BioC 3.1: CHECK report for Rcpi on petty

Package: Rcpi

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.4.0.tar.gz

StartedAt: 2015-10-09 01:28:17 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:32:47 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 270.1 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_1.4.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/Rcpi.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.4.0’
* 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 ... [23s/24s] 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 ... [25s/25s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [13s/13s]
 [14s/13s] 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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (Rcpi)

name	user	system	elapsed
AA2DACOR	0.004	0.001	0.005
AA3DMoRSE	0.003	0.000	0.003
AAACF	0.002	0.000	0.003
AABLOSUM100	0.002	0.001	0.002
AABLOSUM45	0.002	0.000	0.002
AABLOSUM50	0.002	0.000	0.003
AABLOSUM62	0.002	0.000	0.003
AABLOSUM80	0.003	0.000	0.003
AABurden	0.002	0.000	0.003
AACPSA	0.003	0.000	0.003
AAConn	0.002	0.001	0.003
AAConst	0.003	0.001	0.004
AADescAll	0.002	0.001	0.003
AAEdgeAdj	0.002	0.001	0.003
AAEigIdx	0.002	0.001	0.003
AAFGC	0.002	0.001	0.003
AAGETAWAY	0.003	0.001	0.003
AAGeom	0.001	0.000	0.002
AAInfo	0.002	0.000	0.003
AAMOE2D	0.001	0.000	0.002
AAMOE3D	0.002	0.001	0.003
AAMetaInfo	0.002	0.001	0.003
AAMolProp	0.003	0.001	0.003
AAPAM120	0.002	0.000	0.002
AAPAM250	0.002	0.000	0.002
AAPAM30	0.002	0.001	0.004
AAPAM40	0.002	0.000	0.003
AAPAM70	0.002	0.001	0.003
AARDF	0.001	0.001	0.002
AARandic	0.001	0.000	0.003
AATopo	0.002	0.001	0.003
AATopoChg	0.003	0.001	0.004
AAWHIM	0.008	0.001	0.009
AAWalk	0.002	0.001	0.002
AAindex	0.002	0.001	0.002
OptAA3d	0.001	0.000	0.001
Rcpi-package	0.001	0.000	0.002
acc	0.028	0.009	0.037
calcDrugFPSim	0.001	0.001	0.001
calcDrugMCSSim	0.001	0.000	0.001
calcParProtGOSim	0.001	0.000	0.001
calcParProtSeqSim	0.001	0.000	0.001
calcTwoProtGOSim	0.001	0.000	0.001
calcTwoProtSeqSim	0.000	0.000	0.001
checkProt	0.005	0.000	0.005
convMolFormat	0.001	0.001	0.001
extractDrugAIO	0.001	0.000	0.001
extractDrugALOGP	0.001	0.001	0.001
extractDrugAminoAcidCount	0.001	0.000	0.001
extractDrugApol	0.000	0.000	0.001
extractDrugAromaticAtomsCount	0.001	0.000	0.001
extractDrugAromaticBondsCount	0	0	0
extractDrugAtomCount	0.001	0.000	0.001
extractDrugAutocorrelationCharge	0.000	0.000	0.001
extractDrugAutocorrelationMass	0.000	0.001	0.001
extractDrugAutocorrelationPolarizability	0.001	0.000	0.000
extractDrugBCUT	0.001	0.000	0.001
extractDrugBPol	0.001	0.000	0.001
extractDrugBondCount	0.000	0.000	0.001
extractDrugCPSA	0.001	0.000	0.002
extractDrugCarbonTypes	0.001	0.000	0.001
extractDrugChiChain	0.001	0.000	0.000
extractDrugChiCluster	0.001	0.000	0.001
extractDrugChiPath	0.001	0.001	0.000
extractDrugChiPathCluster	0.000	0.000	0.001
extractDrugDescOB	0.001	0.000	0.001
extractDrugECI	0	0	0
extractDrugEstate	0.000	0.000	0.001
extractDrugEstateComplete	0.000	0.000	0.001
extractDrugExtended	0.000	0.000	0.001
extractDrugExtendedComplete	0.001	0.000	0.001
extractDrugFMF	0.001	0.000	0.001
extractDrugFragmentComplexity	0.001	0.000	0.001
extractDrugGraph	0.001	0.000	0.001
extractDrugGraphComplete	0.001	0.000	0.001
extractDrugGravitationalIndex	0.001	0.000	0.001
extractDrugHBondAcceptorCount	0.001	0.000	0.001
