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

Package: Rcpi

Version: 1.19.2

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_1.19.2.tar.gz

StartedAt: 2019-04-09 03:03:49 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:06:41 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 172.5 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_1.19.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Rcpi.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.19.2’
* 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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###   /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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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 -- Tue Apr  9 03:06:29 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 
  7.293   0.336   7.311

name	user	system	elapsed
AA2DACOR	0.016	0.004	0.020
AA3DMoRSE	0.001	0.000	0.002
AAACF	0.002	0.000	0.001
AABLOSUM100	0.002	0.000	0.002
AABLOSUM45	0.001	0.000	0.002
AABLOSUM50	0.001	0.000	0.001
AABLOSUM62	0.001	0.000	0.001
AABLOSUM80	0.001	0.000	0.001
AABurden	0.001	0.000	0.001
AACPSA	0.001	0.000	0.001
AAConn	0.002	0.000	0.002
AAConst	0.002	0.000	0.002
AADescAll	0.001	0.000	0.001
AAEdgeAdj	0.000	0.001	0.001
AAEigIdx	0.000	0.001	0.001
AAFGC	0.001	0.000	0.002
AAGETAWAY	0.001	0.000	0.002
AAGeom	0.001	0.000	0.002
AAInfo	0.001	0.000	0.002
AAMOE2D	0.001	0.000	0.001
AAMOE3D	0.002	0.000	0.001
AAMetaInfo	0.002	0.000	0.001
AAMolProp	0.002	0.000	0.001
AAPAM120	0.002	0.000	0.001
AAPAM250	0.002	0.000	0.001
AAPAM30	0.001	0.000	0.001
AAPAM40	0.001	0.000	0.001
AAPAM70	0.001	0.000	0.001
AARDF	0.001	0.000	0.002
AARandic	0.001	0.000	0.002
AATopo	0.002	0.000	0.002
AATopoChg	0.002	0.000	0.001
AAWHIM	0.002	0.000	0.001
AAWalk	0.001	0.000	0.001
AAindex	0.001	0.000	0.002
OptAA3d	0.000	0.000	0.001
acc	0.011	0.004	0.015
calcDrugFPSim	1.633	0.065	1.858
calcDrugMCSSim	0.004	0.004	0.018
calcParProtGOSim	0	0	0
calcParProtSeqSim	0.006	0.000	0.018
calcTwoProtGOSim	0	0	0
calcTwoProtSeqSim	0.000	0.002	0.002
checkProt	0.001	0.000	0.002
convMolFormat	0.001	0.000	0.000
extractDrugAIO	0.001	0.000	0.001
extractDrugALOGP	0.001	0.000	0.000
extractDrugAminoAcidCount	0.000	0.000	0.001
extractDrugApol	0.001	0.000	0.000
extractDrugAromaticAtomsCount	0.001	0.000	0.001
extractDrugAromaticBondsCount	0.001	0.000	0.000
extractDrugAtomCount	0.000	0.000	0.001
extractDrugAutocorrelationCharge	0.001	0.000	0.000
extractDrugAutocorrelationMass	0.000	0.000	0.001
extractDrugAutocorrelationPolarizability	0.001	0.000	0.000
extractDrugBCUT	0.000	0.000	0.001
extractDrugBPol	0.001	0.000	0.000
extractDrugBondCount	0.000	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	0.000	0.000	0.001
extractDrugChiPath	0.001	0.000	0.001
extractDrugChiPathCluster	0.001	0.000	0.001
extractDrugDescOB	0.099	0.020	0.129
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	0.000	0.001
extractDrugGravitationalIndex	0.000	0.001	0.001
extractDrugHBondAcceptorCount	0.000	0.000	0.001
extractDrugHBondDonorCount	0.000	0.001	0.001
