Multiple platform build/check report for BioC 3.11 - CHECK report for Rcpi on celaya2

Package: Rcpi

Version: 1.23.0

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_1.23.0.tar.gz

StartedAt: 2020-01-16 08:00:05 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 08:04:04 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 238.9 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_1.23.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Rcpi.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.23.0’
* 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/4.0/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) (2019-12-14 r77572) -- "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 -- Thu Jan 16 08:03:50 2020 
*********************************************** 
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 
 10.614   1.511  10.328

name	user	system	elapsed
AA2DACOR	0.025	0.006	0.031
AA3DMoRSE	0.002	0.001	0.003
AAACF	0.002	0.001	0.005
AABLOSUM100	0.002	0.001	0.003
AABLOSUM45	0.002	0.002	0.004
AABLOSUM50	0.002	0.002	0.005
AABLOSUM62	0.003	0.002	0.004
AABLOSUM80	0.002	0.001	0.003
AABurden	0.002	0.001	0.004
AACPSA	0.003	0.002	0.004
AAConn	0.002	0.002	0.004
AAConst	0.002	0.002	0.004
AADescAll	0.002	0.002	0.004
AAEdgeAdj	0.002	0.002	0.003
AAEigIdx	0.002	0.002	0.004
AAFGC	0.002	0.002	0.005
AAGETAWAY	0.002	0.002	0.005
AAGeom	0.002	0.002	0.003
AAInfo	0.002	0.003	0.005
AAMOE2D	0.002	0.002	0.004
AAMOE3D	0.002	0.002	0.004
AAMetaInfo	0.001	0.001	0.003
AAMolProp	0.002	0.001	0.004
AAPAM120	0.002	0.001	0.004
AAPAM250	0.002	0.002	0.004
AAPAM30	0.002	0.002	0.004
AAPAM40	0.003	0.002	0.004
AAPAM70	0.002	0.001	0.003
AARDF	0.002	0.001	0.004
AARandic	0.003	0.002	0.005
AATopo	0.002	0.001	0.003
AATopoChg	0.002	0.002	0.003
AAWHIM	0.001	0.002	0.004
AAWalk	0.002	0.003	0.005
AAindex	0.002	0.002	0.003
OptAA3d	0.000	0.001	0.001
acc	0.024	0.012	0.035
calcDrugFPSim	3.085	1.442	1.637
calcDrugMCSSim	0.008	0.012	0.022
calcParProtGOSim	0.001	0.000	0.001
calcParProtSeqSim	0.008	0.002	0.011
calcTwoProtGOSim	0.000	0.001	0.001
calcTwoProtSeqSim	0.002	0.000	0.002
checkProt	0.001	0.000	0.002
convMolFormat	0.001	0.000	0.001
extractDrugAIO	0.001	0.000	0.001
extractDrugALOGP	0.001	0.000	0.001
extractDrugAminoAcidCount	0.001	0.001	0.001
extractDrugApol	0.001	0.000	0.001
extractDrugAromaticAtomsCount	0.001	0.001	0.001
extractDrugAromaticBondsCount	0.001	0.000	0.000
extractDrugAtomCount	0.001	0.001	0.001
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	0.000	0.001
extractDrugCarbonTypes	0.000	0.000	0.001
extractDrugChiChain	0.001	0.000	0.001
extractDrugChiCluster	0.000	0.000	0.001
extractDrugChiPath	0.001	0.000	0.002
extractDrugChiPathCluster	0.001	0.001	0.002
extractDrugDescOB	0.021	0.002	0.024
extractDrugECI	0.001	0.000	0.001
extractDrugEstate	0.001	0.001	0.002
extractDrugEstateComplete	0.001	0.001	0.001
extractDrugExtended	0.002	0.001	0.002
extractDrugExtendedComplete	0.001	0.001	0.002
extractDrugFMF	0.001	0.001	0.002
extractDrugFragmentComplexity	0.001	0.001	0.001
extractDrugGraph	0.002	0.001	0.002
extractDrugGraphComplete	0.001	0.001	0.001
extractDrugGravitationalIndex	0.001	0.001	0.001
extractDrugHBondAcceptorCount	0.001	0.000	0.002
extractDrugHBondDonorCount	0.002	0.000	0.001
extractDrugHybridization	0.001	0.000	0.001