extractDrugHBondDonorCount	0.001	0.001	0.001
extractDrugHybridization	0.000	0.000	0.001
extractDrugHybridizationComplete	0.001	0.000	0.001
extractDrugHybridizationRatio	0.001	0.000	0.001
extractDrugIPMolecularLearning	0.001	0.000	0.001
extractDrugKR	0.001	0.000	0.001
extractDrugKRComplete	0.001	0.000	0.001
extractDrugKappaShapeIndices	0.001	0.000	0.001
extractDrugKierHallSmarts	0.001	0.000	0.001
extractDrugLargestChain	0.001	0.000	0.001
extractDrugLargestPiSystem	0.001	0.000	0.001
extractDrugLengthOverBreadth	0	0	0
extractDrugLongestAliphaticChain	0.001	0.000	0.001
extractDrugMACCS	0.001	0.001	0.001
extractDrugMACCSComplete	0.001	0.000	0.001
extractDrugMDE	0.001	0.000	0.001
extractDrugMannholdLogP	0.000	0.000	0.001
extractDrugMomentOfInertia	0.000	0.000	0.001
extractDrugOBFP2	0.000	0.000	0.001
extractDrugOBFP3	0.001	0.000	0.000
extractDrugOBFP4	0.001	0.001	0.001
extractDrugOBMACCS	0.000	0.000	0.001
extractDrugPetitjeanNumber	0.000	0.000	0.001
extractDrugPetitjeanShapeIndex	0.001	0.000	0.000
extractDrugPubChem	0.001	0.000	0.001
extractDrugPubChemComplete	0.001	0.000	0.001
extractDrugRotatableBondsCount	0.001	0.000	0.001
extractDrugRuleOfFive	0.001	0.000	0.001
extractDrugShortestPath	0.000	0.000	0.001
extractDrugShortestPathComplete	0.001	0.000	0.002
extractDrugStandard	0.001	0.000	0.001
extractDrugStandardComplete	0.001	0.000	0.001
extractDrugTPSA	0.001	0.000	0.001
extractDrugVABC	0.001	0.000	0.001
extractDrugVAdjMa	0.001	0.000	0.001
extractDrugWHIM	0.000	0.000	0.001
extractDrugWeight	0.001	0.000	0.001
extractDrugWeightedPath	0.001	0.001	0.001
extractDrugWienerNumbers	0.001	0.000	0.001
extractDrugXLogP	0.001	0.000	0.000
extractDrugZagrebIndex	0	0	0
extractPCMBLOSUM	0.026	0.004	0.030
extractPCMDescScales	0.035	0.003	0.038
extractPCMFAScales	0.039	0.004	0.042
extractPCMMDSScales	0.023	0.003	0.026
extractPCMPropScales	0.027	0.004	0.031
extractPCMScales	0.039	0.003	0.043
extractProtAAC	0.005	0.000	0.006
extractProtAPAAC	4.555	0.083	4.628
extractProtCTDC	0.016	0.001	0.019
extractProtCTDD	0.011	0.002	0.012
extractProtCTDT	0.014	0.001	0.014
extractProtCTriad	0.339	0.006	0.346
extractProtDC	0.008	0.004	0.012
extractProtGeary	0.340	0.007	0.348
extractProtMoran	0.336	0.006	0.342
extractProtMoreauBroto	0.316	0.007	0.409
extractProtPAAC	1.385	0.005	1.394
extractProtPSSM	0.001	0.000	0.001
extractProtPSSMAcc	0.001	0.000	0.001
extractProtPSSMFeature	0.001	0.000	0.001
extractProtQSO	2.305	0.015	2.319
extractProtSOCN	2.089	0.011	2.099
extractProtTC	0.103	0.072	0.175
getCPI	0.006	0.001	0.007
getDrug	0	0	0
getFASTAFromKEGG	0.001	0.000	0.001
getFASTAFromUniProt	0.001	0.000	0.001
getMolFromCAS	0.001	0.001	0.001
getMolFromChEMBL	0.001	0.000	0.001
getMolFromDrugBank	0.001	0.001	0.001
getMolFromKEGG	0.001	0.000	0.001
getMolFromPubChem	0.000	0.000	0.001
getPDBFromRCSBPDB	0.001	0.000	0.001
getPPI	0.007	0.002	0.008
getProt	0.001	0.000	0.001
getSeqFromKEGG	0.001	0.000	0.001
getSeqFromRCSBPDB	0.000	0.001	0.001
getSeqFromUniProt	0.001	0.000	0.001
getSmiFromChEMBL	0.000	0.001	0.001
getSmiFromDrugBank	0	0	0
getSmiFromKEGG	0.001	0.001	0.001
getSmiFromPubChem	0.001	0.000	0.001
readFASTA	0.002	0.001	0.002
readMolFromSDF	0.001	0.000	0.001
readMolFromSmi	0.001	0.000	0.001
readPDB	2.161	0.029	2.190
searchDrug	0.000	0.000	0.001
segProt	0.005	0.001	0.006

BioC 3.1: CHECK report for Rcpi on petty

Summary

Command output