Multiple platform build/check report for BioC 3.9 - CHECK report for Rcpi on malbec2

Package: Rcpi

Version: 1.20.1

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Rcpi_1.20.1.tar.gz

StartedAt: 2019-10-16 04:21:05 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:23:59 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 174.6 seconds

RetCode: 0

Status: OK

CheckDir: Rcpi.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Rcpi_1.20.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Rcpi.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Rcpi
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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-pc-linux-gnu (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 04:23:48 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 
  7.309   0.392   7.769

name	user	system	elapsed
AA2DACOR	0.023	0.000	0.023
AA3DMoRSE	0.002	0.000	0.005
AAACF	0.002	0.000	0.002
AABLOSUM100	0.002	0.000	0.001
AABLOSUM45	0.001	0.000	0.001
AABLOSUM50	0.001	0.000	0.001
AABLOSUM62	0.001	0.000	0.002
AABLOSUM80	0.001	0.000	0.002
AABurden	0.001	0.000	0.002
AACPSA	0.001	0.000	0.002
AAConn	0.002	0.000	0.001
AAConst	0.001	0.000	0.001
AADescAll	0.001	0.000	0.001
AAEdgeAdj	0.001	0.000	0.001
AAEigIdx	0.001	0.000	0.001
AAFGC	0.000	0.001	0.001
AAGETAWAY	0.000	0.002	0.001
AAGeom	0.000	0.001	0.002
AAInfo	0.000	0.001	0.002
AAMOE2D	0.000	0.001	0.001
AAMOE3D	0.000	0.001	0.001
AAMetaInfo	0.000	0.001	0.001
AAMolProp	0.000	0.001	0.001
AAPAM120	0.001	0.000	0.001
AAPAM250	0.001	0.000	0.001
AAPAM30	0.001	0.000	0.001
AAPAM40	0.001	0.000	0.001
AAPAM70	0.000	0.001	0.001
AARDF	0.000	0.001	0.001
AARandic	0.001	0.000	0.001
AATopo	0.001	0.000	0.001
AATopoChg	0.001	0.000	0.001
AAWHIM	0.001	0.000	0.001
AAWalk	0.001	0.000	0.001
AAindex	0.001	0.000	0.001
OptAA3d	0	0	0
acc	0.012	0.004	0.016
calcDrugFPSim	1.700	0.081	1.222
calcDrugMCSSim	0.006	0.004	0.091
calcParProtGOSim	0.000	0.000	0.001
calcParProtSeqSim	0.005	0.002	0.193
calcTwoProtGOSim	0.000	0.000	0.001
calcTwoProtSeqSim	0.002	0.000	0.003
checkProt	0.000	0.001	0.002
convMolFormat	0.000	0.001	0.001
extractDrugAIO	0.001	0.000	0.001
extractDrugALOGP	0.001	0.000	0.001
extractDrugAminoAcidCount	0	0	0
extractDrugApol	0.001	0.000	0.001
extractDrugAromaticAtomsCount	0.000	0.000	0.001
extractDrugAromaticBondsCount	0.001	0.000	0.001
extractDrugAtomCount	0.001	0.000	0.001
extractDrugAutocorrelationCharge	0.001	0.000	0.001
extractDrugAutocorrelationMass	0.001	0.000	0.001
extractDrugAutocorrelationPolarizability	0	0	0
extractDrugBCUT	0.001	0.000	0.001
extractDrugBPol	0.001	0.000	0.001
extractDrugBondCount	0.001	0.000	0.001
extractDrugCPSA	0.001	0.000	0.001
extractDrugCarbonTypes	0	0	0
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	0.017	0.008	0.236
extractDrugECI	0.001	0.000	0.001
extractDrugEstate	0.001	0.000	0.001
extractDrugEstateComplete	0.000	0.000	0.001
extractDrugExtended	0.000	0.001	0.001
extractDrugExtendedComplete	0.000	0.001	0.000
extractDrugFMF	0.000	0.000	0.001
extractDrugFragmentComplexity	0.001	0.000	0.001
extractDrugGraph	0.000	0.000	0.001
extractDrugGraphComplete	0.001	0.000	0.001
extractDrugGravitationalIndex	0.000	0.000	0.001
