BioC 3.4: CHECK report for Rcpi on malbec1

Package: Rcpi

Version: 1.10.6

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Rcpi_1.10.6.tar.gz

StartedAt: 2017-04-15 00:45:56 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:48:02 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 125.4 seconds

RetCode: 0

Status: OK

CheckDir: Rcpi.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Rcpi_1.10.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Rcpi.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 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	0.016	0.004	0.022
AA3DMoRSE	0.000	0.000	0.002
AAACF	0.000	0.000	0.002
AABLOSUM100	0.000	0.000	0.002
AABLOSUM45	0.000	0.000	0.002
AABLOSUM50	0.004	0.000	0.002
AABLOSUM62	0.004	0.000	0.002
AABLOSUM80	0.004	0.000	0.002
AABurden	0.004	0.000	0.002
AACPSA	0.004	0.000	0.002
AAConn	0.000	0.000	0.002
AAConst	0.000	0.000	0.002
AADescAll	0.004	0.000	0.002
AAEdgeAdj	0.004	0.000	0.002
AAEigIdx	0.004	0.000	0.001
AAFGC	0.004	0.000	0.002
AAGETAWAY	0.000	0.000	0.002
AAGeom	0.000	0.000	0.001
AAInfo	0.000	0.000	0.002
AAMOE2D	0.004	0.000	0.002
AAMOE3D	0.004	0.000	0.001
AAMetaInfo	0.004	0.000	0.002
AAMolProp	0.000	0.000	0.002
AAPAM120	0.000	0.000	0.003
AAPAM250	0.000	0.000	0.002
AAPAM30	0.000	0.004	0.002
AAPAM40	0.004	0.000	0.001
AAPAM70	0.000	0.000	0.002
AARDF	0.000	0.000	0.002
AARandic	0.000	0.000	0.002
AATopo	0.000	0.004	0.002
AATopoChg	0.004	0.000	0.001
AAWHIM	0.000	0.000	0.002
AAWalk	0.000	0.000	0.002
AAindex	0.000	0.000	0.002
OptAA3d	0.000	0.000	0.001
acc	0.016	0.000	0.017
calcDrugFPSim	2.048	0.060	0.715
calcDrugMCSSim	0.004	0.008	0.007
calcParProtGOSim	0.004	0.000	0.001
calcParProtSeqSim	0.004	0.000	0.004
calcTwoProtGOSim	0	0	0
calcTwoProtSeqSim	0.004	0.000	0.002
checkProt	0.000	0.000	0.002
convMolFormat	0.000	0.000	0.001
extractDrugAIO	0	0	0
extractDrugALOGP	0.004	0.000	0.001
extractDrugAminoAcidCount	0.000	0.000	0.001
extractDrugApol	0.000	0.004	0.001
extractDrugAromaticAtomsCount	0.000	0.000	0.001
extractDrugAromaticBondsCount	0	0	0
extractDrugAtomCount	0.000	0.000	0.001
extractDrugAutocorrelationCharge	0.000	0.000	0.001
extractDrugAutocorrelationMass	0.004	0.000	0.001
extractDrugAutocorrelationPolarizability	0	0	0
extractDrugBCUT	0.000	0.000	0.001
extractDrugBPol	0.004	0.000	0.000
extractDrugBondCount	0.000	0.000	0.001
extractDrugCPSA	0.004	0.000	0.001
extractDrugCarbonTypes	0.000	0.000	0.001
extractDrugChiChain	0.000	0.000	0.001
extractDrugChiCluster	0.004	0.000	0.000
extractDrugChiPath	0.000	0.000	0.001
extractDrugChiPathCluster	0.000	0.000	0.001
extractDrugDescOB	0.204	0.000	0.208
extractDrugECI	0.000	0.000	0.001
extractDrugEstate	0	0	0
extractDrugEstateComplete	0.000	0.000	0.001
extractDrugExtended	0.000	0.000	0.001
extractDrugExtendedComplete	0.004	0.000	0.000
extractDrugFMF	0	0	0
extractDrugFragmentComplexity	0.000	0.000	0.001
extractDrugGraph	0	0	0
extractDrugGraphComplete	0.000	0.000	0.001
extractDrugGravitationalIndex	0.004	0.000	0.001
extractDrugHBondAcceptorCount	0.000	0.000	0.001
extractDrugHBondDonorCount	0.000	0.000	0.001
