BioC 3.6: CHECK report for Rcpi on malbec1

Package: Rcpi

Version: 1.13.4

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Rcpi_1.13.4.tar.gz

StartedAt: 2017-08-16 01:47:21 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:49:29 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 128.5 seconds

RetCode: 0

Status: OK

CheckDir: Rcpi.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Rcpi_1.13.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/Rcpi.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.13.4’
* 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	0.004	0.008	0.013
AA3DMoRSE	0.000	0.000	0.001
AAACF	0.000	0.000	0.001
AABLOSUM100	0.000	0.000	0.001
AABLOSUM45	0.000	0.000	0.001
AABLOSUM50	0.000	0.000	0.001
AABLOSUM62	0.000	0.004	0.001
AABLOSUM80	0.000	0.000	0.001
AABurden	0.000	0.000	0.001
AACPSA	0.000	0.000	0.001
AAConn	0.000	0.000	0.001
AAConst	0.000	0.000	0.001
AADescAll	0.000	0.000	0.001
AAEdgeAdj	0.000	0.000	0.001
AAEigIdx	0.000	0.000	0.001
AAFGC	0.000	0.000	0.001
AAGETAWAY	0.000	0.000	0.001
AAGeom	0.004	0.000	0.001
AAInfo	0.000	0.000	0.001
AAMOE2D	0.004	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	0.002
AAPAM250	0.004	0.000	0.001
AAPAM30	0.000	0.000	0.001
AAPAM40	0.000	0.004	0.001
AAPAM70	0.000	0.000	0.001
AARDF	0.000	0.000	0.001
AARandic	0.000	0.000	0.001
AATopo	0.000	0.000	0.001
AATopoChg	0.004	0.000	0.001
AAWHIM	0.000	0.000	0.001
AAWalk	0.004	0.000	0.001
AAindex	0.000	0.000	0.001
OptAA3d	0.000	0.000	0.001
acc	0.012	0.000	0.009
calcDrugFPSim	2.040	0.036	0.758
calcDrugMCSSim	0.008	0.004	0.010
calcParProtGOSim	0.000	0.000	0.001
calcParProtSeqSim	0.036	0.000	0.038
calcTwoProtGOSim	0.000	0.000	0.001
calcTwoProtSeqSim	0.004	0.000	0.003
checkProt	0.004	0.000	0.003
convMolFormat	0.004	0.000	0.002
extractDrugAIO	0.000	0.000	0.001
extractDrugALOGP	0.000	0.000	0.001
extractDrugAminoAcidCount	0.004	0.000	0.002
extractDrugApol	0.000	0.000	0.002
extractDrugAromaticAtomsCount	0.000	0.000	0.001
extractDrugAromaticBondsCount	0.004	0.000	0.001
extractDrugAtomCount	0.004	0.000	0.002
extractDrugAutocorrelationCharge	0.000	0.000	0.002
extractDrugAutocorrelationMass	0.000	0.000	0.001
extractDrugAutocorrelationPolarizability	0.004	0.000	0.001
extractDrugBCUT	0.000	0.000	0.001
extractDrugBPol	0.000	0.000	0.002
extractDrugBondCount	0.004	0.000	0.001
extractDrugCPSA	0.000	0.000	0.001
extractDrugCarbonTypes	0.000	0.000	0.002
extractDrugChiChain	0.004	0.000	0.002
extractDrugChiCluster	0.000	0.000	0.001
extractDrugChiPath	0.000	0.000	0.001
extractDrugChiPathCluster	0.004	0.000	0.001
extractDrugDescOB	0.248	0.004	0.253
extractDrugECI	0.000	0.000	0.001
extractDrugEstate	0	0	0
extractDrugEstateComplete	0.004	0.000	0.001
extractDrugExtended	0.000	0.000	0.001
extractDrugExtendedComplete	0.000	0.000	0.001
extractDrugFMF	0.000	0.000	0.001
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	0	0
extractDrugHBondDonorCount	0.000	0.000	0.001
extractDrugHybridization	0.000	0.000	0.001
