extractDrugMomentOfInertia	0.001	0.000	0.001
extractDrugOBFP2	0.001	0.000	0.000
extractDrugOBFP3	0.001	0.000	0.001
extractDrugOBFP4	0.000	0.000	0.001
extractDrugOBMACCS	0	0	0
extractDrugPetitjeanNumber	0.000	0.000	0.001
extractDrugPetitjeanShapeIndex	0.000	0.000	0.001
extractDrugPubChem	0.000	0.001	0.000
extractDrugPubChemComplete	0.000	0.000	0.001
extractDrugRotatableBondsCount	0.000	0.000	0.001
extractDrugRuleOfFive	0.000	0.000	0.001
extractDrugShortestPath	0	0	0
extractDrugShortestPathComplete	0.000	0.000	0.001
extractDrugStandard	0.000	0.000	0.001
extractDrugStandardComplete	0.000	0.001	0.000
extractDrugTPSA	0.000	0.000	0.001
extractDrugVABC	0.000	0.000	0.001
extractDrugVAdjMa	0	0	0
extractDrugWHIM	0	0	0
extractDrugWeight	0.000	0.000	0.001
extractDrugWeightedPath	0.000	0.000	0.001
extractDrugWienerNumbers	0	0	0
extractDrugXLogP	0	0	0
extractDrugZagrebIndex	0.000	0.000	0.001
extractPCMBLOSUM	0.018	0.002	0.020
extractPCMDescScales	0.023	0.003	0.025
extractPCMFAScales	0.027	0.003	0.030
extractPCMMDSScales	0.023	0.003	0.026
extractPCMPropScales	0.020	0.001	0.021
extractPCMScales	0.034	0.002	0.036
extractProtAAC	0.006	0.000	0.006
extractProtAPAAC	2.851	0.043	2.911
extractProtCTDC	0.011	0.001	0.011
extractProtCTDD	0.009	0.002	0.010
extractProtCTDT	0.011	0.001	0.013
extractProtCTriad	0.262	0.004	0.276
extractProtDC	0.007	0.003	0.010
extractProtGeary	0.233	0.006	0.240
extractProtMoran	0.236	0.006	0.242
extractProtMoreauBroto	0.235	0.007	0.244
extractProtPAAC	1.126	0.004	1.142
extractProtPSSM	0.001	0.000	0.001
extractProtPSSMAcc	0.001	0.000	0.001
extractProtPSSMFeature	0.001	0.000	0.000
extractProtQSO	1.958	0.008	2.221
extractProtSOCN	1.954	0.007	2.196
extractProtTC	0.064	0.049	0.125
getCPI	0.004	0.001	0.005
getDrug	0	0	0
getFASTAFromKEGG	0.000	0.001	0.003
getFASTAFromUniProt	0.000	0.000	0.001
getMolFromCAS	0.000	0.000	0.001
getMolFromChEMBL	0	0	0
getMolFromDrugBank	0	0	0
getMolFromKEGG	0.000	0.000	0.001
getMolFromPubChem	0.000	0.000	0.001
getPDBFromRCSBPDB	0.000	0.000	0.001
getPPI	0.005	0.001	0.007
getProt	0.000	0.000	0.001
getSeqFromKEGG	0.001	0.000	0.001
getSeqFromRCSBPDB	0.001	0.000	0.001
getSeqFromUniProt	0.001	0.000	0.000
getSmiFromChEMBL	0.001	0.000	0.001
getSmiFromDrugBank	0.001	0.000	0.000
getSmiFromKEGG	0.001	0.000	0.000
getSmiFromPubChem	0.001	0.000	0.001
readFASTA	0.004	0.000	0.004
readMolFromSDF	0.001	0.000	0.000
readMolFromSmi	0	0	0
readPDB	1.426	0.005	1.594
searchDrug	0.000	0.000	0.001
segProt	0.004	0.001	0.007

BioC 3.0: CHECK report for Rcpi on oaxaca

Summary

Command output