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CHECK report for Rcpi on tokay1

This page was generated on 2021-05-06 12:33:08 -0400 (Thu, 06 May 2021).

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 1472/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.26.0  (landing page)
Nan Xiao
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/Rcpi
Branch: RELEASE_3_12
Last Commit: 01c47f5
Last Changed Date: 2020-10-27 10:55:30 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: Rcpi
Version: 1.26.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:Rcpi.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Rcpi_1.26.0.tar.gz
StartedAt: 2021-05-06 06:01:44 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 06:04:46 -0400 (Thu, 06 May 2021)
EllapsedTime: 182.9 seconds
RetCode: 0
Status:   OK   
CheckDir: Rcpi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:Rcpi.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Rcpi_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/Rcpi.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Rcpi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Rcpi' version '1.26.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/Rcpi.Rcheck/00check.log'
for details.



Installation output

Rcpi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch Rcpi
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.12-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
  converting help for package 'Rcpi'
    finding HTML links ... done
    AA2DACOR                                html  
    AA3DMoRSE                               html  
    AAACF                                   html  
    AABLOSUM100                             html  
    AABLOSUM45                              html  
    AABLOSUM50                              html  
    AABLOSUM62                              html  
    AABLOSUM80                              html  
    AABurden                                html  
    AACPSA                                  html  
    AAConn                                  html  
    AAConst                                 html  
    AADescAll                               html  
    AAEdgeAdj                               html  
    AAEigIdx                                html  
    AAFGC                                   html  
    AAGETAWAY                               html  
    AAGeom                                  html  
    AAInfo                                  html  
    AAMOE2D                                 html  
    AAMOE3D                                 html  
    AAMetaInfo                              html  
    AAMolProp                               html  
    AAPAM120                                html  
    AAPAM250                                html  
    AAPAM30                                 html  
    AAPAM40                                 html  
    AAPAM70                                 html  
    AARDF                                   html  
    AARandic                                html  
    AATopo                                  html  
    AATopoChg                               html  
    AAWHIM                                  html  
    AAWalk                                  html  
    AAindex                                 html  
    OptAA3d                                 html  
    Rcpi-package                            html  
    acc                                     html  
    calcDrugFPSim                           html  
    calcDrugMCSSim                          html  
    calcParProtGOSim                        html  
    calcParProtSeqSim                       html  
    calcTwoProtGOSim                        html  
    calcTwoProtSeqSim                       html  
    checkProt                               html  
    convMolFormat                           html  
    extractDrugAIO                          html  
    extractDrugALOGP                        html  
    extractDrugAminoAcidCount               html  
    extractDrugApol                         html  
    extractDrugAromaticAtomsCount           html  
    extractDrugAromaticBondsCount           html  
    extractDrugAtomCount                    html  
    extractDrugAutocorrelationCharge        html  
    extractDrugAutocorrelationMass          html  
    extractDrugAutocorrelationPolarizability
                                            html  
    extractDrugBCUT                         html  
    extractDrugBPol                         html  
    extractDrugBondCount                    html  
    extractDrugCPSA                         html  
    extractDrugCarbonTypes                  html  
    extractDrugChiChain                     html  
    extractDrugChiCluster                   html  
    extractDrugChiPath                      html  
    extractDrugChiPathCluster               html  
    extractDrugDescOB                       html  
    extractDrugECI                          html  
    extractDrugEstate                       html  
    extractDrugEstateComplete               html  