extractDrugHybridizationComplete	0.000	0.000	0.001
extractDrugHybridizationRatio	0.004	0.000	0.001
extractDrugIPMolecularLearning	0.000	0.000	0.001
extractDrugKR	0	0	0
extractDrugKRComplete	0.000	0.000	0.001
extractDrugKappaShapeIndices	0.000	0.000	0.001
extractDrugKierHallSmarts	0.004	0.000	0.001
extractDrugLargestChain	0.000	0.000	0.001
extractDrugLargestPiSystem	0	0	0
extractDrugLengthOverBreadth	0	0	0
extractDrugLongestAliphaticChain	0.000	0.000	0.001
extractDrugMACCS	0.004	0.000	0.001
extractDrugMACCSComplete	0.000	0.000	0.001
extractDrugMDE	0.000	0.000	0.001
extractDrugMannholdLogP	0	0	0
extractDrugMomentOfInertia	0.000	0.000	0.001
extractDrugOBFP2	0.008	0.000	0.009
extractDrugOBFP3	0.000	0.004	0.005
extractDrugOBFP4	0.004	0.004	0.010
extractDrugOBMACCS	0.012	0.000	0.009
extractDrugPetitjeanNumber	0.000	0.000	0.001
extractDrugPetitjeanShapeIndex	0.000	0.000	0.001
extractDrugPubChem	0.000	0.000	0.001
extractDrugPubChemComplete	0.000	0.000	0.001
extractDrugRotatableBondsCount	0.000	0.004	0.000
extractDrugRuleOfFive	0.000	0.000	0.001
extractDrugShortestPath	0	0	0
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	0.000	0.000	0.001
extractDrugVAdjMa	0	0	0
extractDrugWHIM	0.000	0.000	0.001
extractDrugWeight	0.004	0.000	0.001
extractDrugWeightedPath	0.000	0.000	0.001
extractDrugWienerNumbers	0.000	0.000	0.001
extractDrugXLogP	0	0	0
extractDrugZagrebIndex	0.000	0.000	0.001
extractPCMBLOSUM	0.044	0.000	0.041
extractPCMDescScales	0.008	0.000	0.009
extractPCMFAScales	0.012	0.000	0.015
extractPCMMDSScales	0.012	0.000	0.012
extractPCMPropScales	0.020	0.000	0.023
extractPCMScales	0.012	0.000	0.013
extractProtAAC	0.004	0.000	0.002
extractProtAPAAC	0.828	0.020	0.847
extractProtCTDC	0.004	0.000	0.003
extractProtCTDD	0.004	0.000	0.005
extractProtCTDT	0.004	0.000	0.005
extractProtCTriad	0.072	0.000	0.075
extractProtDC	0.004	0.000	0.004
extractProtGeary	0.156	0.000	0.156
extractProtMoran	0.156	0.000	0.155
extractProtMoreauBroto	0.152	0.000	0.152
extractProtPAAC	0.448	0.008	0.457
extractProtPSSM	0.000	0.000	0.001
extractProtPSSMAcc	0.000	0.000	0.001
extractProtPSSMFeature	0.000	0.000	0.001
extractProtQSO	0.788	0.000	0.789
extractProtSOCN	0.764	0.004	0.770
extractProtTC	0.028	0.016	0.043
getCPI	0.004	0.000	0.003
getDrug	0	0	0
getFASTAFromKEGG	0	0	0
getFASTAFromUniProt	0.000	0.000	0.001
getMolFromCAS	0.000	0.000	0.001
getMolFromChEMBL	0.004	0.000	0.001
getMolFromDrugBank	0.000	0.000	0.001
getMolFromKEGG	0.000	0.000	0.001
getMolFromPubChem	0.000	0.000	0.001
getPDBFromRCSBPDB	0	0	0
getPPI	0.000	0.000	0.002
getProt	0	0	0
getSeqFromKEGG	0.000	0.000	0.001
getSeqFromRCSBPDB	0.000	0.000	0.001
getSeqFromUniProt	0.004	0.000	0.001
getSmiFromChEMBL	0.000	0.000	0.001
getSmiFromDrugBank	0	0	0
getSmiFromKEGG	0	0	0
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	1.016	0.000	1.015
searchDrug	0.004	0.000	0.002
segProt	0.004	0.000	0.004

BioC 3.6: CHECK report for Rcpi on malbec1

Summary

Command output