extractDrugHybridization	0.001	0.000	0.001
extractDrugHybridizationComplete	0.001	0.000	0.001
extractDrugHybridizationRatio	0.001	0.000	0.001
extractDrugIPMolecularLearning	0.001	0.000	0.001
extractDrugKR	0.001	0.000	0.001
extractDrugKRComplete	0.001	0.000	0.001
extractDrugKappaShapeIndices	0	0	0
extractDrugKierHallSmarts	0.001	0.000	0.001
extractDrugLargestChain	0	0	0
extractDrugLargestPiSystem	0.001	0.000	0.001
extractDrugLengthOverBreadth	0.000	0.001	0.001
extractDrugLongestAliphaticChain	0.000	0.000	0.001
extractDrugMACCS	0.000	0.001	0.001
extractDrugMACCSComplete	0.001	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	0.007	0.004	0.011
extractDrugOBFP3	0.011	0.008	0.019
extractDrugOBFP4	0.002	0.008	0.010
extractDrugOBMACCS	0.006	0.012	0.018
extractDrugPetitjeanNumber	0.001	0.000	0.001
extractDrugPetitjeanShapeIndex	0.001	0.000	0.001
extractDrugPubChem	0.001	0.000	0.001
extractDrugPubChemComplete	0.001	0.000	0.001
extractDrugRotatableBondsCount	0.001	0.000	0.001
extractDrugRuleOfFive	0	0	0
extractDrugShortestPath	0.001	0.000	0.001
extractDrugShortestPathComplete	0.001	0.000	0.001
extractDrugStandard	0.000	0.001	0.001
extractDrugStandardComplete	0.000	0.000	0.001
extractDrugTPSA	0.000	0.001	0.001
extractDrugVABC	0	0	0
extractDrugVAdjMa	0.001	0.000	0.001
extractDrugWHIM	0.000	0.000	0.001
extractDrugWeight	0.001	0.000	0.001
extractDrugWeightedPath	0.001	0.000	0.001
extractDrugWienerNumbers	0	0	0
extractDrugXLogP	0.001	0.000	0.001
extractDrugZagrebIndex	0.001	0.000	0.000
extractPCMBLOSUM	0.008	0.004	0.012
extractPCMDescScales	0.015	0.000	0.015
extractPCMFAScales	0.020	0.004	0.024
extractPCMMDSScales	0.014	0.000	0.014
extractPCMPropScales	0.010	0.008	0.018
extractPCMScales	0.034	0.000	0.038
extractProtAAC	0.003	0.000	0.003
extractProtAPAAC	1.255	0.008	1.329
extractProtCTDC	0.004	0.000	0.003
extractProtCTDD	0.006	0.000	0.006
extractProtCTDT	0.007	0.000	0.007
extractProtCTriad	0.114	0.000	0.115
extractProtDC	0.006	0.000	0.005
extractProtGeary	0.169	0.000	0.171
extractProtMoran	0.166	0.000	0.167
extractProtMoreauBroto	0.178	0.004	0.184
extractProtPAAC	0.624	0.000	0.635
extractProtPSSM	0.001	0.000	0.001
extractProtPSSMAcc	0.001	0.000	0.001
extractProtPSSMFeature	0.001	0.000	0.001
extractProtQSO	1.154	0.004	1.197
extractProtSOCN	1.356	0.011	1.395
extractProtTC	0.047	0.031	0.078
getCPI	0.004	0.000	0.004
getDrug	0	0	0
getFASTAFromKEGG	0	0	0
getFASTAFromUniProt	0	0	0
getMolFromCAS	0	0	0
getMolFromChEMBL	0	0	0
getMolFromDrugBank	0.001	0.000	0.000
getMolFromKEGG	0.001	0.000	0.000
getMolFromPubChem	0.000	0.000	0.001
getPDBFromRCSBPDB	0.000	0.000	0.001
getPPI	0.004	0.000	0.004
getProt	0	0	0
getSeqFromKEGG	0	0	0
getSeqFromRCSBPDB	0	0	0
getSeqFromUniProt	0	0	0
getSmiFromChEMBL	0	0	0
getSmiFromDrugBank	0	0	0
getSmiFromKEGG	0	0	0
getSmiFromPubChem	0.001	0.000	0.000
readFASTA	0.000	0.002	0.002
readMolFromSDF	0.001	0.001	0.002
readMolFromSmi	0	0	0
readPDB	1.437	0.020	1.476
searchDrug	0.001	0.000	0.001
segProt	0.003	0.000	0.002

CHECK report for Rcpi on malbec2

Summary

Command output

Installation output

Tests output

Example timings