BioC 3.4: CHECK report for Rcpi on morelia

Package: Rcpi

Version: 1.10.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.10.6.tar.gz

StartedAt: 2017-04-15 06:57:37 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 07:00:05 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 147.9 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_1.10.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/Rcpi.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.10.6’
* 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 sizes of PDF files under ‘inst/doc’ ... 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	0.020	0.002	0.023
AA3DMoRSE	0.002	0.000	0.002
AAACF	0.002	0.001	0.002
AABLOSUM100	0.002	0.001	0.002
AABLOSUM45	0.002	0.001	0.002
AABLOSUM50	0.001	0.001	0.002
AABLOSUM62	0.001	0.000	0.003
AABLOSUM80	0.001	0.001	0.003
AABurden	0.002	0.001	0.002
AACPSA	0.001	0.001	0.002
AAConn	0.001	0.000	0.002
AAConst	0.001	0.001	0.002
AADescAll	0.001	0.000	0.001
AAEdgeAdj	0.001	0.001	0.001
AAEigIdx	0.001	0.000	0.002
AAFGC	0.001	0.001	0.001
AAGETAWAY	0.001	0.000	0.001
AAGeom	0.001	0.000	0.002
AAInfo	0.001	0.000	0.002
AAMOE2D	0.001	0.000	0.001
AAMOE3D	0.001	0.000	0.001
AAMetaInfo	0.001	0.000	0.001
AAMolProp	0.001	0.001	0.002
AAPAM120	0.001	0.000	0.001
AAPAM250	0.001	0.001	0.001
AAPAM30	0.001	0.000	0.002
AAPAM40	0.001	0.001	0.001
AAPAM70	0.001	0.000	0.001
AARDF	0.001	0.001	0.001
AARandic	0.001	0.000	0.002
AATopo	0.001	0.001	0.001
AATopoChg	0.001	0.000	0.001
AAWHIM	0.001	0.001	0.002
AAWalk	0.001	0.000	0.001
AAindex	0.001	0.001	0.002
OptAA3d	0	0	0
acc	0.010	0.003	0.013
calcDrugFPSim	2.203	0.101	1.039
calcDrugMCSSim	0.007	0.002	0.010
calcParProtGOSim	0.001	0.000	0.001
calcParProtSeqSim	0.008	0.000	0.008
calcTwoProtGOSim	0.001	0.000	0.001
calcTwoProtSeqSim	0.003	0.000	0.004
checkProt	0.002	0.001	0.003
convMolFormat	0.001	0.000	0.002
extractDrugAIO	0.001	0.000	0.001
extractDrugALOGP	0.001	0.000	0.001
extractDrugAminoAcidCount	0.001	0.000	0.001
extractDrugApol	0.001	0.001	0.001
extractDrugAromaticAtomsCount	0.001	0.000	0.001
extractDrugAromaticBondsCount	0.001	0.000	0.001
extractDrugAtomCount	0.001	0.000	0.001
extractDrugAutocorrelationCharge	0.001	0.001	0.000
extractDrugAutocorrelationMass	0.000	0.000	0.001
extractDrugAutocorrelationPolarizability	0.001	0.000	0.001
extractDrugBCUT	0.000	0.000	0.001
extractDrugBPol	0.001	0.000	0.000
extractDrugBondCount	0.000	0.000	0.001
extractDrugCPSA	0.001	0.000	0.001
extractDrugCarbonTypes	0.001	0.000	0.000
extractDrugChiChain	0.001	0.000	0.001
extractDrugChiCluster	0.001	0.000	0.001
extractDrugChiPath	0.001	0.000	0.000
extractDrugChiPathCluster	0.001	0.000	0.001
extractDrugDescOB	0.150	0.002	0.151
extractDrugECI	0.001	0.000	0.001
extractDrugEstate	0.001	0.000	0.001
extractDrugEstateComplete	0.001	0.000	0.001
extractDrugExtended	0.001	0.000	0.001
extractDrugExtendedComplete	0.001	0.000	0.001
extractDrugFMF	0.001	0.000	0.001
extractDrugFragmentComplexity	0.002	0.000	0.001
extractDrugGraph	0.001	0.001	0.002
extractDrugGraphComplete	0.001	0.000	0.001
extractDrugGravitationalIndex	0.001	0.000	0.001
extractDrugHBondAcceptorCount	0.001	0.000	0.001
extractDrugHBondDonorCount	0.001	0.000	0.002
