BioC 2.14: CHECK report for Rcpi on petty

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: 2014-10-07 23:43:53 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:50:21 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 387.9 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-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 ‘1.0.2’
* 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 ... [33s/33s] 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 ... [35s/36s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
extractProtAPAAC 5.123  0.133   5.341
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [17s/18s]
 [18s/19s] 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	0.048	0.004	0.053
AA3DMoRSE	0.004	0.001	0.005
AAACF	0.003	0.000	0.004
AABLOSUM100	0.002	0.000	0.003
AABLOSUM45	0.003	0.001	0.003
AABLOSUM50	0.003	0.001	0.004
AABLOSUM62	0.004	0.001	0.004
AABLOSUM80	0.003	0.001	0.004
AABurden	0.003	0.001	0.004
AACPSA	0.003	0.001	0.004
AAConn	0.003	0.001	0.003
AAConst	0.002	0.001	0.003
AADescAll	0.004	0.001	0.004
AAEdgeAdj	0.003	0.001	0.003
AAEigIdx	0.003	0.000	0.004
AAFGC	0.004	0.001	0.005
AAGETAWAY	0.003	0.001	0.005
AAGeom	0.003	0.001	0.004
AAInfo	0.003	0.001	0.004
AAMOE2D	0.002	0.001	0.003
AAMOE3D	0.003	0.001	0.003
AAMetaInfo	0.002	0.001	0.003
AAMolProp	0.002	0.001	0.003
AAPAM120	0.004	0.000	0.003
AAPAM250	0.003	0.001	0.004
AAPAM30	0.003	0.001	0.004
AAPAM40	0.003	0.001	0.004
AAPAM70	0.003	0.001	0.004
AARDF	0.003	0.001	0.003
AARandic	0.003	0.001	0.004
AATopo	0.003	0.001	0.004
AATopoChg	0.003	0.000	0.004
AAWHIM	0.003	0.001	0.004
AAWalk	0.003	0.001	0.004
AAindex	0.003	0.001	0.003
OptAA3d	0.001	0.000	0.001
Rcpi-package	0.001	0.000	0.001
acc	0.046	0.008	0.053
calcDrugFPSim	0.001	0.000	0.001
calcDrugMCSSim	0.001	0.000	0.001
calcParProtGOSim	0.000	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	0.008	0.001	0.009
convMolFormat	0.000	0.000	0.001
extractDrugAIO	0.001	0.000	0.001
extractDrugALOGP	0.000	0.000	0.001
extractDrugAminoAcidCount	0.000	0.000	0.001
extractDrugApol	0.001	0.000	0.001
extractDrugAromaticAtomsCount	0.001	0.000	0.001
extractDrugAromaticBondsCount	0.001	0.000	0.001
extractDrugAtomCount	0.001	0.000	0.001
extractDrugAutocorrelationCharge	0.001	0.000	0.001
extractDrugAutocorrelationMass	0.001	0.000	0.001
extractDrugAutocorrelationPolarizability	0.001	0.000	0.001
extractDrugBCUT	0.001	0.000	0.001
extractDrugBPol	0.001	0.000	0.001
extractDrugBondCount	0.001	0.000	0.001
extractDrugCPSA	0.001	0.000	0.001
extractDrugCarbonTypes	0.001	0.000	0.001
extractDrugChiChain	0.001	0.000	0.001
extractDrugChiCluster	0.001	0.000	0.001
extractDrugChiPath	0.001	0.000	0.001
extractDrugChiPathCluster	0.001	0.000	0.002
extractDrugDescOB	0.001	0.000	0.001
extractDrugECI	0.001	0.000	0.001
extractDrugEstate	0.001	0.000	0.001
extractDrugEstateComplete	0.001	0.000	0.002
extractDrugExtended	0.001	0.000	0.000
extractDrugExtendedComplete	0.000	0.000	0.001
extractDrugFMF	0.001	0.000	0.000
extractDrugFragmentComplexity	0.000	0.000	0.001
extractDrugGraph	0.001	0.000	0.001
extractDrugGraphComplete	0.001	0.000	0.001
extractDrugGravitationalIndex	0.000	0.000	0.001
extractDrugHBondAcceptorCount	0.001	0.000	0.001
extractDrugHBondDonorCount	0.001	0.000	0.001
extractDrugHybridization	0.001	0.000	0.001
