BioC 3.5: CHECK report for Rcpi on toluca2

Package: Rcpi

Version: 1.11.6

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.11.6.tar.gz

StartedAt: 2017-04-23 08:43:50 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 08:46:41 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 171.3 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_1.11.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/Rcpi.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.11.6’
* 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	0.019	0.004	0.022
AA3DMoRSE	0.002	0.000	0.002
AAACF	0.001	0.001	0.005
AABLOSUM100	0.002	0.000	0.003
AABLOSUM45	0.001	0.000	0.002
AABLOSUM50	0.001	0.001	0.005
AABLOSUM62	0.001	0.001	0.002
AABLOSUM80	0.002	0.001	0.002
AABurden	0.002	0.001	0.002
AACPSA	0.001	0.001	0.002
AAConn	0.001	0.000	0.002
AAConst	0.002	0.000	0.002
AADescAll	0.002	0.001	0.002
AAEdgeAdj	0.001	0.001	0.002
AAEigIdx	0.002	0.001	0.002
AAFGC	0.002	0.001	0.002
AAGETAWAY	0.002	0.000	0.002
AAGeom	0.001	0.000	0.002
AAInfo	0.002	0.000	0.003
AAMOE2D	0.002	0.000	0.003
AAMOE3D	0.002	0.000	0.002
AAMetaInfo	0.001	0.001	0.002
AAMolProp	0.001	0.001	0.003
AAPAM120	0.002	0.001	0.002
AAPAM250	0.002	0.001	0.002
AAPAM30	0.001	0.001	0.002
AAPAM40	0.001	0.001	0.003
AAPAM70	0.002	0.001	0.002
AARDF	0.002	0.001	0.002
AARandic	0.001	0.001	0.003
AATopo	0.001	0.001	0.002
AATopoChg	0.001	0.001	0.002
AAWHIM	0.002	0.001	0.002
AAWalk	0.002	0.001	0.002
AAindex	0.002	0.001	0.003
OptAA3d	0.001	0.000	0.001
acc	0.017	0.006	0.023
calcDrugFPSim	2.102	0.138	1.167
calcDrugMCSSim	0.010	0.002	0.012
calcParProtGOSim	0.001	0.000	0.001
calcParProtSeqSim	0.039	0.001	0.041
calcTwoProtGOSim	0.001	0.000	0.001
calcTwoProtSeqSim	0.003	0.001	0.003
checkProt	0.002	0.000	0.003
convMolFormat	0.002	0.001	0.001
extractDrugAIO	0.001	0.000	0.002
extractDrugALOGP	0.001	0.000	0.001
extractDrugAminoAcidCount	0.001	0.000	0.001
extractDrugApol	0.001	0.000	0.001
extractDrugAromaticAtomsCount	0.001	0.000	0.001
extractDrugAromaticBondsCount	0.001	0.001	0.001
extractDrugAtomCount	0.001	0.000	0.001
extractDrugAutocorrelationCharge	0.001	0.000	0.002
extractDrugAutocorrelationMass	0.001	0.001	0.001
extractDrugAutocorrelationPolarizability	0.002	0.000	0.001
extractDrugBCUT	0.001	0.000	0.001
extractDrugBPol	0.001	0.000	0.002
extractDrugBondCount	0.001	0.000	0.002
extractDrugCPSA	0.001	0.000	0.001
extractDrugCarbonTypes	0.001	0.000	0.001
extractDrugChiChain	0.001	0.000	0.002
extractDrugChiCluster	0.001	0.000	0.001
extractDrugChiPath	0.001	0.000	0.001
extractDrugChiPathCluster	0.001	0.000	0.002
extractDrugDescOB	0.012	0.002	0.015
extractDrugECI	0.001	0.000	0.001
extractDrugEstate	0.001	0.000	0.001
extractDrugEstateComplete	0.002	0.000	0.001
extractDrugExtended	0.001	0.000	0.001
extractDrugExtendedComplete	0.001	0.001	0.002
extractDrugFMF	0.001	0.000	0.001
extractDrugFragmentComplexity	0.001	0.000	0.002
extractDrugGraph	0.001	0.001	0.001
extractDrugGraphComplete	0.001	0.000	0.001
extractDrugGravitationalIndex	0.001	0.000	0.002
extractDrugHBondAcceptorCount	0.001	0.001	0.001
extractDrugHBondDonorCount	0.001	0.000	0.001
extractDrugHybridization	0.001	0.000	0.001
