BioC 3.0: CHECK report for Rcpi on perceval

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 05:26:39 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 05:32:13 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 333.6 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-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 ‘1.2.0’
* 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 ... [28s/34s] 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 ... [25s/26s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [16s/16s]
 [17s/17s] 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	0.028	0.004	0.034
AA3DMoRSE	0.002	0.000	0.002
AAACF	0.003	0.000	0.003
AABLOSUM100	0.002	0.000	0.003
AABLOSUM45	0.003	0.001	0.003
AABLOSUM50	0.002	0.001	0.004
AABLOSUM62	0.002	0.001	0.004
AABLOSUM80	0.003	0.000	0.003
AABurden	0.002	0.000	0.002
AACPSA	0.002	0.001	0.002
AAConn	0.002	0.001	0.003
AAConst	0.002	0.001	0.002
AADescAll	0.002	0.000	0.002
AAEdgeAdj	0.002	0.000	0.003
AAEigIdx	0.003	0.000	0.003
AAFGC	0.002	0.000	0.003
AAGETAWAY	0.003	0.000	0.004
AAGeom	0.003	0.000	0.003
AAInfo	0.002	0.000	0.003
AAMOE2D	0.002	0.001	0.003
AAMOE3D	0.002	0.001	0.003
AAMetaInfo	0.002	0.001	0.003
AAMolProp	0.002	0.000	0.003
AAPAM120	0.003	0.000	0.002
AAPAM250	0.002	0.001	0.003
AAPAM30	0.002	0.001	0.003
AAPAM40	0.002	0.001	0.003
AAPAM70	0.003	0.001	0.003
AARDF	0.002	0.001	0.003
AARandic	0.002	0.001	0.004
AATopo	0.003	0.001	0.003
AATopoChg	0.003	0.001	0.004
AAWHIM	0.002	0.001	0.002
AAWalk	0.002	0.001	0.003
AAindex	0.002	0.001	0.004
OptAA3d	0.001	0.001	0.000
Rcpi-package	0.001	0.000	0.000
acc	0.022	0.009	0.033
calcDrugFPSim	0.000	0.000	0.001
calcDrugMCSSim	0.001	0.000	0.001
calcParProtGOSim	0.001	0.000	0.001
calcParProtSeqSim	0.001	0.000	0.000
calcTwoProtGOSim	0.000	0.000	0.001
calcTwoProtSeqSim	0.001	0.000	0.001
checkProt	0.006	0.001	0.007
convMolFormat	0.000	0.000	0.001
extractDrugAIO	0.001	0.001	0.001
extractDrugALOGP	0.001	0.000	0.001
extractDrugAminoAcidCount	0.000	0.001	0.001
extractDrugApol	0	0	0
extractDrugAromaticAtomsCount	0.000	0.000	0.001
extractDrugAromaticBondsCount	0.001	0.000	0.001
extractDrugAtomCount	0.000	0.000	0.001
extractDrugAutocorrelationCharge	0.001	0.000	0.001
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	0.001	0.000	0.000
extractDrugCarbonTypes	0.000	0.000	0.001
extractDrugChiChain	0.000	0.000	0.001
extractDrugChiCluster	0	0	0
extractDrugChiPath	0.001	0.000	0.001
extractDrugChiPathCluster	0.000	0.000	0.001
extractDrugDescOB	0	0	0
extractDrugECI	0.001	0.000	0.001
extractDrugEstate	0.001	0.000	0.000
extractDrugEstateComplete	0.000	0.000	0.001
extractDrugExtended	0.000	0.000	0.001
extractDrugExtendedComplete	0.000	0.000	0.001
extractDrugFMF	0	0	0
extractDrugFragmentComplexity	0.001	0.000	0.001
extractDrugGraph	0	0	0
extractDrugGraphComplete	0.001	0.000	0.001
extractDrugGravitationalIndex	0.001	0.000	0.000
extractDrugHBondAcceptorCount	0.001	0.000	0.001
extractDrugHBondDonorCount	0.001	0.000	0.000
extractDrugHybridization	0.001	0.000	0.001
extractDrugHybridizationComplete	0.001	0.000	0.001
extractDrugHybridizationRatio	0.000	0.000	0.001
