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CHECK report for Rcpi on malbec2

This page was generated on 2020-10-17 11:55:32 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Rcpi PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1436/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.24.0
Nan Xiao
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/Rcpi
Branch: RELEASE_3_11
Last Commit: 7bd873b
Last Changed Date: 2020-04-27 14:39:13 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rcpi
Version: 1.24.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings Rcpi_1.24.0.tar.gz
StartedAt: 2020-10-17 04:33:31 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:36:11 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 160.6 seconds
RetCode: 0
Status:  OK 
CheckDir: Rcpi.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings Rcpi_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/Rcpi.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.24.0’
* 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


Installation output

Rcpi.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL Rcpi
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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)

Tests output

Rcpi.Rcheck/tests/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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 -- Sat Oct 17 04:36:03 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 
  8.482   0.359   7.794 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0110.0040.015
AA3DMoRSE0.0010.0000.001
AAACF0.0010.0000.001
AABLOSUM1000.0010.0000.001
AABLOSUM450.0010.0000.001
AABLOSUM500.0010.0000.001
AABLOSUM620.0010.0000.000
AABLOSUM800.0000.0010.001
AABurden0.0000.0010.000
AACPSA0.0000.0010.001
AAConn0.0010.0000.000
AAConst0.0010.0000.001
AADescAll0.0010.0000.001
AAEdgeAdj0.0010.0000.001
AAEigIdx0.0010.0000.001
AAFGC0.0010.0000.001
AAGETAWAY0.0000.0000.001
AAGeom0.0010.0000.001
AAInfo0.0010.0000.001
AAMOE2D0.0010.0000.001
AAMOE3D0.0000.0000.001
AAMetaInfo0.0010.0000.001
AAMolProp0.0010.0000.001
AAPAM1200.0010.0000.001
AAPAM2500.0010.0000.001
AAPAM300.0010.0000.001
AAPAM400.0010.0000.001
AAPAM700.0000.0000.001
AARDF0.0010.0000.001
AARandic0.0010.0000.001
AATopo0.0010.0000.001
AATopoChg0.0010.0000.001
AAWHIM0.0010.0000.000
AAWalk0.0010.0000.001
AAindex0.0000.0000.001
OptAA3d000
acc0.0050.0040.010
calcDrugFPSim2.3800.0941.162
calcDrugMCSSim0.0180.0040.081
calcParProtGOSim000
calcParProtSeqSim0.0090.0000.257
calcTwoProtGOSim000
calcTwoProtSeqSim0.0010.0000.001
checkProt0.0010.0000.001
convMolFormat0.0000.0000.001
extractDrugAIO000
extractDrugALOGP000
extractDrugAminoAcidCount000
extractDrugApol000
extractDrugAromaticAtomsCount000
extractDrugAromaticBondsCount0.0000.0000.001
extractDrugAtomCount0.0000.0000.001
extractDrugAutocorrelationCharge0.0010.0000.000
extractDrugAutocorrelationMass0.0010.0000.001
extractDrugAutocorrelationPolarizability0.0010.0000.001
extractDrugBCUT0.0000.0000.001
extractDrugBPol0.0000.0000.001
extractDrugBondCount0.0000.0000.001
extractDrugCPSA000
extractDrugCarbonTypes0.0010.0000.000
extractDrugChiChain0.0010.0000.000
extractDrugChiCluster0.0010.0000.000
extractDrugChiPath0.0010.0000.001
extractDrugChiPathCluster0.0010.0000.001
extractDrugDescOB0.1200.0360.156
extractDrugECI0.0010.0000.001
extractDrugEstate000
extractDrugEstateComplete000
extractDrugExtended000
extractDrugExtendedComplete000
extractDrugFMF000
extractDrugFragmentComplexity000
extractDrugGraph000
extractDrugGraphComplete000
extractDrugGravitationalIndex000
extractDrugHBondAcceptorCount000
extractDrugHBondDonorCount000
extractDrugHybridization000
extractDrugHybridizationComplete000
extractDrugHybridizationRatio000
extractDrugIPMolecularLearning000
extractDrugKR000
extractDrugKRComplete000
extractDrugKappaShapeIndices000
extractDrugKierHallSmarts000
extractDrugLargestChain0.0000.0000.001
extractDrugLargestPiSystem0.0000.0000.001
extractDrugLengthOverBreadth0.0000.0000.001
extractDrugLongestAliphaticChain0.0000.0000.001
extractDrugMACCS0.0000.0000.001
extractDrugMACCSComplete0.0000.0000.001
extractDrugMDE0.0000.0000.001
extractDrugMannholdLogP0.0000.0000.001
extractDrugMomentOfInertia0.0000.0000.001
extractDrugOBFP20.0050.0040.009
extractDrugOBFP30.3390.0200.358
extractDrugOBFP40.0100.0000.009
extractDrugOBMACCS0.0110.0040.015
extractDrugPetitjeanNumber0.0000.0000.001
extractDrugPetitjeanShapeIndex000
extractDrugPubChem000
extractDrugPubChemComplete000
extractDrugRotatableBondsCount000
extractDrugRuleOfFive000
extractDrugShortestPath000
extractDrugShortestPathComplete000
extractDrugStandard000
extractDrugStandardComplete000
extractDrugTPSA000
extractDrugVABC000
extractDrugVAdjMa000
extractDrugWHIM000
extractDrugWeight000
extractDrugWeightedPath000
extractDrugWienerNumbers0.0000.0000.001
extractDrugXLogP0.0000.0000.001
extractDrugZagrebIndex0.0000.0000.001
extractPCMBLOSUM0.0070.0000.008
extractPCMDescScales0.0090.0000.009
extractPCMFAScales0.0140.0000.013
extractPCMMDSScales0.0070.0000.007
extractPCMPropScales0.0050.0040.009
extractPCMScales0.0100.0040.014
extractProtAAC0.0020.0000.002
extractProtAPAAC0.7410.0450.785
extractProtCTDC0.0020.0000.002
extractProtCTDD0.0040.0000.004
extractProtCTDT0.0040.0000.004
extractProtCTriad0.0730.0080.081
extractProtDC0.0010.0030.004
extractProtGeary0.4480.0040.452
extractProtMoran0.1890.0000.188
extractProtMoreauBroto0.1180.0000.119
extractProtPAAC0.4260.0030.430
extractProtPSSM0.0010.0000.001
extractProtPSSMAcc000
extractProtPSSMFeature0.0010.0000.001
extractProtQSO0.6570.0040.660
extractProtSOCN0.6830.0000.682
extractProtTC0.0380.0360.073
getCPI0.0040.0000.004
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI0.0040.0000.004
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA0.0010.0000.001
readMolFromSDF0.0020.0000.002
readMolFromSmi0.0010.0000.001
readPDB1.1320.0041.151
searchDrug0.0010.0000.001
segProt0.0020.0000.002