Multiple platform build/check report for BioC 3.6 - CHECK report for Rcpi on veracruz1

Package: Rcpi

Version: 1.14.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Rcpi_1.14.1.tar.gz

StartedAt: 2018-04-12 08:24:45 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 08:27:23 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 158.2 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_1.14.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/Rcpi.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.14.1’
* package encoding: UTF-8
* 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 ... 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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)


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage('Rcpi')



RUNIT TEST PROTOCOL -- Thu Apr 12 08:27:13 2018 
*********************************************** 
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Rcpi RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  8.872   0.298   8.624

name	user	system	elapsed
AA2DACOR	0.017	0.003	0.021
AA3DMoRSE	0.002	0.001	0.003
AAACF	0.002	0.001	0.002
AABLOSUM100	0.002	0.001	0.002
AABLOSUM45	0.002	0.001	0.003
AABLOSUM50	0.002	0.001	0.003
AABLOSUM62	0.001	0.001	0.003
AABLOSUM80	0.001	0.001	0.003
AABurden	0.001	0.001	0.003
AACPSA	0.001	0.001	0.003
AAConn	0.002	0.001	0.003
AAConst	0.002	0.001	0.003
AADescAll	0.002	0.001	0.002
AAEdgeAdj	0.001	0.000	0.003
AAEigIdx	0.001	0.000	0.003
AAFGC	0.001	0.001	0.003
AAGETAWAY	0.001	0.001	0.002
AAGeom	0.001	0.001	0.002
AAInfo	0.001	0.001	0.002
AAMOE2D	0.001	0.001	0.002
AAMOE3D	0.001	0.001	0.002
AAMetaInfo	0.002	0.001	0.002
AAMolProp	0.002	0.001	0.003
AAPAM120	0.002	0.001	0.003
AAPAM250	0.002	0.000	0.003
AAPAM30	0.002	0.000	0.003
AAPAM40	0.002	0.000	0.003
AAPAM70	0.002	0.000	0.003
AARDF	0.002	0.000	0.003
AARandic	0.002	0.000	0.003
AATopo	0.002	0.000	0.003
AATopoChg	0.002	0.000	0.003
AAWHIM	0.002	0.001	0.003
AAWalk	0.002	0.001	0.002
AAindex	0.002	0.001	0.002
OptAA3d	0.001	0.000	0.001
acc	0.018	0.005	0.023
calcDrugFPSim	1.601	0.108	0.822
calcDrugMCSSim	0.010	0.002	0.012
calcParProtGOSim	0.001	0.001	0.001
calcParProtSeqSim	0.031	0.001	0.033
calcTwoProtGOSim	0.001	0.000	0.001
calcTwoProtSeqSim	0.003	0.000	0.002
checkProt	0.002	0.000	0.003
convMolFormat	0.001	0.000	0.001
extractDrugAIO	0.002	0.001	0.001
extractDrugALOGP	0.001	0.000	0.002
extractDrugAminoAcidCount	0.001	0.000	0.001
extractDrugApol	0.001	0.000	0.001
extractDrugAromaticAtomsCount	0.001	0.000	0.002
extractDrugAromaticBondsCount	0.001	0.000	0.001
extractDrugAtomCount	0.001	0.000	0.001
extractDrugAutocorrelationCharge	0.002	0.000	0.002
extractDrugAutocorrelationMass	0.001	0.001	0.001
extractDrugAutocorrelationPolarizability	0.001	0.000	0.001
extractDrugBCUT	0.001	0.000	0.001
extractDrugBPol	0.001	0.001	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	0.002
extractDrugChiCluster	0.001	0.000	0.001
extractDrugChiPath	0.001	0.000	0.001
extractDrugChiPathCluster	0.001	0.000	0.001
extractDrugDescOB	0.008	0.003	0.011
extractDrugECI	0.001	0.000	0.001
extractDrugEstate	0.001	0.000	0.001
extractDrugEstateComplete	0.001	0.001	0.002
extractDrugExtended	0.001	0.000	0.001
extractDrugExtendedComplete	0.001	0.000	0.001
extractDrugFMF	0.001	0.001	0.002
extractDrugFragmentComplexity	0.001	0.000	0.000
