BioC 3.2: CHECK report for Rcpi on linux1.bioconductor.org

Package: Rcpi

Version: 1.6.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Rcpi_1.6.0.tar.gz

StartedAt: 2015-10-27 07:17:12 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 07:19:40 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 148.1 seconds

RetCode: 0

Status:  OK

CheckDir: Rcpi.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings Rcpi_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/Rcpi.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.6.0’
* 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 ... [13s/13s] 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 ... [13s/13s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [7s/7s]
 [7s/7s] 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	0.003	0.000	0.003
AA3DMoRSE	0.002	0.000	0.002
AAACF	0.002	0.000	0.001
AABLOSUM100	0.001	0.000	0.001
AABLOSUM45	0.002	0.000	0.002
AABLOSUM50	0.002	0.000	0.002
AABLOSUM62	0.001	0.000	0.001
AABLOSUM80	0.001	0.000	0.001
AABurden	0.002	0.000	0.002
AACPSA	0.002	0.000	0.002
AAConn	0.002	0.000	0.002
AAConst	0.002	0.000	0.002
AADescAll	0.000	0.004	0.002
AAEdgeAdj	0.001	0.000	0.002
AAEigIdx	0.002	0.000	0.001
AAFGC	0.002	0.000	0.001
AAGETAWAY	0.002	0.000	0.001
AAGeom	0.001	0.000	0.001
AAInfo	0.001	0.000	0.002
AAMOE2D	0.002	0.000	0.002
AAMOE3D	0.002	0.000	0.002
AAMetaInfo	0.002	0.000	0.002
AAMolProp	0.002	0.000	0.001
AAPAM120	0.000	0.004	0.001
AAPAM250	0.000	0.000	0.002
AAPAM30	0.000	0.000	0.002
AAPAM40	0.002	0.000	0.001
AAPAM70	0.001	0.000	0.001
AARDF	0.001	0.000	0.002
AARandic	0.002	0.000	0.002
AATopo	0.002	0.000	0.002
AATopoChg	0.002	0.000	0.001
AAWHIM	0.001	0.000	0.001
AAWalk	0.001	0.000	0.002
AAindex	0.002	0.000	0.002
OptAA3d	0.001	0.000	0.001
Rcpi-package	0.001	0.000	0.001
acc	0.014	0.004	0.018
calcDrugFPSim	0.001	0.000	0.001
calcDrugMCSSim	0.001	0.000	0.001
calcParProtGOSim	0.001	0.000	0.000
calcParProtSeqSim	0	0	0
calcTwoProtGOSim	0.001	0.000	0.001
calcTwoProtSeqSim	0.001	0.000	0.001
checkProt	0.003	0.000	0.003
convMolFormat	0.001	0.000	0.001
extractDrugAIO	0.001	0.000	0.000
extractDrugALOGP	0	0	0
extractDrugAminoAcidCount	0.000	0.004	0.001
extractDrugApol	0.000	0.000	0.001
extractDrugAromaticAtomsCount	0	0	0
extractDrugAromaticBondsCount	0	0	0
extractDrugAtomCount	0.001	0.000	0.001
extractDrugAutocorrelationCharge	0.001	0.000	0.001
extractDrugAutocorrelationMass	0.001	0.000	0.000
extractDrugAutocorrelationPolarizability	0	0	0
extractDrugBCUT	0.000	0.000	0.001
extractDrugBPol	0.001	0.000	0.001
extractDrugBondCount	0.001	0.000	0.001
extractDrugCPSA	0	0	0
extractDrugCarbonTypes	0.000	0.000	0.001
extractDrugChiChain	0.001	0.000	0.001
extractDrugChiCluster	0.000	0.000	0.001
extractDrugChiPath	0	0	0
extractDrugChiPathCluster	0.000	0.000	0.001
extractDrugDescOB	0.001	0.000	0.001
extractDrugECI	0.001	0.000	0.000
extractDrugEstate	0	0	0
extractDrugEstateComplete	0.000	0.000	0.001
extractDrugExtended	0.001	0.000	0.001
extractDrugExtendedComplete	0	0	0