extractDrugHBondAcceptorCount	0.001	0.000	0.000
extractDrugHBondDonorCount	0.000	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	0.000	0.001	0.000
extractDrugKR	0.000	0.001	0.001
extractDrugKRComplete	0.000	0.001	0.000
extractDrugKappaShapeIndices	0.000	0.001	0.001
extractDrugKierHallSmarts	0.000	0.000	0.001
extractDrugLargestChain	0.000	0.001	0.001
extractDrugLargestPiSystem	0.000	0.000	0.001
extractDrugLengthOverBreadth	0.000	0.001	0.001
extractDrugLongestAliphaticChain	0.001	0.000	0.001
extractDrugMACCS	0	0	0
extractDrugMACCSComplete	0.001	0.000	0.001
extractDrugMDE	0.001	0.000	0.000
extractDrugMannholdLogP	0.001	0.000	0.001
extractDrugMomentOfInertia	0.001	0.000	0.000
extractDrugOBFP2	0.009	0.000	0.010
extractDrugOBFP3	0.112	0.016	0.129
extractDrugOBFP4	0.003	0.008	0.010
extractDrugOBMACCS	0.007	0.012	0.020
extractDrugPetitjeanNumber	0.001	0.000	0.000
extractDrugPetitjeanShapeIndex	0.001	0.000	0.001
extractDrugPubChem	0.001	0.000	0.000
extractDrugPubChemComplete	0.001	0.000	0.001
extractDrugRotatableBondsCount	0.001	0.000	0.001
extractDrugRuleOfFive	0	0	0
extractDrugShortestPath	0	0	0
extractDrugShortestPathComplete	0.000	0.000	0.001
extractDrugStandard	0.001	0.000	0.001
extractDrugStandardComplete	0.001	0.000	0.000
extractDrugTPSA	0.001	0.000	0.001
extractDrugVABC	0.001	0.000	0.000
extractDrugVAdjMa	0.001	0.000	0.001
extractDrugWHIM	0.001	0.000	0.000
extractDrugWeight	0.000	0.000	0.001
extractDrugWeightedPath	0.001	0.000	0.001
extractDrugWienerNumbers	0.001	0.000	0.000
extractDrugXLogP	0.000	0.000	0.001
extractDrugZagrebIndex	0.001	0.000	0.001
extractPCMBLOSUM	0.012	0.000	0.011
extractPCMDescScales	0.014	0.000	0.014
extractPCMFAScales	0.025	0.000	0.024
extractPCMMDSScales	0.015	0.000	0.017
extractPCMPropScales	0.022	0.004	0.026
extractPCMScales	0.023	0.000	0.024
extractProtAAC	0.003	0.000	0.003
extractProtAPAAC	1.383	0.024	1.429
extractProtCTDC	0.003	0.000	0.003
extractProtCTDD	0.006	0.000	0.006
extractProtCTDT	0.007	0.000	0.007
extractProtCTriad	0.117	0.008	0.126
extractProtDC	0.005	0.000	0.005
extractProtGeary	0.153	0.004	0.157
extractProtMoran	0.146	0.000	0.146
extractProtMoreauBroto	0.149	0.004	0.153
extractProtPAAC	0.529	0.000	0.529
extractProtPSSM	0.001	0.000	0.001
extractProtPSSMAcc	0.001	0.000	0.001
extractProtPSSMFeature	0.001	0.000	0.001
extractProtQSO	1.221	0.000	1.236
extractProtSOCN	1.182	0.004	1.185
extractProtTC	0.048	0.028	0.076
getCPI	0.003	0.000	0.003
getDrug	0	0	0
getFASTAFromKEGG	0	0	0
getFASTAFromUniProt	0	0	0
getMolFromCAS	0.000	0.001	0.000
getMolFromChEMBL	0	0	0
getMolFromDrugBank	0	0	0
getMolFromKEGG	0	0	0
getMolFromPubChem	0.001	0.000	0.000
getPDBFromRCSBPDB	0	0	0
getPPI	0.004	0.000	0.004
getProt	0	0	0
getSeqFromKEGG	0	0	0
getSeqFromRCSBPDB	0	0	0
getSeqFromUniProt	0.000	0.000	0.001
getSmiFromChEMBL	0.000	0.000	0.001
getSmiFromDrugBank	0.001	0.000	0.001
getSmiFromKEGG	0.001	0.000	0.000
getSmiFromPubChem	0	0	0
readFASTA	0.002	0.000	0.001
readMolFromSDF	0.002	0.000	0.002
readMolFromSmi	0.001	0.000	0.001
readPDB	1.491	0.004	1.528
searchDrug	0.001	0.000	0.002
segProt	0.003	0.000	0.002

CHECK report for Rcpi on malbec2

Summary

Command output

Installation output

Tests output

Example timings