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CHECK report for Rcpi on machv2

This page was generated on 2020-10-17 11:59:21 -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: /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_1.24.0.tar.gz
StartedAt: 2020-10-17 04:23:46 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:27:10 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 204.8 seconds
RetCode: 0
Status:  OK 
CheckDir: Rcpi.Rcheck
Warnings: 0

Command output

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### Running 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_1.24.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/Rcpi.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.24.0’
* 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:
###
###   /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)

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-apple-darwin17.0 (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 -- Sat Oct 17 04:26:55 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 
 10.048   0.607   9.122 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0210.0040.025
AA3DMoRSE0.0020.0020.003
AAACF0.0010.0010.002
AABLOSUM1000.0010.0010.003
AABLOSUM450.0010.0010.002
AABLOSUM500.0010.0020.003
AABLOSUM620.0010.0010.002
AABLOSUM800.0010.0000.002
AABurden0.0010.0010.003
AACPSA0.0010.0010.003
AAConn0.0010.0010.002
AAConst0.0020.0010.003
AADescAll0.0010.0010.003
AAEdgeAdj0.0010.0010.003
AAEigIdx0.0020.0020.003
AAFGC0.0010.0020.002
AAGETAWAY0.0010.0010.002
AAGeom0.0010.0010.003
AAInfo0.0020.0010.003
AAMOE2D0.0010.0010.002
AAMOE3D0.0010.0010.003
AAMetaInfo0.0010.0020.003
AAMolProp0.0010.0010.002
AAPAM1200.0010.0010.003
AAPAM2500.0020.0010.003
AAPAM300.0010.0010.003
AAPAM400.0020.0010.003
AAPAM700.0010.0010.003
AARDF0.0020.0010.003
AARandic0.0020.0020.003
AATopo0.0010.0020.003
AATopoChg0.0010.0020.003
AAWHIM0.0010.0010.002
AAWalk0.0020.0010.003
AAindex0.0010.0010.002
OptAA3d0.0000.0000.001
acc0.0180.0130.031
calcDrugFPSim3.3370.2130.959
calcDrugMCSSim0.0130.0040.011
calcParProtGOSim0.0000.0000.001
calcParProtSeqSim0.0080.0030.011
calcTwoProtGOSim0.0000.0010.000
calcTwoProtSeqSim0.0020.0010.003
checkProt0.0020.0010.002
convMolFormat0.0010.0000.002
extractDrugAIO0.0010.0000.002
extractDrugALOGP0.0010.0000.002
extractDrugAminoAcidCount0.0010.0000.001
extractDrugApol0.0010.0000.001
extractDrugAromaticAtomsCount0.0010.0000.001
extractDrugAromaticBondsCount0.0010.0000.001
extractDrugAtomCount0.0000.0000.001
extractDrugAutocorrelationCharge0.0010.0010.002
extractDrugAutocorrelationMass0.0010.0010.002
extractDrugAutocorrelationPolarizability0.0010.0010.001
extractDrugBCUT0.0010.0010.001
extractDrugBPol0.0010.0010.001
extractDrugBondCount0.0010.0010.001
extractDrugCPSA0.0010.0000.002
extractDrugCarbonTypes0.0010.0000.002
extractDrugChiChain0.0010.0000.002
extractDrugChiCluster0.0010.0000.002
extractDrugChiPath0.0010.0000.001
extractDrugChiPathCluster0.0000.0000.001
extractDrugDescOB0.0190.0050.025
extractDrugECI0.0010.0000.001
extractDrugEstate0.0010.0010.001
extractDrugEstateComplete0.0010.0010.001
extractDrugExtended0.0010.0010.001
extractDrugExtendedComplete000