extractDrugHybridizationComplete	0.001	0.000	0.001
extractDrugHybridizationRatio	0.000	0.000	0.001
extractDrugIPMolecularLearning	0.001	0.000	0.001
extractDrugKR	0.000	0.000	0.001
extractDrugKRComplete	0.001	0.000	0.001
extractDrugKappaShapeIndices	0.001	0.001	0.001
extractDrugKierHallSmarts	0.001	0.000	0.002
extractDrugLargestChain	0.001	0.001	0.001
extractDrugLargestPiSystem	0.000	0.000	0.001
extractDrugLengthOverBreadth	0.001	0.000	0.001
extractDrugLongestAliphaticChain	0.001	0.000	0.001
extractDrugMACCS	0.001	0.000	0.001
extractDrugMACCSComplete	0.001	0.000	0.000
extractDrugMDE	0.000	0.000	0.001
extractDrugMannholdLogP	0.001	0.000	0.001
extractDrugMomentOfInertia	0.001	0.000	0.001
extractDrugOBFP2	0.001	0.000	0.001
extractDrugOBFP3	0.001	0.000	0.001
extractDrugOBFP4	0.001	0.000	0.001
extractDrugOBMACCS	0	0	0
extractDrugPetitjeanNumber	0.001	0.000	0.002
extractDrugPetitjeanShapeIndex	0.001	0.000	0.001
extractDrugPubChem	0.001	0.000	0.001
extractDrugPubChemComplete	0.000	0.000	0.001
extractDrugRotatableBondsCount	0.001	0.001	0.001
extractDrugRuleOfFive	0.001	0.000	0.002
extractDrugShortestPath	0.001	0.001	0.001
extractDrugShortestPathComplete	0.000	0.000	0.001
extractDrugStandard	0	0	0
extractDrugStandardComplete	0.000	0.000	0.001
extractDrugTPSA	0.001	0.000	0.001
extractDrugVABC	0.000	0.000	0.001
extractDrugVAdjMa	0	0	0
extractDrugWHIM	0.000	0.000	0.001
extractDrugWeight	0.001	0.000	0.001
extractDrugWeightedPath	0.000	0.001	0.001
extractDrugWienerNumbers	0.001	0.000	0.001
extractDrugXLogP	0.001	0.000	0.001
extractDrugZagrebIndex	0.001	0.000	0.001
extractPCMBLOSUM	0.029	0.005	0.034
extractPCMDescScales	0.309	0.005	0.315
extractPCMFAScales	0.044	0.006	0.050
extractPCMMDSScales	0.034	0.003	0.038
extractPCMPropScales	0.032	0.001	0.034
extractPCMScales	0.055	0.003	0.057
extractProtAAC	0.009	0.001	0.010
extractProtAPAAC	5.123	0.133	5.341
extractProtCTDC	0.016	0.001	0.018
extractProtCTDD	0.015	0.002	0.018
extractProtCTDT	0.020	0.002	0.022
extractProtCTriad	0.390	0.014	0.405
extractProtDC	0.011	0.005	0.017
extractProtGeary	0.400	0.012	0.414
extractProtMoran	0.396	0.011	0.409
extractProtMoreauBroto	0.395	0.012	0.426
extractProtPAAC	2.046	0.011	2.065
extractProtPSSM	0.001	0.000	0.001
extractProtPSSMAcc	0.001	0.000	0.001
extractProtPSSMFeature	0.001	0.000	0.001
extractProtQSO	3.494	0.024	3.716
extractProtSOCN	3.466	0.022	3.625
extractProtTC	0.120	0.082	1.267
getCPI	0.006	0.001	0.008
getDrug	0	0	0
getFASTAFromKEGG	0.001	0.000	0.001
getFASTAFromUniProt	0.001	0.001	0.001
getMolFromCAS	0.000	0.000	0.001
getMolFromChEMBL	0.001	0.001	0.001
getMolFromDrugBank	0.001	0.000	0.001
getMolFromKEGG	0.001	0.000	0.001
getMolFromPubChem	0.001	0.000	0.001
getPDBFromRCSBPDB	0.001	0.000	0.001
getPPI	0.008	0.002	0.009
getProt	0.001	0.001	0.001
getSeqFromKEGG	0.000	0.000	0.001
getSeqFromRCSBPDB	0.001	0.000	0.001
getSeqFromUniProt	0.001	0.000	0.001
getSmiFromChEMBL	0.001	0.000	0.001
getSmiFromDrugBank	0.002	0.000	0.001
getSmiFromKEGG	0.001	0.000	0.001
getSmiFromPubChem	0.001	0.000	0.002
readFASTA	0.005	0.001	0.005
readMolFromSDF	0.001	0.000	0.001
readMolFromSmi	0.001	0.000	0.001
readPDB	3.152	0.013	3.198
searchDrug	0.001	0.000	0.001
segProt	0.007	0.001	0.009

BioC 2.14: CHECK report for Rcpi on petty

Summary

Command output