Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2022-04-13 12:07:11 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for Rcpi on tokay2


To the developers/maintainers of the Rcpi package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rcpi.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1547/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.30.0  (landing page)
Nan Xiao
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: RELEASE_3_14
git_last_commit: d21a4c1
git_last_commit_date: 2021-10-26 12:12:30 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Rcpi
Version: 1.30.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:Rcpi.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Rcpi_1.30.0.tar.gz
StartedAt: 2022-04-13 01:18:46 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 01:22:34 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 228.5 seconds
RetCode: 0
Status:   OK  
CheckDir: Rcpi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:Rcpi.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings Rcpi_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/Rcpi.Rcheck'
* using R version 4.1.3 (2022-03-10)
* 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 '1.30.0'
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
calcDrugFPSim 3.05   0.41    15.8
* 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-3.14-bioc/meat/Rcpi.Rcheck/00check.log'
for details.



Installation output

Rcpi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch Rcpi
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.14-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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 -- Wed Apr 13 01:22:21 2022 
*********************************************** 
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 
   7.45    0.65    7.62 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR000
AA3DMoRSE000
AAACF000
AABLOSUM100000
AABLOSUM450.020.000.02
AABLOSUM50000
AABLOSUM62000
AABLOSUM800.000.020.01
AABurden000
AACPSA000
AAConn0.010.000.02
AAConst000
AADescAll000
AAEdgeAdj0.000.010.01
AAEigIdx000
AAFGC000
AAGETAWAY0.000.020.02
AAGeom000
AAInfo000
AAMOE2D0.000.010.01
AAMOE3D000
AAMetaInfo000
AAMolProp0.000.020.02
AAPAM120000
AAPAM250000
AAPAM300.000.010.01
AAPAM40000
AAPAM70000
AARDF000
AARandic0.000.020.02
AATopo000
AATopoChg000
AAWHIM0.000.010.02
AAWalk000
AAindex000
OptAA3d000
acc0.020.000.01
calcDrugFPSim 3.05 0.4115.80
calcDrugMCSSim0.000.000.03
calcParProtGOSim000
calcParProtSeqSim0.010.000.02
calcTwoProtGOSim000
calcTwoProtSeqSim000
checkProt0.000.020.01
convMolFormat000
extractDrugAIO000
extractDrugALOGP000
extractDrugAminoAcidCount000
extractDrugApol000
extractDrugAromaticAtomsCount000
extractDrugAromaticBondsCount000
extractDrugAtomCount000
extractDrugAutocorrelationCharge000
extractDrugAutocorrelationMass000
extractDrugAutocorrelationPolarizability000
extractDrugBCUT000
extractDrugBPol000
extractDrugBondCount000
extractDrugCPSA000
extractDrugCarbonTypes000
extractDrugChiChain0.020.000.02
extractDrugChiCluster000
extractDrugChiPath000
extractDrugChiPathCluster000
extractDrugDescOB000
extractDrugECI0.020.000.01
extractDrugEstate000
extractDrugEstateComplete000
extractDrugExtended000
extractDrugExtendedComplete000
extractDrugFMF000
extractDrugFragmentComplexity000
extractDrugGraph0.010.000.02
extractDrugGraphComplete000
extractDrugGravitationalIndex000
extractDrugHBondAcceptorCount000
extractDrugHBondDonorCount000
extractDrugHybridization000
extractDrugHybridizationComplete000
extractDrugHybridizationRatio000
extractDrugIPMolecularLearning000
extractDrugKR000
extractDrugKRComplete000
extractDrugKappaShapeIndices000
extractDrugKierHallSmarts000
extractDrugLargestChain000
extractDrugLargestPiSystem000
extractDrugLengthOverBreadth000
extractDrugLongestAliphaticChain000
extractDrugMACCS000
extractDrugMACCSComplete000
extractDrugMDE000
extractDrugMannholdLogP0.020.000.02
extractDrugMomentOfInertia000
extractDrugOBFP2000
extractDrugOBFP30.010.000.01
extractDrugOBFP4000
extractDrugOBMACCS000
extractDrugPetitjeanNumber000
extractDrugPetitjeanShapeIndex0.010.000.01
extractDrugPubChem000
extractDrugPubChemComplete000
extractDrugRotatableBondsCount000
extractDrugRuleOfFive000
extractDrugShortestPath000
extractDrugShortestPathComplete000
extractDrugStandard000
extractDrugStandardComplete000
extractDrugTPSA000
extractDrugVABC000
extractDrugVAdjMa000
extractDrugWHIM000
extractDrugWeight000
extractDrugWeightedPath000
extractDrugWienerNumbers000
extractDrugXLogP000
extractDrugZagrebIndex000
extractPCMBLOSUM0.020.000.02
extractPCMDescScales0.000.020.02
extractPCMFAScales0.010.010.03
extractPCMMDSScales0.030.000.03
extractPCMPropScales0.020.000.01
extractPCMScales0.030.020.05
extractProtAAC000
extractProtAPAAC1.160.001.23
extractProtCTDC000
extractProtCTDD000
extractProtCTDT0.010.000.02
extractProtCTriad0.110.030.14
extractProtDC0.020.000.02
extractProtGeary0.220.000.22
extractProtMoran0.170.000.17
extractProtMoreauBroto0.150.000.15
extractProtPAAC0.410.000.41
extractProtPSSM000
extractProtPSSMAcc000
extractProtPSSMFeature000
extractProtQSO0.860.000.86
extractProtSOCN0.780.000.78
extractProtTC0.030.030.06
getCPI000
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI000
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA000
readMolFromSDF000
readMolFromSmi0.000.020.02
readPDB1.250.001.47
searchDrug000
segProt000