BioC 2.14: CHECK report for Rcpi on morelia

Package: Rcpi

Version: 1.0.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Rcpi_1.0.2.tar.gz

StartedAt: 2014-10-08 01:02:55 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 01:06:46 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 231.0 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 --no-multiarch Rcpi_1.0.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/Rcpi.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ‘1.0.2’
* 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 ... [19s/21s] 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 ... [20s/20s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [10s/11s]
 [11s/11s] 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

* 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	0.025	0.001	0.026
AA3DMoRSE	0.002	0.000	0.002
AAACF	0.002	0.001	0.003
AABLOSUM100	0.002	0.000	0.003
AABLOSUM45	0.002	0.001	0.002
AABLOSUM50	0.002	0.000	0.002
AABLOSUM62	0.002	0.000	0.002
AABLOSUM80	0.002	0.001	0.003
AABurden	0.002	0.000	0.003
AACPSA	0.002	0.000	0.002
AAConn	0.002	0.001	0.003
AAConst	0.002	0.001	0.003
AADescAll	0.002	0.000	0.002
AAEdgeAdj	0.002	0.001	0.002
AAEigIdx	0.002	0.000	0.002
AAFGC	0.002	0.000	0.002
AAGETAWAY	0.002	0.001	0.002
AAGeom	0.002	0.000	0.003
AAInfo	0.002	0.000	0.003
AAMOE2D	0.002	0.000	0.003
AAMOE3D	0.002	0.000	0.002
AAMetaInfo	0.002	0.001	0.002
AAMolProp	0.002	0.000	0.002
AAPAM120	0.001	0.001	0.002
AAPAM250	0.002	0.000	0.002
AAPAM30	0.002	0.001	0.003
AAPAM40	0.001	0.000	0.002
AAPAM70	0.002	0.001	0.002
AARDF	0.002	0.000	0.002
AARandic	0.002	0.001	0.002
AATopo	0.002	0.000	0.002
AATopoChg	0.002	0.000	0.002
AAWHIM	0.002	0.000	0.003
AAWalk	0.002	0.000	0.003
AAindex	0.002	0.000	0.002
OptAA3d	0.001	0.000	0.001
Rcpi-package	0.001	0.000	0.001
acc	0.020	0.004	0.029
calcDrugFPSim	0.001	0.000	0.000
calcDrugMCSSim	0.000	0.000	0.001
calcParProtGOSim	0	0	0
calcParProtSeqSim	0.000	0.000	0.001
calcTwoProtGOSim	0.001	0.000	0.000
calcTwoProtSeqSim	0.001	0.000	0.001
checkProt	0.006	0.001	0.007
convMolFormat	0.001	0.001	0.001
extractDrugAIO	0.001	0.000	0.001
extractDrugALOGP	0	0	0
extractDrugAminoAcidCount	0.000	0.001	0.001
extractDrugApol	0	0	0
extractDrugAromaticAtomsCount	0.000	0.000	0.001
extractDrugAromaticBondsCount	0.000	0.000	0.001
extractDrugAtomCount	0.001	0.000	0.001
extractDrugAutocorrelationCharge	0.001	0.000	0.001
extractDrugAutocorrelationMass	0.001	0.000	0.000
extractDrugAutocorrelationPolarizability	0.000	0.000	0.001
extractDrugBCUT	0	0	0
extractDrugBPol	0.001	0.000	0.001
extractDrugBondCount	0.001	0.000	0.001
extractDrugCPSA	0.000	0.000	0.001
extractDrugCarbonTypes	0.001	0.000	0.001
extractDrugChiChain	0	0	0
extractDrugChiCluster	0.001	0.000	0.001
extractDrugChiPath	0.000	0.000	0.001
extractDrugChiPathCluster	0	0	0
extractDrugDescOB	0.001	0.000	0.001
extractDrugECI	0.001	0.000	0.000
extractDrugEstate	0.000	0.000	0.001
extractDrugEstateComplete	0.000	0.000	0.001
extractDrugExtended	0.001	0.000	0.000
extractDrugExtendedComplete	0.001	0.000	0.001
extractDrugFMF	0.000	0.000	0.001
extractDrugFragmentComplexity	0.001	0.000	0.001
extractDrugGraph	0	0	0
extractDrugGraphComplete	0.001	0.000	0.001
extractDrugGravitationalIndex	0.001	0.000	0.001
extractDrugHBondAcceptorCount	0.000	0.000	0.001