extractDrugFMF0.0010.0000.001
extractDrugFragmentComplexity0.0010.0000.001
extractDrugGraph0.0000.0000.002
extractDrugGraphComplete0.0010.0000.001
extractDrugGravitationalIndex0.0010.0010.001
extractDrugHBondAcceptorCount0.0010.0010.001
extractDrugHBondDonorCount0.0010.0010.001
extractDrugHybridization0.0010.0010.002
extractDrugHybridizationComplete0.0010.0010.002
extractDrugHybridizationRatio0.0010.0010.001
extractDrugIPMolecularLearning0.0010.0010.001
extractDrugKR0.0010.0000.001
extractDrugKRComplete0.0010.0000.002
extractDrugKappaShapeIndices0.0010.0010.001
extractDrugKierHallSmarts0.0010.0010.001
extractDrugLargestChain0.0000.0000.001
extractDrugLargestPiSystem0.0010.0000.001
extractDrugLengthOverBreadth0.0010.0000.000
extractDrugLongestAliphaticChain000
extractDrugMACCS0.0010.0010.001
extractDrugMACCSComplete0.0000.0010.001
extractDrugMDE0.0010.0000.001
extractDrugMannholdLogP0.0010.0000.001
extractDrugMomentOfInertia0.0010.0000.001
extractDrugOBFP20.0080.0030.012
extractDrugOBFP30.0130.0050.018
extractDrugOBFP40.0070.0030.009
extractDrugOBMACCS0.1010.0040.105
extractDrugPetitjeanNumber0.0010.0010.001
extractDrugPetitjeanShapeIndex0.0010.0010.001
extractDrugPubChem0.0010.0010.001
extractDrugPubChemComplete0.0010.0010.001
extractDrugRotatableBondsCount0.0010.0000.002
extractDrugRuleOfFive0.0010.0000.002
extractDrugShortestPath0.0010.0000.002
extractDrugShortestPathComplete0.0010.0000.001
extractDrugStandard0.0010.0000.001
extractDrugStandardComplete0.0020.0000.001
extractDrugTPSA0.0010.0000.001
extractDrugVABC0.0010.0010.001
extractDrugVAdjMa0.0010.0010.001
extractDrugWHIM0.0000.0000.001
extractDrugWeight0.0000.0010.001
extractDrugWeightedPath0.0010.0010.002
extractDrugWienerNumbers0.0010.0000.001
extractDrugXLogP0.0010.0000.001
extractDrugZagrebIndex0.0010.0000.002
extractPCMBLOSUM0.0140.0030.016
extractPCMDescScales0.0150.0020.016
extractPCMFAScales0.0320.0070.038
extractPCMMDSScales0.0130.0020.015
extractPCMPropScales0.0180.0030.020
extractPCMScales0.0290.0040.032
extractProtAAC0.0030.0020.005
extractProtAPAAC1.4700.0361.508
extractProtCTDC0.0040.0010.005
extractProtCTDD0.0050.0030.007
extractProtCTDT0.0080.0010.009
extractProtCTriad0.1640.0170.181
extractProtDC0.0070.0100.016
extractProtGeary0.2540.0170.270
extractProtMoran0.2330.0110.244
extractProtMoreauBroto0.2310.0140.246
extractProtPAAC0.8160.0080.824
extractProtPSSM0.0010.0000.002
extractProtPSSMAcc0.0010.0000.002
extractProtPSSMFeature0.0010.0000.002
extractProtQSO1.6730.0131.687
extractProtSOCN1.6480.0121.660
extractProtTC0.0730.1310.204
getCPI0.0030.0020.005
getDrug000
getFASTAFromKEGG0.0000.0010.000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank0.0010.0000.000
getMolFromKEGG0.0000.0010.000
getMolFromPubChem0.0000.0000.001
getPDBFromRCSBPDB0.0000.0000.001
getPPI0.0050.0030.009
getProt0.0000.0000.001
getSeqFromKEGG0.0010.0000.000
getSeqFromRCSBPDB000
getSeqFromUniProt0.0000.0010.000
getSmiFromChEMBL0.0000.0000.001
getSmiFromDrugBank0.0000.0000.001
getSmiFromKEGG0.0010.0000.000
getSmiFromPubChem0.0010.0000.000
readFASTA0.0010.0010.002
readMolFromSDF0.0020.0010.003
readMolFromSmi0.0010.0000.001
readPDB1.4030.0031.406
searchDrug0.0010.0000.002
segProt0.0030.0010.003