Multiple platform build/check report for BioC 3.10 - CHECK report for Rcpi on merida1

Package: Rcpi

Version: 1.22.0

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_1.22.0.tar.gz

StartedAt: 2020-04-15 05:00:27 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:03:23 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 175.7 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_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/Rcpi.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.22.0’
* 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/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 Apr 15 05:03:07 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 
  8.194   0.590   7.473

name	user	system	elapsed
AA2DACOR	0.004	0.002	0.005
AA3DMoRSE	0.001	0.001	0.001
AAACF	0.002	0.001	0.003
AABLOSUM100	0.001	0.001	0.003
AABLOSUM45	0.002	0.000	0.004
AABLOSUM50	0.002	0.001	0.002
AABLOSUM62	0.001	0.001	0.002
AABLOSUM80	0.001	0.001	0.002
AABurden	0.001	0.001	0.002
AACPSA	0.000	0.001	0.002
AAConn	0.001	0.001	0.001
AAConst	0.001	0.000	0.002
AADescAll	0.001	0.001	0.002
AAEdgeAdj	0.001	0.001	0.002
AAEigIdx	0.002	0.001	0.002
AAFGC	0.001	0.001	0.002
AAGETAWAY	0.001	0.001	0.003
AAGeom	0.002	0.001	0.003
AAInfo	0.001	0.001	0.002
AAMOE2D	0.002	0.001	0.003
AAMOE3D	0.001	0.002	0.003
AAMetaInfo	0.001	0.000	0.002
AAMolProp	0.001	0.000	0.001
AAPAM120	0.001	0.001	0.002
AAPAM250	0.001	0.001	0.002
AAPAM30	0.002	0.001	0.002
AAPAM40	0.001	0.001	0.002
AAPAM70	0.002	0.001	0.003
AARDF	0.001	0.001	0.003
AARandic	0.002	0.001	0.002
AATopo	0.001	0.001	0.002
AATopoChg	0.001	0.001	0.002
AAWHIM	0.002	0.001	0.003
AAWalk	0.001	0.001	0.002
AAindex	0.001	0.000	0.001
OptAA3d	0	0	0
acc	0.021	0.008	0.028
calcDrugFPSim	3.087	0.495	0.937
calcDrugMCSSim	0.018	0.007	0.013
calcParProtGOSim	0.001	0.000	0.001
calcParProtSeqSim	0.017	0.001	0.010
calcTwoProtGOSim	0.001	0.000	0.001
calcTwoProtSeqSim	0.002	0.000	0.003
checkProt	0.004	0.001	0.003
convMolFormat	0.001	0.000	0.002
extractDrugAIO	0.023	0.000	0.013
extractDrugALOGP	0.001	0.000	0.001
extractDrugAminoAcidCount	0.001	0.000	0.001
extractDrugApol	0.001	0.000	0.002
extractDrugAromaticAtomsCount	0.001	0.000	0.002
extractDrugAromaticBondsCount	0.001	0.000	0.001
extractDrugAtomCount	0.001	0.000	0.001
extractDrugAutocorrelationCharge	0.001	0.001	0.002
extractDrugAutocorrelationMass	0.001	0.000	0.001
extractDrugAutocorrelationPolarizability	0.001	0.001	0.001
extractDrugBCUT	0.001	0.000	0.002
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	0.001
extractDrugChiCluster	0.001	0.000	0.001
extractDrugChiPath	0.001	0.000	0.001
extractDrugChiPathCluster	0.001	0.000	0.001
extractDrugDescOB	0.008	0.001	0.009
extractDrugECI	0.001	0.000	0.001
extractDrugEstate	0.001	0.000	0.001
extractDrugEstateComplete	0.001	0.000	0.001
extractDrugExtended	0.001	0.000	0.001
extractDrugExtendedComplete	0.001	0.000	0.001
extractDrugFMF	0.001	0.000	0.001
extractDrugFragmentComplexity	0.001	0.000	0.001
extractDrugGraph	0.001	0.000	0.001
extractDrugGraphComplete	0.001	0.001	0.001
extractDrugGravitationalIndex	0.001	0.000	0.001
extractDrugHBondAcceptorCount	0.001	0.001	0.001
extractDrugHBondDonorCount	0.001	0.000	0.001
extractDrugHybridization	0.001	0.001	0.001
