Multiple platform build/check report for BioC 3.9 - CHECK report for Rcpi on celaya2

Package: Rcpi

Version: 1.19.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rcpi_1.19.2.tar.gz

StartedAt: 2019-04-09 04:48:27 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:51:57 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 210.3 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 --install=check:Rcpi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Rcpi_1.19.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Rcpi.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.19.2’
* 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 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 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Rcpi
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Rcpi’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rcpi)


R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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 -- Tue Apr  9 04:51:41 2019 
*********************************************** 
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 
  9.809   1.279   9.510

name	user	system	elapsed
AA2DACOR	0.020	0.005	0.025
AA3DMoRSE	0.002	0.001	0.003
AAACF	0.001	0.001	0.003
AABLOSUM100	0.003	0.003	0.006
AABLOSUM45	0.002	0.001	0.004
AABLOSUM50	0.002	0.002	0.003
AABLOSUM62	0.002	0.002	0.003
AABLOSUM80	0.001	0.001	0.002
AABurden	0.002	0.001	0.004
AACPSA	0.002	0.002	0.005
AAConn	0.003	0.002	0.005
AAConst	0.002	0.001	0.003
AADescAll	0.002	0.001	0.003
AAEdgeAdj	0.001	0.001	0.003
AAEigIdx	0.002	0.002	0.005
AAFGC	0.003	0.001	0.004
AAGETAWAY	0.002	0.002	0.004
AAGeom	0.002	0.002	0.003
AAInfo	0.002	0.002	0.004
AAMOE2D	0.002	0.002	0.004
AAMOE3D	0.002	0.001	0.004
AAMetaInfo	0.002	0.001	0.003
AAMolProp	0.002	0.001	0.003
AAPAM120	0.001	0.001	0.002
AAPAM250	0.002	0.001	0.002
AAPAM30	0.002	0.002	0.004
AAPAM40	0.002	0.002	0.004
AAPAM70	0.002	0.001	0.004
AARDF	0.002	0.001	0.004
AARandic	0.001	0.001	0.003
AATopo	0.001	0.001	0.003
AATopoChg	0.002	0.001	0.004
AAWHIM	0.002	0.002	0.005
AAWalk	0.002	0.001	0.003
AAindex	0.002	0.002	0.004
OptAA3d	0.000	0.001	0.001
acc	0.024	0.013	0.037
calcDrugFPSim	2.807	1.243	1.439
calcDrugMCSSim	0.007	0.009	0.018
calcParProtGOSim	0.000	0.000	0.001
calcParProtSeqSim	0.009	0.003	0.012
calcTwoProtGOSim	0.001	0.000	0.001
calcTwoProtSeqSim	0.003	0.001	0.004
checkProt	0.002	0.001	0.003
convMolFormat	0.002	0.001	0.002
extractDrugAIO	0.001	0.000	0.002
extractDrugALOGP	0.001	0.000	0.001
extractDrugAminoAcidCount	0.001	0.000	0.002
extractDrugApol	0.002	0.000	0.001
extractDrugAromaticAtomsCount	0.001	0.000	0.002
extractDrugAromaticBondsCount	0.002	0.000	0.001
extractDrugAtomCount	0.001	0.000	0.002
extractDrugAutocorrelationCharge	0.002	0.000	0.001
extractDrugAutocorrelationMass	0.001	0.000	0.002
extractDrugAutocorrelationPolarizability	0.002	0.000	0.002
extractDrugBCUT	0.001	0.001	0.002
extractDrugBPol	0.002	0.001	0.002
extractDrugBondCount	0.001	0.001	0.001
extractDrugCPSA	0.002	0.001	0.002
extractDrugCarbonTypes	0.001	0.001	0.002
extractDrugChiChain	0.001	0.001	0.001
extractDrugChiCluster	0.002	0.001	0.002
extractDrugChiPath	0.001	0.001	0.001
extractDrugChiPathCluster	0.001	0.001	0.002
extractDrugDescOB	0.012	0.011	0.024
extractDrugECI	0.001	0.000	0.002
extractDrugEstate	0.001	0.000	0.002
extractDrugEstateComplete	0.001	0.001	0.001
extractDrugExtended	0.001	0.000	0.001
extractDrugExtendedComplete	0.001	0.000	0.001
extractDrugFMF	0.001	0.001	0.002
extractDrugFragmentComplexity	0.001	0.001	0.002
