BioC 3.5: CHECK report for Rcpi on malbec2

Package: Rcpi

Version: 1.12.6

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Rcpi_1.12.6.tar.gz

StartedAt: 2017-10-18 01:52:29 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 01:54:46 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 137.2 seconds

RetCode: 0

Status: OK

CheckDir: Rcpi.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings Rcpi_1.12.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/Rcpi.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.12.6’
* package encoding: UTF-8
* 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	0.000	0.015
AA3DMoRSE	0.000	0.000	0.001
AAACF	0.000	0.000	0.002
AABLOSUM100	0.000	0.000	0.001
AABLOSUM45	0.000	0.000	0.001
AABLOSUM50	0.000	0.000	0.001
AABLOSUM62	0.000	0.000	0.001
AABLOSUM80	0.000	0.000	0.001
AABurden	0.004	0.000	0.001
AACPSA	0.000	0.000	0.001
AAConn	0.004	0.000	0.001
AAConst	0.000	0.000	0.001
AADescAll	0.004	0.000	0.001
AAEdgeAdj	0.000	0.000	0.002
AAEigIdx	0.000	0.000	0.001
AAFGC	0.000	0.000	0.001
AAGETAWAY	0.004	0.000	0.001
AAGeom	0.000	0.000	0.001
AAInfo	0.004	0.000	0.001
AAMOE2D	0.000	0.000	0.001
AAMOE3D	0.000	0.000	0.001
AAMetaInfo	0.000	0.000	0.001
AAMolProp	0.000	0.000	0.001
AAPAM120	0.000	0.000	0.001
AAPAM250	0.000	0.000	0.001
AAPAM30	0.004	0.000	0.001
AAPAM40	0.000	0.000	0.001
AAPAM70	0.000	0.004	0.001
AARDF	0.000	0.000	0.002
AARandic	0.000	0.000	0.001
AATopo	0.000	0.000	0.001
AATopoChg	0.000	0.000	0.001
AAWHIM	0.000	0.000	0.001
AAWalk	0.000	0.000	0.001
AAindex	0.004	0.000	0.001
OptAA3d	0	0	0
acc	0.012	0.000	0.010
calcDrugFPSim	2.072	0.060	1.718
calcDrugMCSSim	0.024	0.000	0.024
calcParProtGOSim	0.000	0.000	0.002
calcParProtSeqSim	0.036	0.000	0.038
calcTwoProtGOSim	0.004	0.000	0.002
calcTwoProtSeqSim	0.004	0.000	0.003
checkProt	0.004	0.000	0.002
convMolFormat	0.000	0.000	0.002
extractDrugAIO	0.000	0.000	0.002
extractDrugALOGP	0.004	0.000	0.001
extractDrugAminoAcidCount	0.000	0.000	0.002
extractDrugApol	0.000	0.004	0.001
extractDrugAromaticAtomsCount	0.000	0.000	0.002
extractDrugAromaticBondsCount	0.000	0.000	0.001
extractDrugAtomCount	0.004	0.000	0.002
extractDrugAutocorrelationCharge	0.000	0.000	0.001
extractDrugAutocorrelationMass	0.000	0.000	0.002
extractDrugAutocorrelationPolarizability	0.000	0.004	0.002
extractDrugBCUT	0.000	0.000	0.001
extractDrugBPol	0.000	0.000	0.001
extractDrugBondCount	0.004	0.000	0.002
extractDrugCPSA	0.000	0.000	0.001
extractDrugCarbonTypes	0.000	0.000	0.002
extractDrugChiChain	0.004	0.000	0.001
extractDrugChiCluster	0.000	0.000	0.002
extractDrugChiPath	0.000	0.000	0.001
extractDrugChiPathCluster	0.004	0.000	0.002
extractDrugDescOB	0.272	0.016	0.290
extractDrugECI	0.000	0.000	0.001
extractDrugEstate	0.004	0.000	0.001
extractDrugEstateComplete	0.000	0.000	0.002
extractDrugExtended	0.000	0.000	0.001
extractDrugExtendedComplete	0.004	0.000	0.003
extractDrugFMF	0.000	0.000	0.002
extractDrugFragmentComplexity	0.000	0.000	0.001
extractDrugGraph	0.004	0.000	0.001
extractDrugGraphComplete	0.000	0.000	0.001
extractDrugGravitationalIndex	0.004	0.000	0.001
extractDrugHBondAcceptorCount	0.004	0.000	0.003
extractDrugHBondDonorCount	0.000	0.000	0.001
