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

Package: Rcpi

Version: 1.20.1

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_1.20.1.tar.gz

StartedAt: 2019-10-16 06:03:48 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:07:33 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 224.3 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_1.20.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/Rcpi.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.20.1’
* 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 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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
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 -- Wed Oct 16 06:07:18 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 
  9.779   1.374   9.438

name	user	system	elapsed
AA2DACOR	0.020	0.006	0.027
AA3DMoRSE	0.002	0.001	0.003
AAACF	0.002	0.002	0.005
AABLOSUM100	0.002	0.002	0.003
AABLOSUM45	0.002	0.002	0.004
AABLOSUM50	0.002	0.001	0.004
AABLOSUM62	0.002	0.002	0.004
AABLOSUM80	0.002	0.002	0.003
AABurden	0.002	0.002	0.004
AACPSA	0.001	0.001	0.003
AAConn	0.002	0.001	0.003
AAConst	0.002	0.001	0.003
AADescAll	0.002	0.002	0.005
AAEdgeAdj	0.002	0.001	0.003
AAEigIdx	0.002	0.002	0.003
AAFGC	0.002	0.002	0.003
AAGETAWAY	0.002	0.002	0.004
AAGeom	0.002	0.002	0.003
AAInfo	0.002	0.002	0.004
AAMOE2D	0.002	0.001	0.004
AAMOE3D	0.001	0.001	0.003
AAMetaInfo	0.002	0.001	0.004
AAMolProp	0.001	0.001	0.003
AAPAM120	0.002	0.002	0.004
AAPAM250	0.002	0.002	0.004
AAPAM30	0.002	0.002	0.004
AAPAM40	0.002	0.002	0.004
AAPAM70	0.001	0.001	0.003
AARDF	0.001	0.002	0.004
AARandic	0.002	0.002	0.004
AATopo	0.002	0.001	0.004
AATopoChg	0.002	0.002	0.003
AAWHIM	0.001	0.002	0.004
AAWalk	0.002	0.002	0.004
AAindex	0.002	0.002	0.004
OptAA3d	0.001	0.000	0.001
acc	0.023	0.012	0.035
calcDrugFPSim	3.045	1.450	1.539
calcDrugMCSSim	0.007	0.010	0.020
calcParProtGOSim	0.000	0.000	0.001
calcParProtSeqSim	0.009	0.002	0.013
calcTwoProtGOSim	0.000	0.001	0.001
calcTwoProtSeqSim	0.002	0.001	0.004
checkProt	0.002	0.001	0.002
convMolFormat	0.001	0.000	0.002
extractDrugAIO	0.001	0.001	0.002
extractDrugALOGP	0.001	0.001	0.002
extractDrugAminoAcidCount	0.002	0.000	0.002
extractDrugApol	0.001	0.000	0.001
extractDrugAromaticAtomsCount	0.001	0.000	0.001
extractDrugAromaticBondsCount	0.001	0.000	0.000
extractDrugAtomCount	0.001	0.000	0.002
extractDrugAutocorrelationCharge	0.001	0.000	0.002
extractDrugAutocorrelationMass	0.001	0.000	0.002
extractDrugAutocorrelationPolarizability	0.001	0.000	0.001
extractDrugBCUT	0.001	0.001	0.001
extractDrugBPol	0.001	0.000	0.002
extractDrugBondCount	0.001	0.000	0.002
extractDrugCPSA	0.001	0.000	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	0.010	0.009	0.020
extractDrugECI	0.001	0.000	0.002
extractDrugEstate	0.001	0.000	0.002
extractDrugEstateComplete	0.000	0.001	0.001
extractDrugExtended	0.001	0.001	0.001
extractDrugExtendedComplete	0.002	0.001	0.002
extractDrugFMF	0.001	0.001	0.001
extractDrugFragmentComplexity	0.001	0.001	0.001
extractDrugGraph	0.001	0.001	0.001
extractDrugGraphComplete	0.001	0.000	0.001
extractDrugGravitationalIndex	0.001	0.000	0.001
extractDrugHBondAcceptorCount	0.001	0.000	0.002
extractDrugHBondDonorCount	0.001	0.001	0.001
extractDrugHybridization	0.001	0.000	0.002
