BioC 3.2: CHECK report for Rcpi on perceval

Package: Rcpi

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.6.0.tar.gz

StartedAt: 2015-10-27 11:30:31 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 11:33:48 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 197.7 seconds

RetCode: 0

Status: OK

CheckDir: Rcpi.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Rcpi.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* 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 ‘1.6.0’
* 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 ... [18s/18s] 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 ... [18s/18s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [10s/9s]
 [10s/10s] 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	0.004
AA3DMoRSE	0.002	0.000	0.002
AAACF	0.002	0.001	0.002
AABLOSUM100	0.001	0.000	0.002
AABLOSUM45	0.002	0.000	0.002
AABLOSUM50	0.002	0.001	0.002
AABLOSUM62	0.002	0.000	0.002
AABLOSUM80	0.002	0.000	0.003
AABurden	0.001	0.001	0.002
AACPSA	0.002	0.000	0.002
AAConn	0.002	0.001	0.002
AAConst	0.002	0.000	0.002
AADescAll	0.002	0.000	0.002
AAEdgeAdj	0.002	0.001	0.002
AAEigIdx	0.002	0.000	0.001
AAFGC	0.002	0.001	0.002
AAGETAWAY	0.002	0.000	0.002
AAGeom	0.002	0.001	0.002
AAInfo	0.002	0.000	0.001
AAMOE2D	0.002	0.001	0.002
AAMOE3D	0.002	0.000	0.002
AAMetaInfo	0.002	0.000	0.002
AAMolProp	0.002	0.001	0.002
AAPAM120	0.002	0.000	0.002
AAPAM250	0.002	0.001	0.002
AAPAM30	0.002	0.000	0.002
AAPAM40	0.002	0.000	0.002
AAPAM70	0.002	0.001	0.002
AARDF	0.002	0.000	0.002
AARandic	0.002	0.000	0.002
AATopo	0.002	0.001	0.002
AATopoChg	0.001	0.000	0.002
AAWHIM	0.001	0.001	0.002
AAWalk	0.002	0.000	0.002
AAindex	0.002	0.000	0.002
OptAA3d	0.000	0.000	0.001
Rcpi-package	0.000	0.000	0.001
acc	0.021	0.007	0.028
calcDrugFPSim	0.001	0.000	0.001
calcDrugMCSSim	0	0	0
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	0.004	0.001	0.004
convMolFormat	0.001	0.000	0.000
extractDrugAIO	0.001	0.000	0.001
extractDrugALOGP	0.001	0.000	0.001
extractDrugAminoAcidCount	0.001	0.000	0.000
extractDrugApol	0	0	0
extractDrugAromaticAtomsCount	0.001	0.000	0.001
extractDrugAromaticBondsCount	0.001	0.000	0.000
extractDrugAtomCount	0.001	0.000	0.001
extractDrugAutocorrelationCharge	0.001	0.000	0.000
extractDrugAutocorrelationMass	0	0	0
extractDrugAutocorrelationPolarizability	0.001	0.001	0.001
extractDrugBCUT	0.001	0.000	0.000
extractDrugBPol	0.001	0.000	0.001
extractDrugBondCount	0.001	0.000	0.001
extractDrugCPSA	0.001	0.000	0.000
extractDrugCarbonTypes	0.001	0.000	0.000
extractDrugChiChain	0.001	0.000	0.000
extractDrugChiCluster	0	0	0
extractDrugChiPath	0.001	0.000	0.000
extractDrugChiPathCluster	0.001	0.000	0.001
extractDrugDescOB	0.001	0.000	0.001
extractDrugECI	0.001	0.000	0.001
extractDrugEstate	0	0	0
extractDrugEstateComplete	0.000	0.000	0.001
extractDrugExtended	0.000	0.000	0.001
extractDrugExtendedComplete	0.000	0.000	0.001
extractDrugFMF	0	0	0
extractDrugFragmentComplexity	0.001	0.000	0.001
extractDrugGraph	0.001	0.000	0.001
extractDrugGraphComplete	0.001	0.000	0.000
extractDrugGravitationalIndex	0.001	0.000	0.001
extractDrugHBondAcceptorCount	0.001	0.000	0.001
extractDrugHBondDonorCount	0.001	0.000	0.000
extractDrugHybridization	0.001	0.000	0.001
