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This page was generated on 2024-10-18 20:42 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
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

Package 1701/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.40.3  (landing page)
Nan Xiao
Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: RELEASE_3_19
git_last_commit: e93f6a2
git_last_commit_date: 2024-09-09 23:48:11 -0400 (Mon, 09 Sep 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for Rcpi on kjohnson1

To the developers/maintainers of the Rcpi package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: Rcpi
Version: 1.40.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rcpi_1.40.3.tar.gz
StartedAt: 2024-10-18 08:51:04 -0400 (Fri, 18 Oct 2024)
EndedAt: 2024-10-18 08:53:32 -0400 (Fri, 18 Oct 2024)
EllapsedTime: 148.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Rcpi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Rcpi_1.40.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Rcpi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.40.3’
* 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 code 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rcpi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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
*** copying figures
** 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/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> library(testthat)
> library(Rcpi)

> 
> test_check("Rcpi")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 22 ]
> 
> proc.time()
   user  system elapsed 
  7.581   0.623   7.344 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0020.0020.003
AA3DMoRSE0.0010.0010.003
AAACF0.0010.0010.002
AABLOSUM1000.0000.0010.002
AABLOSUM450.0000.0020.002
AABLOSUM500.0010.0010.002
AABLOSUM620.0010.0020.001
AABLOSUM800.0010.0010.002
AABurden0.0010.0010.002
AACPSA0.0010.0010.002
AAConn0.0010.0010.002
AAConst0.0020.0020.003
AADescAll0.0010.0010.002
AAEdgeAdj0.0000.0010.002
AAEigIdx0.0010.0010.002
AAFGC0.0010.0010.002
AAGETAWAY0.0010.0010.002
AAGeom0.0010.0020.002
AAInfo0.0010.0010.002
AAMOE2D0.0010.0010.002
AAMOE3D0.0010.0010.002
AAMetaInfo0.0010.0010.001
AAMolProp0.0010.0010.002
AAPAM1200.0010.0010.002
AAPAM2500.0010.0010.002
AAPAM300.0010.0010.002
AAPAM400.0010.0020.004
AAPAM700.0010.0020.002
AARDF0.0010.0010.002
AARandic0.0000.0010.002
AATopo0.0010.0010.002
AATopoChg0.0010.0010.002
AAWHIM0.0010.0010.003
AAWalk0.0000.0010.002
AAindex0.0000.0010.002
OptAA3d0.0000.0010.000
acc0.0090.0050.014
calcDrugFPSim000
calcDrugMCSSim0.0030.0030.006
calcParProtGOSim0.0010.0000.001
calcParProtSeqSim0.0060.0030.009
calcTwoProtGOSim0.0010.0000.000
calcTwoProtSeqSim0.0020.0010.002
checkProt0.0010.0010.001
convMolFormat0.0000.0000.001
extractDrugAIO0.0000.0000.001
extractDrugALOGP0.0000.0010.002
extractDrugAminoAcidCount0.0000.0000.001
extractDrugApol0.0000.0000.001
extractDrugAromaticAtomsCount0.0000.0000.001
extractDrugAromaticBondsCount0.0000.0000.001
extractDrugAtomCount0.0000.0000.001
extractDrugAutocorrelationCharge0.0000.0000.001
extractDrugAutocorrelationMass0.0000.0010.000
extractDrugAutocorrelationPolarizability0.0000.0000.001
extractDrugBCUT0.0010.0010.001
extractDrugBPol0.0010.0000.001
extractDrugBondCount0.0010.0010.001
extractDrugCPSA0.0010.0000.001
extractDrugCarbonTypes0.0010.0010.001
extractDrugChiChain0.0010.0000.000
extractDrugChiCluster0.0000.0010.001