extractDrugHBondDonorCount	0.001	0.001	0.001
extractDrugHybridization	0	0	0
extractDrugHybridizationComplete	0.001	0.000	0.000
extractDrugHybridizationRatio	0.001	0.001	0.001
extractDrugIPMolecularLearning	0	0	0
extractDrugKR	0.000	0.000	0.001
extractDrugKRComplete	0.001	0.001	0.000
extractDrugKappaShapeIndices	0.001	0.000	0.001
extractDrugKierHallSmarts	0.001	0.000	0.001
extractDrugLargestChain	0.001	0.000	0.000
extractDrugLargestPiSystem	0.001	0.000	0.001
extractDrugLengthOverBreadth	0.001	0.000	0.001
extractDrugLongestAliphaticChain	0.001	0.000	0.000
extractDrugMACCS	0.001	0.001	0.001
extractDrugMACCSComplete	0.001	0.000	0.001
extractDrugMDE	0.001	0.000	0.000
extractDrugMannholdLogP	0.000	0.000	0.001
extractDrugMomentOfInertia	0	0	0
extractDrugOBFP2	0.000	0.000	0.001
extractDrugOBFP3	0	0	0
extractDrugOBFP4	0.000	0.000	0.001
extractDrugOBMACCS	0.000	0.000	0.001
extractDrugPetitjeanNumber	0	0	0
extractDrugPetitjeanShapeIndex	0.001	0.000	0.001
extractDrugPubChem	0.000	0.000	0.001
extractDrugPubChemComplete	0.001	0.000	0.000
extractDrugRotatableBondsCount	0.001	0.000	0.000
extractDrugRuleOfFive	0.001	0.000	0.001
extractDrugShortestPath	0.001	0.000	0.000
extractDrugShortestPathComplete	0.001	0.000	0.000
extractDrugStandard	0.001	0.000	0.001
extractDrugStandardComplete	0.001	0.001	0.000
extractDrugTPSA	0.001	0.000	0.000
extractDrugVABC	0.001	0.000	0.001
extractDrugVAdjMa	0	0	0
extractDrugWHIM	0.000	0.000	0.001
extractDrugWeight	0	0	0
extractDrugWeightedPath	0.000	0.000	0.001
extractDrugWienerNumbers	0.000	0.000	0.001
extractDrugXLogP	0.001	0.000	0.000
extractDrugZagrebIndex	0.001	0.000	0.001
extractPCMBLOSUM	0.019	0.002	0.021
extractPCMDescScales	0.022	0.002	0.024
extractPCMFAScales	0.192	0.002	0.194
extractPCMMDSScales	0.018	0.003	0.021
extractPCMPropScales	0.024	0.001	0.025
extractPCMScales	0.033	0.002	0.035
extractProtAAC	0.005	0.001	0.006
extractProtAPAAC	2.869	0.038	2.909
extractProtCTDC	0.011	0.000	0.011
extractProtCTDD	0.009	0.001	0.010
extractProtCTDT	0.015	0.001	0.016
extractProtCTriad	0.270	0.011	0.280
extractProtDC	0.007	0.003	0.010
extractProtGeary	0.248	0.006	0.255
extractProtMoran	0.248	0.007	0.254
extractProtMoreauBroto	0.240	0.006	0.247
extractProtPAAC	1.166	0.008	1.170
extractProtPSSM	0.001	0.000	0.001
extractProtPSSMAcc	0	0	0
extractProtPSSMFeature	0.000	0.000	0.001
extractProtQSO	1.974	0.015	1.996
extractProtSOCN	1.991	0.011	2.016
extractProtTC	0.074	0.051	0.125
getCPI	0.004	0.001	0.006
getDrug	0.001	0.000	0.001
getFASTAFromKEGG	0.001	0.000	0.000
getFASTAFromUniProt	0.001	0.000	0.001
getMolFromCAS	0.001	0.000	0.001
getMolFromChEMBL	0.001	0.000	0.000
getMolFromDrugBank	0.001	0.000	0.001
getMolFromKEGG	0.001	0.000	0.001
getMolFromPubChem	0.001	0.000	0.000
getPDBFromRCSBPDB	0.001	0.000	0.000
getPPI	0.005	0.001	0.006
getProt	0	0	0
getSeqFromKEGG	0.000	0.000	0.001
getSeqFromRCSBPDB	0.000	0.000	0.001
getSeqFromUniProt	0	0	0
getSmiFromChEMBL	0.000	0.000	0.001
getSmiFromDrugBank	0.000	0.000	0.001
getSmiFromKEGG	0	0	0
getSmiFromPubChem	0.000	0.000	0.001
readFASTA	0.003	0.001	0.003
readMolFromSDF	0.001	0.000	0.001
readMolFromSmi	0.000	0.000	0.001
readPDB	1.880	0.004	1.901
searchDrug	0.001	0.000	0.001
segProt	0.005	0.001	0.006

BioC 2.14: CHECK report for Rcpi on morelia

Summary

Command output