extractDrugGraph	0.000	0.000	0.001
extractDrugGraphComplete	0.001	0.000	0.001
extractDrugGravitationalIndex	0.001	0.000	0.000
extractDrugHBondAcceptorCount	0.000	0.000	0.001
extractDrugHBondDonorCount	0.001	0.000	0.001
extractDrugHybridization	0.001	0.000	0.001
extractDrugHybridizationComplete	0.001	0.001	0.002
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	0.000
extractDrugKappaShapeIndices	0.001	0.000	0.001
extractDrugKierHallSmarts	0.002	0.000	0.002
extractDrugLargestChain	0.001	0.000	0.001
extractDrugLargestPiSystem	0.001	0.000	0.001
extractDrugLengthOverBreadth	0.001	0.000	0.001
extractDrugLongestAliphaticChain	0.001	0.000	0.001
extractDrugMACCS	0.001	0.000	0.002
extractDrugMACCSComplete	0.001	0.000	0.001
extractDrugMDE	0.001	0.001	0.001
extractDrugMannholdLogP	0.001	0.000	0.001
extractDrugMomentOfInertia	0.001	0.000	0.001
extractDrugOBFP2	0.008	0.001	0.008
extractDrugOBFP3	0.008	0.000	0.008
extractDrugOBFP4	0.009	0.001	0.009
extractDrugOBMACCS	0.203	0.001	0.204
extractDrugPetitjeanNumber	0.000	0.000	0.001
extractDrugPetitjeanShapeIndex	0.001	0.000	0.001
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	0.001	0.000	0.001
extractDrugShortestPathComplete	0.001	0.000	0.004
extractDrugStandard	0.001	0.001	0.001
extractDrugStandardComplete	0.001	0.000	0.002
extractDrugTPSA	0.001	0.000	0.001
extractDrugVABC	0.002	0.001	0.001
extractDrugVAdjMa	0.001	0.000	0.001
extractDrugWHIM	0.002	0.001	0.001
extractDrugWeight	0.001	0.000	0.001
extractDrugWeightedPath	0.001	0.000	0.002
extractDrugWienerNumbers	0.001	0.001	0.001
extractDrugXLogP	0.001	0.000	0.002
extractDrugZagrebIndex	0.001	0.000	0.001
extractPCMBLOSUM	0.053	0.001	0.054
extractPCMDescScales	0.014	0.001	0.016
extractPCMFAScales	0.018	0.003	0.021
extractPCMMDSScales	0.014	0.002	0.015
extractPCMPropScales	0.037	0.001	0.039
extractPCMScales	0.017	0.003	0.020
extractProtAAC	0.003	0.000	0.004
extractProtAPAAC	1.246	0.040	1.314
extractProtCTDC	0.003	0.001	0.003
extractProtCTDD	0.007	0.001	0.008
extractProtCTDT	0.006	0.001	0.006
extractProtCTriad	0.114	0.012	0.126
extractProtDC	0.004	0.002	0.006
extractProtGeary	0.216	0.007	0.227
extractProtMoran	0.209	0.006	0.220
extractProtMoreauBroto	0.207	0.006	0.217
extractProtPAAC	0.682	0.008	0.714
extractProtPSSM	0.002	0.000	0.002
extractProtPSSMAcc	0.001	0.000	0.002
extractProtPSSMFeature	0.001	0.000	0.003
extractProtQSO	1.169	0.010	1.195
extractProtSOCN	1.244	0.023	1.288
extractProtTC	0.064	0.051	0.117
getCPI	0.003	0.000	0.004
getDrug	0.000	0.001	0.001
getFASTAFromKEGG	0.000	0.000	0.001
getFASTAFromUniProt	0.001	0.000	0.001
getMolFromCAS	0	0	0
getMolFromChEMBL	0.001	0.000	0.000
getMolFromDrugBank	0	0	0
getMolFromKEGG	0.000	0.000	0.001
getMolFromPubChem	0.001	0.000	0.000
getPDBFromRCSBPDB	0.001	0.000	0.000
getPPI	0.003	0.001	0.003
getProt	0.001	0.000	0.001
getSeqFromKEGG	0.000	0.000	0.001
getSeqFromRCSBPDB	0.000	0.001	0.001
getSeqFromUniProt	0	0	0
getSmiFromChEMBL	0	0	0
getSmiFromDrugBank	0.000	0.001	0.001
getSmiFromKEGG	0.001	0.000	0.001
getSmiFromPubChem	0.001	0.000	0.001
readFASTA	0.002	0.001	0.003
readMolFromSDF	0.003	0.000	0.002
readMolFromSmi	0.001	0.000	0.001
readPDB	1.147	0.009	1.176
searchDrug	0.002	0.000	0.002
segProt	0.003	0.001	0.004

CHECK report for Rcpi on veracruz1

Summary

Command output

Installation output

Tests output

Example timings