extractDrugChiPath0.0000.0000.001
extractDrugChiPathCluster0.0000.0010.001
extractDrugDescOB0.0110.0040.016
extractDrugECI0.0010.0010.002
extractDrugEstate0.0010.0000.001
extractDrugEstateComplete0.0010.0010.001
extractDrugExtended0.0010.0000.000
extractDrugExtendedComplete0.0010.0000.001
extractDrugFMF0.0010.0000.000
extractDrugFragmentComplexity0.0010.0000.001
extractDrugGraph0.0010.0000.001
extractDrugGraphComplete0.0010.0000.001
extractDrugGravitationalIndex0.0010.0010.001
extractDrugHBondAcceptorCount0.0010.0000.001
extractDrugHBondDonorCount0.0010.0010.001
extractDrugHybridization0.0010.0000.001
extractDrugHybridizationComplete0.0010.0000.001
extractDrugHybridizationRatio0.0010.0000.001
extractDrugIPMolecularLearning0.0010.0000.001
extractDrugKR0.0000.0010.001
extractDrugKRComplete0.0000.0000.001
extractDrugKappaShapeIndices0.0000.0010.001
extractDrugKierHallSmarts0.0000.0000.001
extractDrugLargestChain0.0000.0000.001
extractDrugLargestPiSystem0.0000.0000.001
extractDrugLengthOverBreadth0.0000.0000.001
extractDrugLongestAliphaticChain0.0000.0000.001
extractDrugMACCS0.0010.0000.000
extractDrugMACCSComplete0.0010.0000.001
extractDrugMDE0.0010.0000.001
extractDrugMannholdLogP0.0010.0000.001
extractDrugMomentOfInertia0.0010.0000.001
extractDrugOBFP20.0050.0030.008
extractDrugOBFP30.0060.0030.009
extractDrugOBFP40.0050.0040.009
extractDrugOBMACCS0.0040.0030.008
extractDrugPetitjeanNumber0.0010.0010.002
extractDrugPetitjeanShapeIndex0.0000.0000.001
extractDrugPubChem0.0010.0000.002
extractDrugPubChemComplete0.0010.0010.001
extractDrugRotatableBondsCount0.0010.0000.001
extractDrugRuleOfFive0.0010.0000.001
extractDrugShortestPath0.0010.0000.000
extractDrugShortestPathComplete0.0010.0000.001
extractDrugStandard0.0010.0010.000
extractDrugStandardComplete0.0010.0000.001
extractDrugTPSA0.0010.0010.000
extractDrugVABC0.0010.0000.001
extractDrugVAdjMa0.0010.0010.001
extractDrugWHIM0.0010.0000.001
extractDrugWeight0.0010.0000.001
extractDrugWeightedPath0.0010.0010.001
extractDrugWienerNumbers0.0010.0000.001
extractDrugXLogP0.0010.0010.001
extractDrugZagrebIndex0.0010.0000.001
extractPCMBLOSUM0.1220.0060.127
extractPCMDescScales0.0130.0020.014
extractPCMFAScales0.0180.0050.022
extractPCMMDSScales0.0110.0030.013
extractPCMPropScales0.0130.0020.015
extractPCMScales0.0280.0080.035
extractProtAAC0.0030.0000.003
extractProtAPAAC0.7420.0230.770
extractProtCTDC0.0030.0000.003
extractProtCTDD0.0020.0000.002
extractProtCTDT0.0050.0010.005
extractProtCTriad0.0910.0120.104
extractProtDC0.0040.0040.011
extractProtGeary0.1200.0090.131
extractProtMoran0.1100.0080.120
extractProtMoreauBroto0.1170.0100.127
extractProtPAAC0.3690.0100.380
extractProtPSSM0.0020.0010.001
extractProtPSSMAcc0.0010.0010.001
extractProtPSSMFeature0.0010.0000.001
extractProtQSO0.6530.0170.671
extractProtSOCN1.0490.0271.079
extractProtTC0.0310.0750.110
getCPI0.0020.0010.003
getDrug000
getFASTAFromKEGG0.0000.0010.000
getFASTAFromUniProt0.0010.0000.000
getMolFromCAS000
getMolFromChEMBL0.0000.0010.000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem0.0000.0010.000
getPDBFromRCSBPDB000
getPPI0.0020.0020.004
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt0.0010.0000.000
getSmiFromChEMBL000
getSmiFromDrugBank0.0000.0000.001
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA0.0020.0010.001
readMolFromSDF0.0020.0010.003
readMolFromSmi0.0010.0000.001
readPDB0.7660.0040.774
searchDrug0.0020.0010.003
segProt0.0010.0010.003