extractDrugHybridization	0.004	0.000	0.001
extractDrugHybridizationComplete	0.000	0.000	0.001
extractDrugHybridizationRatio	0.000	0.000	0.001
extractDrugIPMolecularLearning	0.000	0.000	0.001
extractDrugKR	0.004	0.000	0.001
extractDrugKRComplete	0.000	0.000	0.001
extractDrugKappaShapeIndices	0.004	0.000	0.001
extractDrugKierHallSmarts	0.004	0.000	0.002
extractDrugLargestChain	0.000	0.000	0.001
extractDrugLargestPiSystem	0.000	0.000	0.001
extractDrugLengthOverBreadth	0.004	0.000	0.001
extractDrugLongestAliphaticChain	0.000	0.000	0.001
extractDrugMACCS	0.000	0.000	0.001
extractDrugMACCSComplete	0.004	0.000	0.001
extractDrugMDE	0.000	0.000	0.001
extractDrugMannholdLogP	0.000	0.000	0.002
extractDrugMomentOfInertia	0.004	0.000	0.002
extractDrugOBFP2	0.008	0.004	0.012
extractDrugOBFP3	0.008	0.004	0.012
extractDrugOBFP4	0.012	0.000	0.008
extractDrugOBMACCS	0.008	0.004	0.012
extractDrugPetitjeanNumber	0.004	0.000	0.001
extractDrugPetitjeanShapeIndex	0.000	0.000	0.001
extractDrugPubChem	0.000	0.000	0.002
extractDrugPubChemComplete	0.000	0.000	0.002
extractDrugRotatableBondsCount	0.000	0.000	0.002
extractDrugRuleOfFive	0.004	0.000	0.001
extractDrugShortestPath	0.000	0.000	0.001
extractDrugShortestPathComplete	0.000	0.000	0.002
extractDrugStandard	0.000	0.000	0.002
extractDrugStandardComplete	0.004	0.000	0.001
extractDrugTPSA	0.000	0.000	0.001
extractDrugVABC	0.000	0.000	0.001
extractDrugVAdjMa	0.004	0.000	0.001
extractDrugWHIM	0.000	0.000	0.001
extractDrugWeight	0.000	0.000	0.001
extractDrugWeightedPath	0.004	0.000	0.001
extractDrugWienerNumbers	0.000	0.000	0.002
extractDrugXLogP	0.000	0.000	0.001
extractDrugZagrebIndex	0.000	0.000	0.001
extractPCMBLOSUM	0.068	0.004	0.075
extractPCMDescScales	0.02	0.00	0.02
extractPCMFAScales	0.024	0.000	0.024
extractPCMMDSScales	0.016	0.000	0.014
extractPCMPropScales	0.024	0.000	0.022
extractPCMScales	0.016	0.000	0.015
extractProtAAC	0.004	0.000	0.002
extractProtAPAAC	0.892	0.028	0.920
extractProtCTDC	0.004	0.000	0.002
extractProtCTDD	0.004	0.000	0.004
extractProtCTDT	0.004	0.000	0.004
extractProtCTriad	0.064	0.020	0.082
extractProtDC	0.000	0.004	0.004
extractProtGeary	0.152	0.008	0.158
extractProtMoran	0.148	0.004	0.149
extractProtMoreauBroto	0.136	0.000	0.138
extractProtPAAC	0.472	0.004	0.476
extractProtPSSM	0.000	0.000	0.001
extractProtPSSMAcc	0.004	0.000	0.001
extractProtPSSMFeature	0.000	0.000	0.001
extractProtQSO	0.888	0.004	0.890
extractProtSOCN	0.808	0.000	0.808
extractProtTC	0.028	0.012	0.040
getCPI	0.004	0.000	0.003
getDrug	0	0	0
getFASTAFromKEGG	0.004	0.000	0.000
getFASTAFromUniProt	0	0	0
getMolFromCAS	0	0	0
getMolFromChEMBL	0	0	0
getMolFromDrugBank	0	0	0
getMolFromKEGG	0	0	0
getMolFromPubChem	0	0	0
getPDBFromRCSBPDB	0	0	0
getPPI	0.000	0.000	0.003
getProt	0.000	0.000	0.001
getSeqFromKEGG	0.000	0.000	0.001
getSeqFromRCSBPDB	0	0	0
getSeqFromUniProt	0	0	0
getSmiFromChEMBL	0.004	0.000	0.000
getSmiFromDrugBank	0	0	0
getSmiFromKEGG	0	0	0
getSmiFromPubChem	0	0	0
readFASTA	0.004	0.000	0.001
readMolFromSDF	0.000	0.000	0.001
readMolFromSmi	0.000	0.000	0.001
readPDB	1.008	0.000	1.010
searchDrug	0.000	0.000	0.002
segProt	0.004	0.000	0.003

BioC 3.5: CHECK report for Rcpi on malbec2

Summary

Command output