extractDrugGraph	0.001	0.001	0.001
extractDrugGraphComplete	0.001	0.000	0.002
extractDrugGravitationalIndex	0.001	0.000	0.002
extractDrugHBondAcceptorCount	0.001	0.000	0.002
extractDrugHBondDonorCount	0.001	0.000	0.001
extractDrugHybridization	0.001	0.000	0.001
extractDrugHybridizationComplete	0.001	0.000	0.001
extractDrugHybridizationRatio	0.000	0.001	0.001
extractDrugIPMolecularLearning	0.001	0.000	0.001
extractDrugKR	0.001	0.000	0.001
extractDrugKRComplete	0.000	0.000	0.001
extractDrugKappaShapeIndices	0.001	0.000	0.001
extractDrugKierHallSmarts	0.001	0.001	0.001
extractDrugLargestChain	0.001	0.001	0.001
extractDrugLargestPiSystem	0.000	0.000	0.001
extractDrugLengthOverBreadth	0.001	0.000	0.001
extractDrugLongestAliphaticChain	0.001	0.001	0.002
extractDrugMACCS	0.001	0.001	0.002
extractDrugMACCSComplete	0.001	0.000	0.001
extractDrugMDE	0.001	0.000	0.002
extractDrugMannholdLogP	0.000	0.000	0.002
extractDrugMomentOfInertia	0.002	0.000	0.002
extractDrugOBFP2	0.109	0.001	0.110
extractDrugOBFP3	0.005	0.000	0.005
extractDrugOBFP4	0.009	0.008	0.017
extractDrugOBMACCS	0.016	0.001	0.017
extractDrugPetitjeanNumber	0.001	0.001	0.002
extractDrugPetitjeanShapeIndex	0.001	0.000	0.002
extractDrugPubChem	0.001	0.000	0.002
extractDrugPubChemComplete	0.001	0.000	0.001
extractDrugRotatableBondsCount	0.001	0.001	0.001
extractDrugRuleOfFive	0.001	0.000	0.001
extractDrugShortestPath	0.001	0.000	0.001
extractDrugShortestPathComplete	0.002	0.001	0.001
extractDrugStandard	0.001	0.001	0.002
extractDrugStandardComplete	0.002	0.001	0.001
extractDrugTPSA	0.001	0.000	0.001
extractDrugVABC	0.001	0.000	0.001
extractDrugVAdjMa	0.002	0.000	0.002
extractDrugWHIM	0.001	0.000	0.001
extractDrugWeight	0.001	0.000	0.001
extractDrugWeightedPath	0.001	0.000	0.001
extractDrugWienerNumbers	0.001	0.000	0.001
extractDrugXLogP	0.001	0.000	0.001
extractDrugZagrebIndex	0.000	0.001	0.001
extractPCMBLOSUM	0.015	0.005	0.020
extractPCMDescScales	0.018	0.005	0.023
extractPCMFAScales	0.022	0.006	0.029
extractPCMMDSScales	0.016	0.006	0.022
extractPCMPropScales	0.019	0.005	0.024
extractPCMScales	0.034	0.014	0.048
extractProtAAC	0.003	0.001	0.003
extractProtAPAAC	1.166	0.033	1.199
extractProtCTDC	0.003	0.000	0.003
extractProtCTDD	0.009	0.003	0.013
extractProtCTDT	0.009	0.002	0.010
extractProtCTriad	0.148	0.029	0.176
extractProtDC	0.008	0.006	0.014
extractProtGeary	0.260	0.023	0.282
extractProtMoran	0.279	0.013	0.292
extractProtMoreauBroto	0.251	0.025	0.276
extractProtPAAC	0.890	0.009	0.896
extractProtPSSM	0.001	0.000	0.002
extractProtPSSMAcc	0.001	0.001	0.002
extractProtPSSMFeature	0.001	0.001	0.003
extractProtQSO	2.179	0.037	2.215
extractProtSOCN	1.713	0.024	1.736
extractProtTC	0.083	0.088	0.171
getCPI	0.003	0.002	0.004
getDrug	0	0	0
getFASTAFromKEGG	0.000	0.001	0.000
getFASTAFromUniProt	0.000	0.000	0.001
getMolFromCAS	0	0	0
getMolFromChEMBL	0	0	0
getMolFromDrugBank	0.000	0.000	0.001
getMolFromKEGG	0	0	0
getMolFromPubChem	0	0	0
getPDBFromRCSBPDB	0.000	0.001	0.001
getPPI	0.003	0.002	0.005
getProt	0	0	0
getSeqFromKEGG	0	0	0
getSeqFromRCSBPDB	0	0	0
getSeqFromUniProt	0.000	0.001	0.001
getSmiFromChEMBL	0.001	0.000	0.000
getSmiFromDrugBank	0.001	0.000	0.000
getSmiFromKEGG	0.001	0.000	0.001
getSmiFromPubChem	0	0	0
readFASTA	0.002	0.000	0.002
readMolFromSDF	0.001	0.001	0.002
readMolFromSmi	0.001	0.000	0.001
readPDB	1.049	0.012	1.063
searchDrug	0.002	0.000	0.002
segProt	0.003	0.001	0.004

CHECK report for Rcpi on celaya2

Summary

Command output

Installation output

Tests output

Example timings