    extractDrugExtended                     html  
    extractDrugExtendedComplete             html  
    extractDrugFMF                          html  
    extractDrugFragmentComplexity           html  
    extractDrugGraph                        html  
    extractDrugGraphComplete                html  
    extractDrugGravitationalIndex           html  
    extractDrugHBondAcceptorCount           html  
    extractDrugHBondDonorCount              html  
    extractDrugHybridization                html  
    extractDrugHybridizationComplete        html  
    extractDrugHybridizationRatio           html  
    extractDrugIPMolecularLearning          html  
    extractDrugKR                           html  
    extractDrugKRComplete                   html  
    extractDrugKappaShapeIndices            html  
    extractDrugKierHallSmarts               html  
    extractDrugLargestChain                 html  
    extractDrugLargestPiSystem              html  
    extractDrugLengthOverBreadth            html  
    extractDrugLongestAliphaticChain        html  
    extractDrugMACCS                        html  
    extractDrugMACCSComplete                html  
    extractDrugMDE                          html  
    extractDrugMannholdLogP                 html  
    extractDrugMomentOfInertia              html  
    extractDrugOBFP2                        html  
    extractDrugOBFP3                        html  
    extractDrugOBFP4                        html  
    extractDrugOBMACCS                      html  
    extractDrugPetitjeanNumber              html  
    extractDrugPetitjeanShapeIndex          html  
    extractDrugPubChem                      html  
    extractDrugPubChemComplete              html  
    extractDrugRotatableBondsCount          html  
    extractDrugRuleOfFive                   html  
    extractDrugShortestPath                 html  
    extractDrugShortestPathComplete         html  
    extractDrugStandard                     html  
    extractDrugStandardComplete             html  
    extractDrugTPSA                         html  
    extractDrugVABC                         html  
    extractDrugVAdjMa                       html  
    extractDrugWHIM                         html  
    extractDrugWeight                       html  
    extractDrugWeightedPath                 html  
    extractDrugWienerNumbers                html  
    extractDrugXLogP                        html  
    extractDrugZagrebIndex                  html  
    extractPCMBLOSUM                        html  
    extractPCMDescScales                    html  
    extractPCMFAScales                      html  
    extractPCMMDSScales                     html  
    extractPCMPropScales                    html  
    extractPCMScales                        html  
    extractProtAAC                          html  
    extractProtAPAAC                        html  
    extractProtCTDC                         html  
    extractProtCTDD                         html  
    extractProtCTDT                         html  
    extractProtCTriad                       html  
    extractProtDC                           html  
    extractProtGeary                        html  
    extractProtMoran                        html  
    extractProtMoreauBroto                  html  
    extractProtPAAC                         html  
    extractProtPSSM                         html  
    extractProtPSSMAcc                      html  
    extractProtPSSMFeature                  html  
    extractProtQSO                          html  
    extractProtSOCN                         html  
    extractProtTC                           html  
    getCPI                                  html  
    getDrug                                 html  
    getFASTAFromKEGG                        html  
    getFASTAFromUniProt                     html  
    getMolFromCAS                           html  
    getMolFromChEMBL                        html  
    getMolFromDrugBank                      html  
    getMolFromKEGG                          html  
    getMolFromPubChem                       html  
    getPDBFromRCSBPDB                       html  
    getPPI                                  html  
    getProt                                 html  
    getSeqFromKEGG                          html  
    getSeqFromRCSBPDB                       html  
    getSeqFromUniProt                       html  
    getSmiFromChEMBL                        html  
    getSmiFromDrugBank                      html  
    getSmiFromKEGG                          html  
    getSmiFromPubChem                       html  
    readFASTA                               html  
    readMolFromSDF                          html  
    readMolFromSmi                          html  
    readPDB                                 html  
    searchDrug                              html  
    segProt                                 html  
** 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)
Making 'packages.html' ... done