extractDrugHybridizationComplete	0.001	0.001	0.001
extractDrugHybridizationRatio	0.002	0.000	0.002
extractDrugIPMolecularLearning	0.001	0.000	0.001
extractDrugKR	0.001	0.001	0.001
extractDrugKRComplete	0.001	0.000	0.001
extractDrugKappaShapeIndices	0.001	0.000	0.001
extractDrugKierHallSmarts	0.000	0.001	0.001
extractDrugLargestChain	0.001	0.001	0.002
extractDrugLargestPiSystem	0.001	0.000	0.001
extractDrugLengthOverBreadth	0.001	0.000	0.002
extractDrugLongestAliphaticChain	0.001	0.000	0.002
extractDrugMACCS	0.001	0.000	0.002
extractDrugMACCSComplete	0.001	0.000	0.001
extractDrugMDE	0.001	0.001	0.001
extractDrugMannholdLogP	0.002	0.001	0.002
extractDrugMomentOfInertia	0.001	0.001	0.001
extractDrugOBFP2	0.012	0.011	0.022
extractDrugOBFP3	0.021	0.001	0.022
extractDrugOBFP4	0.006	0.001	0.007
extractDrugOBMACCS	0.128	0.002	0.129
extractDrugPetitjeanNumber	0.001	0.000	0.001
extractDrugPetitjeanShapeIndex	0.001	0.000	0.002
extractDrugPubChem	0.002	0.000	0.001
extractDrugPubChemComplete	0.001	0.000	0.002
extractDrugRotatableBondsCount	0.002	0.000	0.002
extractDrugRuleOfFive	0.001	0.000	0.001
extractDrugShortestPath	0.002	0.000	0.002
extractDrugShortestPathComplete	0.001	0.001	0.001
extractDrugStandard	0.002	0.001	0.002
extractDrugStandardComplete	0.001	0.001	0.001
extractDrugTPSA	0.001	0.001	0.001
extractDrugVABC	0.001	0.000	0.002
extractDrugVAdjMa	0.001	0.000	0.001
extractDrugWHIM	0.001	0.000	0.001
extractDrugWeight	0.001	0.000	0.002
extractDrugWeightedPath	0.001	0.000	0.001
extractDrugWienerNumbers	0.001	0.001	0.002
extractDrugXLogP	0.001	0.001	0.002
extractDrugZagrebIndex	0.001	0.000	0.001
extractPCMBLOSUM	0.017	0.003	0.020
extractPCMDescScales	0.023	0.006	0.029
extractPCMFAScales	0.033	0.008	0.041
extractPCMMDSScales	0.041	0.014	0.055
extractPCMPropScales	0.016	0.003	0.019
extractPCMScales	0.024	0.006	0.030
extractProtAAC	0.004	0.001	0.005
extractProtAPAAC	1.217	0.053	1.271
extractProtCTDC	0.003	0.000	0.003
extractProtCTDD	0.006	0.002	0.008
extractProtCTDT	0.006	0.002	0.008
extractProtCTriad	0.195	0.030	0.224
extractProtDC	0.008	0.006	0.014
extractProtGeary	0.273	0.024	0.298
extractProtMoran	0.287	0.025	0.310
extractProtMoreauBroto	0.258	0.028	0.285
extractProtPAAC	0.670	0.004	0.673
extractProtPSSM	0.001	0.000	0.002
extractProtPSSMAcc	0.002	0.000	0.002
extractProtPSSMFeature	0.002	0.000	0.002
extractProtQSO	1.818	0.025	1.841
extractProtSOCN	1.956	0.032	1.985
extractProtTC	0.142	0.158	0.300
getCPI	0.005	0.002	0.008
getDrug	0.000	0.000	0.001
getFASTAFromKEGG	0.000	0.000	0.001
getFASTAFromUniProt	0.000	0.000	0.001
getMolFromCAS	0.000	0.001	0.001
getMolFromChEMBL	0.000	0.000	0.001
getMolFromDrugBank	0	0	0
getMolFromKEGG	0.001	0.001	0.000
getMolFromPubChem	0	0	0
getPDBFromRCSBPDB	0.001	0.000	0.000
getPPI	0.005	0.003	0.008
getProt	0.001	0.001	0.000
getSeqFromKEGG	0	0	0
getSeqFromRCSBPDB	0.001	0.000	0.001
getSeqFromUniProt	0.000	0.000	0.001
getSmiFromChEMBL	0.001	0.000	0.000
getSmiFromDrugBank	0.000	0.000	0.001
getSmiFromKEGG	0.001	0.000	0.000
getSmiFromPubChem	0.000	0.001	0.001
readFASTA	0.002	0.001	0.002
readMolFromSDF	0.002	0.001	0.003
readMolFromSmi	0.001	0.001	0.002
readPDB	1.347	0.006	1.354
searchDrug	0.002	0.000	0.003
segProt	0.005	0.002	0.006

CHECK report for Rcpi on celaya2

Summary

Command output

Installation output

Tests output

Example timings