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This page was generated on 2024-11-09 21:31 -0500 (Sat, 09 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4505
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4538
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4486
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1686/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.42.0  (landing page)
Nan Xiao
Snapshot Date: 2024-11-08 13:40 -0500 (Fri, 08 Nov 2024)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: RELEASE_3_20
git_last_commit: c03a28c
git_last_commit_date: 2024-10-29 09:50:50 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for Rcpi on kjohnson3

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: 1.42.0
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_1.42.0.tar.gz
StartedAt: 2024-11-09 10:51:34 -0500 (Sat, 09 Nov 2024)
EndedAt: 2024-11-09 10:56:00 -0500 (Sat, 09 Nov 2024)
EllapsedTime: 265.5 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_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-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 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.42.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 
  2.217   0.180   2.033 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0000.0000.001
AA3DMoRSE0.0000.0010.001
AAACF000
AABLOSUM1000.0000.0010.001
AABLOSUM450.0000.0000.001
AABLOSUM500.0010.0010.000
AABLOSUM620.0000.0000.001
AABLOSUM800.0000.0000.001
AABurden000
AACPSA0.0010.0000.001
AAConn0.0000.0010.001
AAConst000
AADescAll0.0000.0000.001
AAEdgeAdj0.0000.0010.001
AAEigIdx000
AAFGC0.0000.0010.001
AAGETAWAY0.0000.0000.001
AAGeom000
AAInfo0.0000.0010.001
AAMOE2D0.0000.0000.001
AAMOE3D0.0010.0010.000
AAMetaInfo0.0000.0000.001
AAMolProp000
AAPAM1200.0000.0010.000
AAPAM2500.0010.0000.001
AAPAM300.0000.0010.000
AAPAM40000
AAPAM700.0000.0000.001
AARDF0.0010.0010.000
AARandic000
AATopo0.0000.0010.001
AATopoChg000
AAWHIM0.0010.0000.000
AAWalk0.0000.0010.001
AAindex000
OptAA3d000
acc0.0030.0020.004
calcDrugFPSim000
calcDrugMCSSim0.0010.0010.002
calcParProtGOSim0.0000.0000.001
calcParProtSeqSim0.0020.0010.002
calcTwoProtGOSim000
calcTwoProtSeqSim000
checkProt0.0010.0000.001
convMolFormat000
extractDrugAIO0.0000.0010.001
extractDrugALOGP0.0010.0000.000
extractDrugAminoAcidCount000
extractDrugApol000
extractDrugAromaticAtomsCount000
extractDrugAromaticBondsCount0.0010.0000.001
extractDrugAtomCount000
extractDrugAutocorrelationCharge0.0000.0000.001
extractDrugAutocorrelationMass000
extractDrugAutocorrelationPolarizability0.0010.0000.000
extractDrugBCUT000
extractDrugBPol000
extractDrugBondCount0.0000.0000.001
extractDrugCPSA0.0010.0000.000
extractDrugCarbonTypes0.0000.0000.001
extractDrugChiChain000
extractDrugChiCluster000
extractDrugChiPath0.0010.0000.001
extractDrugChiPathCluster000
extractDrugDescOB0.0040.0020.005
extractDrugECI0.0000.0000.001
extractDrugEstate000
extractDrugEstateComplete0.0000.0000.001
extractDrugExtended000
extractDrugExtendedComplete000
extractDrugFMF000
extractDrugFragmentComplexity000
extractDrugGraph0.0000.0000.001
extractDrugGraphComplete000
extractDrugGravitationalIndex000
extractDrugHBondAcceptorCount000
extractDrugHBondDonorCount0.0000.0010.000
extractDrugHybridization0.0000.0000.001
extractDrugHybridizationComplete000
extractDrugHybridizationRatio0.0010.0000.000
extractDrugIPMolecularLearning000
extractDrugKR000
extractDrugKRComplete0.0000.0000.001
extractDrugKappaShapeIndices0.0010.0000.000
extractDrugKierHallSmarts000
extractDrugLargestChain000
extractDrugLargestPiSystem000
extractDrugLengthOverBreadth0.0010.0000.001
extractDrugLongestAliphaticChain000
extractDrugMACCS0.0000.0010.000
extractDrugMACCSComplete000
extractDrugMDE0.0010.0000.000
extractDrugMannholdLogP0.0000.0000.001
extractDrugMomentOfInertia000
extractDrugOBFP20.0020.0010.003
extractDrugOBFP30.0030.0020.004
extractDrugOBFP40.0010.0010.003
extractDrugOBMACCS0.0020.0010.003
extractDrugPetitjeanNumber000
extractDrugPetitjeanShapeIndex0.0000.0000.001
extractDrugPubChem000
extractDrugPubChemComplete0.0010.0000.000
extractDrugRotatableBondsCount000
extractDrugRuleOfFive000
extractDrugShortestPath0.0000.0000.001
extractDrugShortestPathComplete0.0010.0010.000
extractDrugStandard0.0000.0000.001
extractDrugStandardComplete000
extractDrugTPSA000
extractDrugVABC0.0010.0000.000
extractDrugVAdjMa000
extractDrugWHIM0.0000.0010.001
extractDrugWeight000
extractDrugWeightedPath0.0010.0000.000
extractDrugWienerNumbers000
extractDrugXLogP000
extractDrugZagrebIndex0.0000.0000.001
extractPCMBLOSUM0.0320.0010.032
extractPCMDescScales0.0040.0010.004
extractPCMFAScales0.0050.0010.005
extractPCMMDSScales0.0030.0010.003
extractPCMPropScales0.0030.0000.004
extractPCMScales0.0080.0010.009
extractProtAAC0.0000.0000.001
extractProtAPAAC0.2450.0060.250
extractProtCTDC0.0010.0000.001
extractProtCTDD0.0010.0000.001
extractProtCTDT0.0010.0000.001
extractProtCTriad0.0280.0040.030
extractProtDC0.0010.0010.002
extractProtGeary0.0370.0030.040
extractProtMoran0.0330.0020.035
extractProtMoreauBroto0.0360.0030.038
extractProtPAAC0.1090.0030.111
extractProtPSSM000
extractProtPSSMAcc0.0010.0000.001
extractProtPSSMFeature000
extractProtQSO0.1890.0050.194
extractProtSOCN0.1880.0040.191
extractProtTC0.0080.0240.031
getCPI0.0000.0000.001
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI0.0000.0010.001
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL0.0000.0010.000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA0.0010.0000.001
readMolFromSDF0.0000.0000.001
readMolFromSmi0.0010.0010.000
readPDB0.2260.0010.228
searchDrug0.0000.0010.000
segProt0.0010.0000.001