extractDrugHybridization	0.000	0.000	0.002
extractDrugHybridizationComplete	0	0	0
extractDrugHybridizationRatio	0.000	0.004	0.001
extractDrugIPMolecularLearning	0	0	0
extractDrugKR	0.000	0.000	0.001
extractDrugKRComplete	0.000	0.000	0.001
extractDrugKappaShapeIndices	0.000	0.000	0.001
extractDrugKierHallSmarts	0.004	0.000	0.000
extractDrugLargestChain	0.000	0.000	0.001
extractDrugLargestPiSystem	0.004	0.000	0.000
extractDrugLengthOverBreadth	0.000	0.000	0.001
extractDrugLongestAliphaticChain	0	0	0
extractDrugMACCS	0.000	0.000	0.001
extractDrugMACCSComplete	0	0	0
extractDrugMDE	0.000	0.000	0.001
extractDrugMannholdLogP	0.000	0.000	0.001
extractDrugMomentOfInertia	0.000	0.000	0.001
extractDrugOBFP2	0.008	0.000	0.008
extractDrugOBFP3	0.004	0.004	0.009
extractDrugOBFP4	0.008	0.000	0.009
extractDrugOBMACCS	0.004	0.004	0.010
extractDrugPetitjeanNumber	0.000	0.000	0.001
extractDrugPetitjeanShapeIndex	0	0	0
extractDrugPubChem	0.000	0.000	0.002
extractDrugPubChemComplete	0.000	0.000	0.001
extractDrugRotatableBondsCount	0.004	0.000	0.001
extractDrugRuleOfFive	0.000	0.000	0.001
extractDrugShortestPath	0.000	0.004	0.001
extractDrugShortestPathComplete	0	0	0
extractDrugStandard	0.000	0.000	0.001
extractDrugStandardComplete	0.000	0.000	0.001
extractDrugTPSA	0.000	0.000	0.001
extractDrugVABC	0	0	0
extractDrugVAdjMa	0.000	0.000	0.001
extractDrugWHIM	0.004	0.000	0.001
extractDrugWeight	0	0	0
extractDrugWeightedPath	0.000	0.000	0.001
extractDrugWienerNumbers	0.000	0.000	0.001
extractDrugXLogP	0	0	0
extractDrugZagrebIndex	0.000	0.004	0.001
extractPCMBLOSUM	0.008	0.000	0.010
extractPCMDescScales	0.008	0.000	0.011
extractPCMFAScales	0.016	0.000	0.018
extractPCMMDSScales	0.012	0.000	0.010
extractPCMPropScales	0.012	0.000	0.012
extractPCMScales	0.020	0.000	0.019
extractProtAAC	0.004	0.000	0.002
extractProtAPAAC	1.992	0.004	1.997
extractProtCTDC	0.004	0.000	0.003
extractProtCTDD	0.008	0.000	0.005
extractProtCTDT	0.004	0.000	0.005
extractProtCTriad	0.076	0.008	0.083
extractProtDC	0.004	0.000	0.004
extractProtGeary	0.112	0.004	0.117
extractProtMoran	0.120	0.000	0.117
extractProtMoreauBroto	0.112	0.004	0.117
extractProtPAAC	0.548	0.004	0.553
extractProtPSSM	0.000	0.000	0.001
extractProtPSSMAcc	0.000	0.000	0.001
extractProtPSSMFeature	0.000	0.000	0.001
extractProtQSO	0.864	0.000	0.861
extractProtSOCN	0.828	0.000	0.828
extractProtTC	0.028	0.016	0.044
getCPI	0.004	0.000	0.002
getDrug	0	0	0
getFASTAFromKEGG	0	0	0
getFASTAFromUniProt	0	0	0
getMolFromCAS	0	0	0
getMolFromChEMBL	0	0	0
getMolFromDrugBank	0	0	0
getMolFromKEGG	0.004	0.000	0.000
getMolFromPubChem	0	0	0
getPDBFromRCSBPDB	0	0	0
getPPI	0.004	0.000	0.002
getProt	0	0	0
getSeqFromKEGG	0	0	0
getSeqFromRCSBPDB	0	0	0
getSeqFromUniProt	0	0	0
getSmiFromChEMBL	0	0	0
getSmiFromDrugBank	0	0	0
getSmiFromKEGG	0.004	0.000	0.000
getSmiFromPubChem	0	0	0
readFASTA	0.000	0.000	0.001
readMolFromSDF	0.004	0.000	0.001
readMolFromSmi	0.000	0.000	0.001
readPDB	0.952	0.000	0.952
searchDrug	0.000	0.000	0.001
segProt	0.004	0.000	0.002

BioC 3.4: CHECK report for Rcpi on malbec1

Summary

Command output