extractDrugHybridization	0.001	0.000	0.001
extractDrugHybridizationComplete	0.001	0.000	0.002
extractDrugHybridizationRatio	0.002	0.000	0.002
extractDrugIPMolecularLearning	0.001	0.001	0.002
extractDrugKR	0.001	0.000	0.001
extractDrugKRComplete	0	0	0
extractDrugKappaShapeIndices	0.001	0.000	0.001
extractDrugKierHallSmarts	0.000	0.000	0.001
extractDrugLargestChain	0.001	0.000	0.001
extractDrugLargestPiSystem	0.000	0.000	0.001
extractDrugLengthOverBreadth	0.001	0.000	0.002
extractDrugLongestAliphaticChain	0.001	0.001	0.001
extractDrugMACCS	0.001	0.000	0.001
extractDrugMACCSComplete	0.001	0.000	0.001
extractDrugMDE	0.001	0.000	0.001
extractDrugMannholdLogP	0.002	0.000	0.002
extractDrugMomentOfInertia	0.001	0.001	0.002
extractDrugOBFP2	0.010	0.002	0.013
extractDrugOBFP3	0.005	0.001	0.005
extractDrugOBFP4	0.007	0.000	0.007
extractDrugOBMACCS	0.010	0.001	0.011
extractDrugPetitjeanNumber	0.001	0.000	0.001
extractDrugPetitjeanShapeIndex	0.001	0.001	0.001
extractDrugPubChem	0.001	0.000	0.001
extractDrugPubChemComplete	0.001	0.000	0.002
extractDrugRotatableBondsCount	0.001	0.000	0.002
extractDrugRuleOfFive	0.001	0.000	0.002
extractDrugShortestPath	0.001	0.000	0.001
extractDrugShortestPathComplete	0.001	0.000	0.002
extractDrugStandard	0.001	0.000	0.001
extractDrugStandardComplete	0.001	0.001	0.001
extractDrugTPSA	0.001	0.000	0.000
extractDrugVABC	0.002	0.000	0.002
extractDrugVAdjMa	0.001	0.000	0.001
extractDrugWHIM	0.001	0.000	0.001
extractDrugWeight	0.001	0.000	0.001
extractDrugWeightedPath	0.001	0.001	0.002
extractDrugWienerNumbers	0.002	0.000	0.002
extractDrugXLogP	0.001	0.000	0.002
extractDrugZagrebIndex	0.002	0.000	0.002
extractPCMBLOSUM	0.013	0.002	0.015
extractPCMDescScales	0.015	0.001	0.016
extractPCMFAScales	0.028	0.003	0.031
extractPCMMDSScales	0.015	0.002	0.017
extractPCMPropScales	0.017	0.001	0.019
extractPCMScales	0.028	0.002	0.031
extractProtAAC	0.003	0.000	0.004
extractProtAPAAC	2.218	0.049	2.266
extractProtCTDC	0.003	0.000	0.003
extractProtCTDD	0.005	0.001	0.006
extractProtCTDT	0.007	0.001	0.008
extractProtCTriad	0.133	0.008	0.141
extractProtDC	0.005	0.002	0.007
extractProtGeary	0.190	0.004	0.192
extractProtMoran	0.159	0.006	0.165
extractProtMoreauBroto	0.159	0.005	0.163
extractProtPAAC	0.816	0.014	0.831
extractProtPSSM	0.001	0.001	0.002
extractProtPSSMAcc	0.001	0.000	0.001
extractProtPSSMFeature	0.002	0.000	0.002
extractProtQSO	1.536	0.014	1.549
extractProtSOCN	1.546	0.010	1.557
extractProtTC	0.050	0.042	0.093
getCPI	0.003	0.000	0.004
getDrug	0.001	0.000	0.001
getFASTAFromKEGG	0.001	0.000	0.001
getFASTAFromUniProt	0.000	0.000	0.001
getMolFromCAS	0.000	0.000	0.001
getMolFromChEMBL	0	0	0
getMolFromDrugBank	0	0	0
getMolFromKEGG	0	0	0
getMolFromPubChem	0.001	0.000	0.000
getPDBFromRCSBPDB	0.000	0.001	0.001
getPPI	0.004	0.001	0.005
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	0.001
getSmiFromChEMBL	0.000	0.000	0.001
getSmiFromDrugBank	0.000	0.000	0.001
getSmiFromKEGG	0	0	0
getSmiFromPubChem	0	0	0
readFASTA	0.002	0.000	0.003
readMolFromSDF	0.003	0.001	0.003
readMolFromSmi	0.001	0.000	0.002
readPDB	1.134	0.010	1.145
searchDrug	0.002	0.001	0.003
segProt	0.003	0.000	0.004

BioC 3.4: CHECK report for Rcpi on morelia

Summary

Command output