extractDrugHybridizationComplete	0.001	0.001	0.001
extractDrugHybridizationRatio	0.001	0.000	0.001
extractDrugIPMolecularLearning	0.002	0.000	0.002
extractDrugKR	0.001	0.000	0.002
extractDrugKRComplete	0.002	0.000	0.002
extractDrugKappaShapeIndices	0.001	0.001	0.001
extractDrugKierHallSmarts	0.001	0.000	0.001
extractDrugLargestChain	0.001	0.000	0.001
extractDrugLargestPiSystem	0.001	0.001	0.001
extractDrugLengthOverBreadth	0.001	0.000	0.001
extractDrugLongestAliphaticChain	0.002	0.000	0.001
extractDrugMACCS	0.001	0.000	0.001
extractDrugMACCSComplete	0.001	0.000	0.001
extractDrugMDE	0.001	0.000	0.001
extractDrugMannholdLogP	0.001	0.001	0.001
extractDrugMomentOfInertia	0.001	0.000	0.001
extractDrugOBFP2	0.011	0.000	0.011
extractDrugOBFP3	0.01	0.00	0.01
extractDrugOBFP4	0.010	0.001	0.010
extractDrugOBMACCS	0.009	0.000	0.009
extractDrugPetitjeanNumber	0.002	0.001	0.001
extractDrugPetitjeanShapeIndex	0.001	0.000	0.001
extractDrugPubChem	0.001	0.000	0.001
extractDrugPubChemComplete	0.001	0.000	0.001
extractDrugRotatableBondsCount	0.001	0.000	0.002
extractDrugRuleOfFive	0.001	0.000	0.001
extractDrugShortestPath	0.001	0.000	0.001
extractDrugShortestPathComplete	0.001	0.000	0.001
extractDrugStandard	0.001	0.000	0.001
extractDrugStandardComplete	0.001	0.000	0.002
extractDrugTPSA	0.001	0.000	0.001
extractDrugVABC	0.001	0.000	0.001
extractDrugVAdjMa	0.001	0.000	0.001
extractDrugWHIM	0.001	0.000	0.001
extractDrugWeight	0.001	0.000	0.001
extractDrugWeightedPath	0.001	0.000	0.001
extractDrugWienerNumbers	0.001	0.000	0.001
extractDrugXLogP	0.001	0.001	0.002
extractDrugZagrebIndex	0.001	0.000	0.001
extractPCMBLOSUM	0.072	0.002	0.076
extractPCMDescScales	0.015	0.002	0.018
extractPCMFAScales	0.217	0.003	0.223
extractPCMMDSScales	0.013	0.002	0.015
extractPCMPropScales	0.039	0.002	0.042
extractPCMScales	0.025	0.003	0.028
extractProtAAC	0.002	0.001	0.003
extractProtAPAAC	1.566	0.021	1.608
extractProtCTDC	0.003	0.000	0.004
extractProtCTDD	0.007	0.001	0.008
extractProtCTDT	0.007	0.001	0.008
extractProtCTriad	0.133	0.010	0.145
extractProtDC	0.005	0.002	0.008
extractProtGeary	0.293	0.006	0.305
extractProtMoran	0.288	0.005	0.297
extractProtMoreauBroto	0.291	0.010	0.306
extractProtPAAC	0.895	0.008	0.910
extractProtPSSM	0.001	0.000	0.002
extractProtPSSMAcc	0.002	0.000	0.002
extractProtPSSMFeature	0.001	0.001	0.002
extractProtQSO	1.556	0.014	1.577
extractProtSOCN	1.593	0.009	1.609
extractProtTC	0.053	0.043	0.097
getCPI	0.003	0.001	0.004
getDrug	0	0	0
getFASTAFromKEGG	0.001	0.000	0.001
getFASTAFromUniProt	0.000	0.001	0.001
getMolFromCAS	0.001	0.000	0.001
getMolFromChEMBL	0.001	0.000	0.000
getMolFromDrugBank	0.001	0.000	0.000
getMolFromKEGG	0.001	0.000	0.000
getMolFromPubChem	0.001	0.000	0.000
getPDBFromRCSBPDB	0.001	0.000	0.000
getPPI	0.003	0.000	0.003
getProt	0.000	0.001	0.001
getSeqFromKEGG	0	0	0
getSeqFromRCSBPDB	0	0	0
getSeqFromUniProt	0	0	0
getSmiFromChEMBL	0	0	0
getSmiFromDrugBank	0	0	0
getSmiFromKEGG	0.000	0.000	0.001
getSmiFromPubChem	0.000	0.000	0.001
readFASTA	0.002	0.000	0.002
readMolFromSDF	0.002	0.000	0.002
readMolFromSmi	0.001	0.001	0.000
readPDB	1.236	0.008	1.256
searchDrug	0.002	0.000	0.002
segProt	0.003	0.001	0.003