extractDrugFMF	0.000	0.000	0.001
extractDrugFragmentComplexity	0.001	0.000	0.001
extractDrugGraph	0.001	0.000	0.000
extractDrugGraphComplete	0	0	0
extractDrugGravitationalIndex	0.000	0.000	0.001
extractDrugHBondAcceptorCount	0.001	0.000	0.001
extractDrugHBondDonorCount	0.001	0.000	0.000
extractDrugHybridization	0	0	0
extractDrugHybridizationComplete	0.000	0.000	0.001
extractDrugHybridizationRatio	0.001	0.000	0.001
extractDrugIPMolecularLearning	0.001	0.000	0.000
extractDrugKR	0	0	0
extractDrugKRComplete	0.000	0.000	0.001
extractDrugKappaShapeIndices	0.001	0.000	0.001
extractDrugKierHallSmarts	0.001	0.000	0.000
extractDrugLargestChain	0	0	0
extractDrugLargestPiSystem	0.001	0.000	0.001
extractDrugLengthOverBreadth	0.001	0.000	0.001
extractDrugLongestAliphaticChain	0	0	0
extractDrugMACCS	0	0	0
extractDrugMACCSComplete	0.001	0.000	0.001
extractDrugMDE	0.001	0.000	0.001
extractDrugMannholdLogP	0	0	0
extractDrugMomentOfInertia	0	0	0
extractDrugOBFP2	0.000	0.000	0.001
extractDrugOBFP3	0.001	0.000	0.000
extractDrugOBFP4	0	0	0
extractDrugOBMACCS	0.000	0.000	0.001
extractDrugPetitjeanNumber	0.001	0.000	0.001
extractDrugPetitjeanShapeIndex	0.001	0.000	0.000
extractDrugPubChem	0	0	0
extractDrugPubChemComplete	0.000	0.000	0.001
extractDrugRotatableBondsCount	0.001	0.000	0.001
extractDrugRuleOfFive	0.001	0.000	0.000
extractDrugShortestPath	0	0	0
extractDrugShortestPathComplete	0.000	0.000	0.001
extractDrugStandard	0.001	0.000	0.001
extractDrugStandardComplete	0.001	0.000	0.000
extractDrugTPSA	0	0	0
extractDrugVABC	0.000	0.000	0.001
extractDrugVAdjMa	0.000	0.000	0.001
extractDrugWHIM	0.000	0.000	0.001
extractDrugWeight	0.000	0.000	0.001
extractDrugWeightedPath	0.001	0.000	0.001
extractDrugWienerNumbers	0.001	0.000	0.001
extractDrugXLogP	0.001	0.000	0.000
extractDrugZagrebIndex	0	0	0
extractPCMBLOSUM	0.015	0.008	0.022
extractPCMDescScales	0.018	0.000	0.017
extractPCMFAScales	0.024	0.000	0.024
extractPCMMDSScales	0.016	0.004	0.019
extractPCMPropScales	0.014	0.004	0.017
extractPCMScales	0.029	0.000	0.029
extractProtAAC	0.000	0.004	0.004
extractProtAPAAC	1.911	0.000	1.913
extractProtCTDC	0.005	0.000	0.004
extractProtCTDD	0.000	0.004	0.004
extractProtCTDT	0.006	0.000	0.005
extractProtCTriad	0.159	0.000	0.159
extractProtDC	0.000	0.004	0.004
extractProtGeary	0.113	0.004	0.117
extractProtMoran	0.111	0.000	0.110
extractProtMoreauBroto	0.135	0.008	0.143
extractProtPAAC	0.856	0.000	0.856
extractProtPSSM	0	0	0
extractProtPSSMAcc	0	0	0
extractProtPSSMFeature	0	0	0
extractProtQSO	1.113	0.000	1.115
extractProtSOCN	1.099	0.000	1.098
extractProtTC	0.026	0.028	0.054
getCPI	0.003	0.000	0.002
getDrug	0.001	0.000	0.000
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	0	0
getPDBFromRCSBPDB	0	0	0
getPPI	0.000	0.000	0.003
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	0	0
getSmiFromPubChem	0	0	0
readFASTA	0.000	0.000	0.001
readMolFromSDF	0	0	0
readMolFromSmi	0	0	0
readPDB	1.532	0.020	1.554
searchDrug	0.001	0.000	0.000
segProt	0.003	0.000	0.003