Tests output

Rcpi.Rcheck/tests/runTests.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 -- Thu May 06 06:04:34 2021 
*********************************************** 
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 
   8.01    0.51    8.20 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.020.000.01
AA3DMoRSE000
AAACF000
AABLOSUM100000
AABLOSUM45000
AABLOSUM50000
AABLOSUM62000
AABLOSUM80000
AABurden000
AACPSA000
AAConn0.000.010.02
AAConst000
AADescAll000
AAEdgeAdj000
AAEigIdx0.000.020.01
AAFGC000
AAGETAWAY000
AAGeom000
AAInfo000
AAMOE2D000
AAMOE3D000
AAMetaInfo000
AAMolProp0.010.000.01
AAPAM120000
AAPAM250000
AAPAM30000
AAPAM400.000.020.02
AAPAM70000
AARDF000
AARandic000
AATopo0.000.010.02
AATopoChg000
AAWHIM000
AAWalk000
AAindex0.020.000.01
OptAA3d000
acc000
calcDrugFPSim2.200.201.61
calcDrugMCSSim0.020.000.02
calcParProtGOSim000
calcParProtSeqSim000
calcTwoProtGOSim000
calcTwoProtSeqSim000
checkProt0.010.000.01
convMolFormat000
extractDrugAIO000
extractDrugALOGP000
extractDrugAminoAcidCount000
extractDrugApol000
extractDrugAromaticAtomsCount000
extractDrugAromaticBondsCount000
extractDrugAtomCount000
extractDrugAutocorrelationCharge000
extractDrugAutocorrelationMass000
extractDrugAutocorrelationPolarizability000
extractDrugBCUT0.000.020.02
extractDrugBPol000
extractDrugBondCount000
extractDrugCPSA000
extractDrugCarbonTypes000
extractDrugChiChain000
extractDrugChiCluster000
extractDrugChiPath000
extractDrugChiPathCluster000
extractDrugDescOB000
extractDrugECI000
extractDrugEstate000
extractDrugEstateComplete000
extractDrugExtended000
extractDrugExtendedComplete000
extractDrugFMF000
extractDrugFragmentComplexity000
extractDrugGraph000
extractDrugGraphComplete000
extractDrugGravitationalIndex000
extractDrugHBondAcceptorCount000
extractDrugHBondDonorCount0.010.000.02
extractDrugHybridization000
extractDrugHybridizationComplete000
extractDrugHybridizationRatio000
extractDrugIPMolecularLearning000
extractDrugKR000
extractDrugKRComplete000
extractDrugKappaShapeIndices000
extractDrugKierHallSmarts000
extractDrugLargestChain000
extractDrugLargestPiSystem000
extractDrugLengthOverBreadth000
extractDrugLongestAliphaticChain000
extractDrugMACCS000
extractDrugMACCSComplete000
extractDrugMDE000
extractDrugMannholdLogP000
extractDrugMomentOfInertia000
extractDrugOBFP2000
extractDrugOBFP3000
extractDrugOBFP40.000.020.02
extractDrugOBMACCS0.000.010.02
extractDrugPetitjeanNumber000
extractDrugPetitjeanShapeIndex000
extractDrugPubChem000
extractDrugPubChemComplete000
extractDrugRotatableBondsCount000
extractDrugRuleOfFive000
extractDrugShortestPath000
extractDrugShortestPathComplete000
extractDrugStandard000
extractDrugStandardComplete0.020.000.01
extractDrugTPSA000
extractDrugVABC000
extractDrugVAdjMa000
extractDrugWHIM000
extractDrugWeight000
extractDrugWeightedPath000
extractDrugWienerNumbers000
extractDrugXLogP000
extractDrugZagrebIndex000
extractPCMBLOSUM0.010.000.02
extractPCMDescScales0.020.000.01
extractPCMFAScales0.010.000.02
extractPCMMDSScales0.020.000.01
extractPCMPropScales000
extractPCMScales0.150.000.16
extractProtAAC000
extractProtAPAAC1.490.001.48
extractProtCTDC000
extractProtCTDD0.010.000.02
extractProtCTDT000
extractProtCTriad0.160.000.15
extractProtDC000
extractProtGeary0.220.000.22
extractProtMoran0.190.030.22
extractProtMoreauBroto0.20.00.2
extractProtPAAC0.750.000.75
extractProtPSSM000
extractProtPSSMAcc000
extractProtPSSMFeature0.020.000.01
extractProtQSO1.090.001.10
extractProtSOCN0.860.000.86
extractProtTC0.050.020.06
getCPI000
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI000
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA000
readMolFromSDF000
readMolFromSmi000
readPDB1.190.001.20
searchDrug000
segProt000