Multiple platform build/check report for BioC 3.9 - CHECK report for Rcpi on merida2

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 03:12:37 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:15:18 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 161.3 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) (2018-11-27 r75683)
* 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’ ...
** 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
* DONE (Rcpi)


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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 -- Tue Apr  9 03:15:07 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 
  7.802   0.564   7.238

name	user	system	elapsed
AA2DACOR	0.086	0.003	0.089
AA3DMoRSE	0.001	0.001	0.002
AAACF	0.001	0.000	0.001
AABLOSUM100	0.001	0.000	0.002
AABLOSUM45	0.001	0.001	0.001
AABLOSUM50	0.001	0.001	0.002
AABLOSUM62	0.002	0.001	0.002
AABLOSUM80	0.001	0.001	0.002
AABurden	0.001	0.000	0.002
AACPSA	0.001	0.000	0.002
AAConn	0.001	0.001	0.001
AAConst	0.001	0.001	0.002
AADescAll	0.001	0.001	0.001
AAEdgeAdj	0.002	0.001	0.003
AAEigIdx	0.001	0.001	0.002
AAFGC	0.002	0.001	0.002
AAGETAWAY	0.001	0.001	0.002
AAGeom	0.002	0.001	0.002
AAInfo	0.002	0.001	0.002
AAMOE2D	0.001	0.001	0.002
AAMOE3D	0.002	0.001	0.003
AAMetaInfo	0.002	0.001	0.002
AAMolProp	0.002	0.001	0.002
AAPAM120	0.001	0.001	0.003
AAPAM250	0.002	0.001	0.003
AAPAM30	0.001	0.001	0.002
AAPAM40	0.002	0.001	0.002
AAPAM70	0.001	0.001	0.003
AARDF	0.001	0.000	0.002
AARandic	0.002	0.001	0.002
AATopo	0.001	0.001	0.002
AATopoChg	0.002	0.001	0.002
AAWHIM	0.001	0.001	0.003
AAWalk	0.002	0.000	0.002
AAindex	0.001	0.000	0.002
OptAA3d	0.000	0.000	0.001
acc	0.013	0.004	0.018
calcDrugFPSim	2.259	0.282	0.808
calcDrugMCSSim	0.005	0.004	0.010
calcParProtGOSim	0.000	0.000	0.001
calcParProtSeqSim	0.005	0.001	0.006
calcTwoProtGOSim	0.000	0.000	0.001
calcTwoProtSeqSim	0.002	0.001	0.002
checkProt	0.002	0.000	0.002
convMolFormat	0.001	0.000	0.001
extractDrugAIO	0.000	0.000	0.001
extractDrugALOGP	0.001	0.001	0.001
extractDrugAminoAcidCount	0.001	0.000	0.001
extractDrugApol	0.001	0.001	0.001
extractDrugAromaticAtomsCount	0.001	0.000	0.002
extractDrugAromaticBondsCount	0.001	0.001	0.001
extractDrugAtomCount	0.001	0.000	0.002
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	0.000	0.000	0.001
extractDrugCPSA	0.001	0.001	0.001
extractDrugCarbonTypes	0.001	0.000	0.002
extractDrugChiChain	0.001	0.001	0.001
extractDrugChiCluster	0.001	0.000	0.001
extractDrugChiPath	0.001	0.000	0.001
extractDrugChiPathCluster	0.001	0.000	0.001
extractDrugDescOB	0.008	0.005	0.013
extractDrugECI	0.000	0.000	0.001
extractDrugEstate	0.001	0.000	0.001
extractDrugEstateComplete	0.001	0.000	0.001
extractDrugExtended	0.000	0.000	0.001
extractDrugExtendedComplete	0.001	0.000	0.001
extractDrugFMF	0.001	0.000	0.000
extractDrugFragmentComplexity	0.000	0.000	0.001
extractDrugGraph	0.001	0.001	0.001
extractDrugGraphComplete	0.001	0.000	0.001
extractDrugGravitationalIndex	0.001	0.001	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	0.001	0.001	0.001
extractDrugKRComplete	0.001	0.000	0.002
extractDrugKappaShapeIndices	0.001	0.001	0.001
extractDrugKierHallSmarts	0.000	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	0.001	0.001
extractDrugMACCS	0.001	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	0.001
extractDrugOBFP2	0.016	0.002	0.018
extractDrugOBFP3	0.006	0.000	0.006
extractDrugOBFP4	0.005	0.001	0.006
extractDrugOBMACCS	0.009	0.002	0.011
extractDrugPetitjeanNumber	0.001	0.001	0.001
extractDrugPetitjeanShapeIndex	0.000	0.000	0.001
extractDrugPubChem	0	0	0
extractDrugPubChemComplete	0.001	0.000	0.001
extractDrugRotatableBondsCount	0.001	0.000	0.001
extractDrugRuleOfFive	0.001	0.000	0.001
extractDrugShortestPath	0.000	0.000	0.001
extractDrugShortestPathComplete	0.000	0.000	0.001
extractDrugStandard	0.001	0.000	0.001
extractDrugStandardComplete	0.001	0.001	0.001
extractDrugTPSA	0.000	0.000	0.001
extractDrugVABC	0.001	0.000	0.001
extractDrugVAdjMa	0.001	0.000	0.001
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	0.000	0.000	0.002
extractDrugZagrebIndex	0.001	0.000	0.001
extractPCMBLOSUM	0.009	0.001	0.010
extractPCMDescScales	0.019	0.003	0.022
extractPCMFAScales	0.024	0.002	0.027
extractPCMMDSScales	0.010	0.002	0.012
extractPCMPropScales	0.018	0.002	0.019
extractPCMScales	0.034	0.004	0.038
extractProtAAC	0.003	0.000	0.003
extractProtAPAAC	1.144	0.023	1.177
extractProtCTDC	0.004	0.000	0.004
extractProtCTDD	0.008	0.002	0.010
extractProtCTDT	0.007	0.000	0.008
extractProtCTriad	0.140	0.014	0.155
extractProtDC	0.007	0.005	0.012
extractProtGeary	0.214	0.007	0.222
extractProtMoran	0.151	0.006	0.159
extractProtMoreauBroto	0.426	0.006	0.436
extractProtPAAC	0.619	0.036	0.662
extractProtPSSM	0.001	0.000	0.001
extractProtPSSMAcc	0.001	0.000	0.001
extractProtPSSMFeature	0.001	0.001	0.002
extractProtQSO	1.333	0.032	1.377
extractProtSOCN	1.270	0.011	1.284
extractProtTC	0.074	0.057	0.129
getCPI	0.003	0.001	0.004
getDrug	0	0	0
getFASTAFromKEGG	0	0	0
getFASTAFromUniProt	0	0	0
getMolFromCAS	0.001	0.001	0.001
getMolFromChEMBL	0.000	0.000	0.001
getMolFromDrugBank	0.000	0.000	0.001
getMolFromKEGG	0	0	0
getMolFromPubChem	0	0	0
getPDBFromRCSBPDB	0	0	0
getPPI	0.002	0.001	0.004
getProt	0.000	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	0	0
getSmiFromKEGG	0	0	0
getSmiFromPubChem	0	0	0
readFASTA	0.001	0.000	0.001
readMolFromSDF	0.002	0.001	0.002
readMolFromSmi	0.000	0.000	0.001
readPDB	1.044	0.004	1.056
searchDrug	0.002	0.000	0.002
segProt	0.002	0.001	0.003

CHECK report for Rcpi on merida2

Summary

Command output

Installation output

Tests output

Example timings