extractDrugIPMolecularLearning	0	0	0
extractDrugKR	0.001	0.000	0.001
extractDrugKRComplete	0.001	0.000	0.001
extractDrugKappaShapeIndices	0.000	0.000	0.001
extractDrugKierHallSmarts	0.000	0.000	0.001
extractDrugLargestChain	0.001	0.000	0.001
extractDrugLargestPiSystem	0.001	0.000	0.000
extractDrugLengthOverBreadth	0.000	0.000	0.001
extractDrugLongestAliphaticChain	0.000	0.000	0.001
extractDrugMACCS	0	0	0
extractDrugMACCSComplete	0.001	0.000	0.001
extractDrugMDE	0.001	0.000	0.002
extractDrugMannholdLogP	0.001	0.000	0.001
extractDrugMomentOfInertia	0.001	0.000	0.001
extractDrugOBFP2	0.001	0.000	0.001
extractDrugOBFP3	0.001	0.001	0.001
extractDrugOBFP4	0.001	0.001	0.001
extractDrugOBMACCS	0.001	0.000	0.000
extractDrugPetitjeanNumber	0.001	0.000	0.001
extractDrugPetitjeanShapeIndex	0.001	0.000	0.001
extractDrugPubChem	0.001	0.000	0.000
extractDrugPubChemComplete	0.001	0.000	0.001
extractDrugRotatableBondsCount	0.001	0.000	0.000
extractDrugRuleOfFive	0.001	0.000	0.000
extractDrugShortestPath	0.000	0.000	0.001
extractDrugShortestPathComplete	0.000	0.000	0.001
extractDrugStandard	0.001	0.000	0.000
extractDrugStandardComplete	0.001	0.000	0.000
extractDrugTPSA	0.001	0.001	0.001
extractDrugVABC	0.001	0.000	0.000
extractDrugVAdjMa	0.001	0.000	0.001
extractDrugWHIM	0.001	0.000	0.001
extractDrugWeight	0.001	0.000	0.000
extractDrugWeightedPath	0.000	0.000	0.001
extractDrugWienerNumbers	0.001	0.000	0.001
extractDrugXLogP	0.001	0.000	0.001
extractDrugZagrebIndex	0.001	0.000	0.000
extractPCMBLOSUM	0.018	0.004	0.024
extractPCMDescScales	0.019	0.003	0.023
extractPCMFAScales	0.032	0.004	0.036
extractPCMMDSScales	0.018	0.001	0.019
extractPCMPropScales	0.022	0.001	0.023
extractPCMScales	0.041	0.003	0.044
extractProtAAC	0.006	0.001	0.007
extractProtAPAAC	3.368	0.103	3.460
extractProtCTDC	0.008	0.001	0.010
extractProtCTDD	0.008	0.002	0.010
extractProtCTDT	0.016	0.001	0.018
extractProtCTriad	0.244	0.008	0.254
extractProtDC	0.007	0.004	0.011
extractProtGeary	0.247	0.013	0.263
extractProtMoran	0.253	0.009	0.264
extractProtMoreauBroto	0.230	0.012	0.243
extractProtPAAC	1.268	0.007	1.278
extractProtPSSM	0.000	0.001	0.000
extractProtPSSMAcc	0	0	0
extractProtPSSMFeature	0.001	0.001	0.000
extractProtQSO	2.080	0.032	2.116
extractProtSOCN	2.056	0.015	2.070
extractProtTC	0.075	0.068	0.145
getCPI	0.004	0.001	0.005
getDrug	0.000	0.000	0.001
getFASTAFromKEGG	0.000	0.000	0.001
getFASTAFromUniProt	0.000	0.000	0.001
getMolFromCAS	0	0	0
getMolFromChEMBL	0	0	0
getMolFromDrugBank	0.000	0.001	0.000
getMolFromKEGG	0	0	0
getMolFromPubChem	0.000	0.001	0.000
getPDBFromRCSBPDB	0.000	0.000	0.001
getPPI	0.005	0.001	0.005
getProt	0.000	0.000	0.001
getSeqFromKEGG	0.000	0.000	0.001
getSeqFromRCSBPDB	0.001	0.000	0.000
getSeqFromUniProt	0.001	0.000	0.000
getSmiFromChEMBL	0.000	0.000	0.001
getSmiFromDrugBank	0	0	0
getSmiFromKEGG	0.001	0.000	0.001
getSmiFromPubChem	0	0	0
readFASTA	0.003	0.001	0.005
readMolFromSDF	0.001	0.000	0.001
readMolFromSmi	0.000	0.000	0.001
readPDB	1.342	0.011	1.352
searchDrug	0	0	0
segProt	0.005	0.002	0.007

BioC 3.0: CHECK report for Rcpi on perceval

Summary

Command output