extractDrugHybridizationComplete	0.000	0.000	0.001
extractDrugHybridizationRatio	0.000	0.000	0.001
extractDrugIPMolecularLearning	0.000	0.000	0.001
extractDrugKR	0	0	0
extractDrugKRComplete	0	0	0
extractDrugKappaShapeIndices	0.000	0.001	0.000
extractDrugKierHallSmarts	0.001	0.000	0.000
extractDrugLargestChain	0.001	0.000	0.001
extractDrugLargestPiSystem	0.001	0.001	0.001
extractDrugLengthOverBreadth	0.001	0.000	0.000
extractDrugLongestAliphaticChain	0	0	0
extractDrugMACCS	0.000	0.000	0.001
extractDrugMACCSComplete	0.000	0.000	0.001
extractDrugMDE	0.001	0.000	0.001
extractDrugMannholdLogP	0.001	0.000	0.001
extractDrugMomentOfInertia	0.001	0.000	0.000
extractDrugOBFP2	0.001	0.001	0.001
extractDrugOBFP3	0.001	0.000	0.001
extractDrugOBFP4	0.000	0.000	0.001
extractDrugOBMACCS	0.000	0.000	0.001
extractDrugPetitjeanNumber	0	0	0
extractDrugPetitjeanShapeIndex	0.001	0.000	0.000
extractDrugPubChem	0.001	0.000	0.001
extractDrugPubChemComplete	0.001	0.000	0.001
extractDrugRotatableBondsCount	0	0	0
extractDrugRuleOfFive	0.001	0.000	0.001
extractDrugShortestPath	0.001	0.000	0.000
extractDrugShortestPathComplete	0.001	0.001	0.001
extractDrugStandard	0.001	0.000	0.001
extractDrugStandardComplete	0.001	0.000	0.000
extractDrugTPSA	0.001	0.000	0.000
extractDrugVABC	0	0	0
extractDrugVAdjMa	0.000	0.000	0.001
extractDrugWHIM	0.001	0.000	0.001
extractDrugWeight	0.001	0.000	0.001
extractDrugWeightedPath	0.000	0.000	0.001
extractDrugWienerNumbers	0.000	0.000	0.001
extractDrugXLogP	0	0	0
extractDrugZagrebIndex	0	0	0
extractPCMBLOSUM	0.026	0.004	0.030
extractPCMDescScales	0.018	0.003	0.021
extractPCMFAScales	0.029	0.005	0.033
extractPCMMDSScales	0.021	0.005	0.026
extractPCMPropScales	0.021	0.004	0.026
extractPCMScales	0.033	0.003	0.037
extractProtAAC	0.003	0.001	0.004
extractProtAPAAC	2.756	0.073	2.827
extractProtCTDC	0.010	0.001	0.010
extractProtCTDD	0.007	0.001	0.008
extractProtCTDT	0.009	0.000	0.009
extractProtCTriad	0.241	0.003	0.243
extractProtDC	0.006	0.003	0.008
extractProtGeary	0.216	0.004	0.220
extractProtMoran	0.217	0.004	0.221
extractProtMoreauBroto	0.211	0.004	0.216
extractProtPAAC	0.983	0.003	0.979
extractProtPSSM	0.000	0.000	0.001
extractProtPSSMAcc	0.001	0.000	0.001
extractProtPSSMFeature	0.001	0.000	0.001
extractProtQSO	1.702	0.012	1.714
extractProtSOCN	1.694	0.009	1.702
extractProtTC	0.072	0.050	0.121
getCPI	0.004	0.001	0.004
getDrug	0.001	0.000	0.000
getFASTAFromKEGG	0.000	0.000	0.001
getFASTAFromUniProt	0.001	0.000	0.001
getMolFromCAS	0.001	0.000	0.000
getMolFromChEMBL	0	0	0
getMolFromDrugBank	0	0	0
getMolFromKEGG	0.001	0.000	0.000
getMolFromPubChem	0.000	0.001	0.001
getPDBFromRCSBPDB	0.000	0.000	0.001
getPPI	0.004	0.001	0.005
getProt	0.000	0.001	0.001
getSeqFromKEGG	0.001	0.000	0.001
getSeqFromRCSBPDB	0.001	0.000	0.001
getSeqFromUniProt	0.000	0.001	0.001
getSmiFromChEMBL	0.000	0.000	0.001
getSmiFromDrugBank	0.001	0.000	0.001
getSmiFromKEGG	0.001	0.000	0.001
getSmiFromPubChem	0.000	0.000	0.001
readFASTA	0.001	0.000	0.002
readMolFromSDF	0.001	0.001	0.000
readMolFromSmi	0.001	0.000	0.000
readPDB	1.538	0.028	1.565
searchDrug	0	0	0
segProt	0.004	0.000	0.004

BioC 3.2: CHECK report for Rcpi on perceval

Summary

Command output