extractDrugHybridizationComplete	0.002	0.000	0.002
extractDrugHybridizationRatio	0.001	0.001	0.002
extractDrugIPMolecularLearning	0.129	0.002	0.130
extractDrugKR	0.002	0.000	0.002
extractDrugKRComplete	0.001	0.000	0.001
extractDrugKappaShapeIndices	0.001	0.000	0.002
extractDrugKierHallSmarts	0.002	0.001	0.002
extractDrugLargestChain	0.001	0.001	0.001
extractDrugLargestPiSystem	0.002	0.001	0.002
extractDrugLengthOverBreadth	0.001	0.001	0.002
extractDrugLongestAliphaticChain	0.001	0.000	0.002
extractDrugMACCS	0.001	0.000	0.001
extractDrugMACCSComplete	0.001	0.000	0.002
extractDrugMDE	0.002	0.001	0.002
extractDrugMannholdLogP	0.001	0.001	0.002
extractDrugMomentOfInertia	0.001	0.001	0.001
extractDrugOBFP2	0.008	0.001	0.009
extractDrugOBFP3	0.008	0.001	0.008
extractDrugOBFP4	0.011	0.009	0.020
extractDrugOBMACCS	0.020	0.001	0.022
extractDrugPetitjeanNumber	0.001	0.000	0.001
extractDrugPetitjeanShapeIndex	0.001	0.000	0.001
extractDrugPubChem	0.000	0.001	0.001
extractDrugPubChemComplete	0.001	0.000	0.002
extractDrugRotatableBondsCount	0.001	0.000	0.002
extractDrugRuleOfFive	0.001	0.000	0.001
extractDrugShortestPath	0.002	0.000	0.001
extractDrugShortestPathComplete	0.001	0.000	0.002
extractDrugStandard	0.001	0.001	0.002
extractDrugStandardComplete	0.002	0.001	0.002
extractDrugTPSA	0.001	0.001	0.001
extractDrugVABC	0.002	0.001	0.002
extractDrugVAdjMa	0.001	0.001	0.002
extractDrugWHIM	0.001	0.001	0.001
extractDrugWeight	0.001	0.000	0.001
extractDrugWeightedPath	0.001	0.000	0.002
extractDrugWienerNumbers	0.001	0.000	0.001
extractDrugXLogP	0.001	0.000	0.002
extractDrugZagrebIndex	0.001	0.000	0.002
extractPCMBLOSUM	0.014	0.002	0.016
extractPCMDescScales	0.022	0.004	0.026
extractPCMFAScales	0.034	0.010	0.044
extractPCMMDSScales	0.023	0.008	0.031
extractPCMPropScales	0.021	0.003	0.024
extractPCMScales	0.048	0.010	0.058
extractProtAAC	0.003	0.001	0.004
extractProtAPAAC	1.430	0.046	1.476
extractProtCTDC	0.003	0.000	0.003
extractProtCTDD	0.006	0.001	0.008
extractProtCTDT	0.006	0.001	0.008
extractProtCTriad	0.193	0.036	0.229
extractProtDC	0.009	0.008	0.017
extractProtGeary	0.217	0.019	0.236
extractProtMoran	0.209	0.018	0.225
extractProtMoreauBroto	0.638	0.018	0.655
extractProtPAAC	0.959	0.085	1.043
extractProtPSSM	0.002	0.000	0.002
extractProtPSSMAcc	0.002	0.001	0.002
extractProtPSSMFeature	0.002	0.001	0.002
extractProtQSO	2.077	0.048	2.123
extractProtSOCN	1.946	0.027	1.971
extractProtTC	0.137	0.147	0.283
getCPI	0.005	0.002	0.008
getDrug	0.000	0.000	0.001
getFASTAFromKEGG	0.001	0.001	0.001
getFASTAFromUniProt	0	0	0
getMolFromCAS	0.000	0.000	0.001
getMolFromChEMBL	0.001	0.000	0.000
getMolFromDrugBank	0	0	0
getMolFromKEGG	0.001	0.001	0.001
getMolFromPubChem	0	0	0
getPDBFromRCSBPDB	0.001	0.000	0.000
getPPI	0.005	0.004	0.009
getProt	0.000	0.001	0.000
getSeqFromKEGG	0	0	0
getSeqFromRCSBPDB	0.001	0.000	0.001
getSeqFromUniProt	0	0	0
getSmiFromChEMBL	0	0	0
getSmiFromDrugBank	0.000	0.001	0.000
getSmiFromKEGG	0.000	0.000	0.001
getSmiFromPubChem	0.000	0.000	0.001
readFASTA	0.002	0.001	0.003
readMolFromSDF	0.003	0.001	0.004
readMolFromSmi	0.001	0.000	0.001
readPDB	1.296	0.013	1.309
searchDrug	0.001	0.001	0.002
segProt	0.002	0.001	0.004

CHECK report for Rcpi on celaya2

Summary

Command output

Installation output

Tests output

Example timings