extractDrugHybridizationComplete	0.001	0.000	0.001
extractDrugHybridizationRatio	0.001	0.001	0.001
extractDrugIPMolecularLearning	0.001	0.000	0.001
extractDrugKR	0.000	0.000	0.002
extractDrugKRComplete	0.001	0.000	0.001
extractDrugKappaShapeIndices	0.001	0.000	0.001
extractDrugKierHallSmarts	0.001	0.000	0.001
extractDrugLargestChain	0.001	0.000	0.001
extractDrugLargestPiSystem	0.001	0.000	0.001
extractDrugLengthOverBreadth	0.001	0.001	0.002
extractDrugLongestAliphaticChain	0.001	0.000	0.001
extractDrugMACCS	0.001	0.001	0.001
extractDrugMACCSComplete	0.001	0.000	0.001
extractDrugMDE	0.001	0.001	0.001
extractDrugMannholdLogP	0.001	0.000	0.001
extractDrugMomentOfInertia	0.001	0.001	0.001
extractDrugOBFP2	0.010	0.005	0.015
extractDrugOBFP3	0.107	0.003	0.111
extractDrugOBFP4	0.008	0.001	0.009
extractDrugOBMACCS	0.007	0.000	0.008
extractDrugPetitjeanNumber	0.001	0.000	0.001
extractDrugPetitjeanShapeIndex	0.001	0.001	0.001
extractDrugPubChem	0.001	0.000	0.002
extractDrugPubChemComplete	0.001	0.001	0.001
extractDrugRotatableBondsCount	0.000	0.000	0.001
extractDrugRuleOfFive	0.001	0.001	0.001
extractDrugShortestPath	0.001	0.000	0.001
extractDrugShortestPathComplete	0.001	0.001	0.001
extractDrugStandard	0.001	0.000	0.001
extractDrugStandardComplete	0.001	0.000	0.001
extractDrugTPSA	0.001	0.000	0.002
extractDrugVABC	0.001	0.000	0.000
extractDrugVAdjMa	0.001	0.000	0.001
extractDrugWHIM	0.000	0.000	0.001
extractDrugWeight	0.001	0.000	0.001
extractDrugWeightedPath	0.000	0.000	0.001
extractDrugWienerNumbers	0.001	0.000	0.001
extractDrugXLogP	0.001	0.000	0.001
extractDrugZagrebIndex	0.001	0.000	0.001
extractPCMBLOSUM	0.012	0.002	0.014
extractPCMDescScales	0.024	0.001	0.025
extractPCMFAScales	0.024	0.003	0.027
extractPCMMDSScales	0.012	0.002	0.015
extractPCMPropScales	0.013	0.002	0.016
extractPCMScales	0.025	0.004	0.028
extractProtAAC	0.002	0.001	0.003
extractProtAPAAC	1.132	0.022	1.199
extractProtCTDC	0.004	0.001	0.004
extractProtCTDD	0.007	0.001	0.009
extractProtCTDT	0.007	0.000	0.008
extractProtCTriad	0.136	0.013	0.153
extractProtDC	0.004	0.002	0.007
extractProtGeary	0.472	0.008	0.482
extractProtMoran	0.185	0.009	0.197
extractProtMoreauBroto	0.176	0.016	0.193
extractProtPAAC	0.728	0.022	0.756
extractProtPSSM	0.001	0.000	0.002
extractProtPSSMAcc	0.002	0.000	0.002
extractProtPSSMFeature	0.001	0.001	0.002
extractProtQSO	1.413	0.050	1.472
extractProtSOCN	1.323	0.015	1.349
extractProtTC	0.076	0.061	0.137
getCPI	0.003	0.001	0.004
getDrug	0.000	0.000	0.001
getFASTAFromKEGG	0.000	0.001	0.001
getFASTAFromUniProt	0.000	0.000	0.001
getMolFromCAS	0.000	0.000	0.001
getMolFromChEMBL	0.000	0.000	0.001
getMolFromDrugBank	0	0	0
getMolFromKEGG	0.001	0.000	0.000
getMolFromPubChem	0	0	0
getPDBFromRCSBPDB	0	0	0
getPPI	0.004	0.001	0.005
getProt	0	0	0
getSeqFromKEGG	0	0	0
getSeqFromRCSBPDB	0	0	0
getSeqFromUniProt	0	0	0
getSmiFromChEMBL	0.000	0.000	0.001
getSmiFromDrugBank	0	0	0
getSmiFromKEGG	0	0	0
getSmiFromPubChem	0.000	0.000	0.001
readFASTA	0.002	0.000	0.002
readMolFromSDF	0.001	0.000	0.002
readMolFromSmi	0.001	0.000	0.001
readPDB	1.100	0.007	1.113
searchDrug	0.002	0.000	0.002
segProt	0.003	0.001	0.005

CHECK report for Rcpi on merida1

Summary

Command output

Installation output

Tests output

Example timings