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This page was generated on 2025-10-27 12:45 -0400 (Mon, 27 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4637
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 1733/2361HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.45.0  (landing page)
Nan Xiao
Snapshot Date: 2025-10-26 13:45 -0400 (Sun, 26 Oct 2025)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: devel
git_last_commit: dba81ab
git_last_commit_date: 2025-04-15 10:29:42 -0400 (Tue, 15 Apr 2025)
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 1.45.0
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_1.45.0.tar.gz
StartedAt: 2025-10-26 21:20:50 -0400 (Sun, 26 Oct 2025)
EndedAt: 2025-10-26 21:23:06 -0400 (Sun, 26 Oct 2025)
EllapsedTime: 135.7 seconds
RetCode: 0
Status:   OK  
CheckDir: Rcpi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Rcpi.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.45.0’
* 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 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/4.5-arm64/Resources/library’
* installing *source* package ‘Rcpi’ ...
** this is package ‘Rcpi’ version ‘1.45.0’
** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 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 
  2.071   0.184   1.871 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0000.0000.001
AA3DMoRSE000
AAACF000
AABLOSUM1000.0000.0000.001
AABLOSUM450.0010.0010.001
AABLOSUM500.0000.0000.001
AABLOSUM620.0000.0010.000
AABLOSUM80000
AABurden0.0000.0010.001
AACPSA0.0000.0000.001
AAConn000
AAConst000
AADescAll0.0000.0000.001
AAEdgeAdj0.0000.0010.001
AAEigIdx000
AAFGC0.0010.0010.000
AAGETAWAY0.0000.0000.001
AAGeom0.0000.0010.000
AAInfo000
AAMOE2D0.0010.0010.001
AAMOE3D0.0000.0000.001
AAMetaInfo000
AAMolProp0.0000.0010.001
AAPAM1200.0000.0000.001
AAPAM2500.0000.0010.000
AAPAM300.0000.0000.001
AAPAM400.0000.0000.001
AAPAM70000
AARDF0.0000.0000.001
AARandic0.0000.0010.001
AATopo000
AATopoChg0.0000.0000.001
AAWHIM0.0000.0000.001
AAWalk000
AAindex0.0010.0010.001
OptAA3d000
acc0.0020.0010.004
calcDrugFPSim000
calcDrugMCSSim0.0000.0000.002
calcParProtGOSim0.0010.0010.000
calcParProtSeqSim0.0010.0000.003
calcTwoProtGOSim000
calcTwoProtSeqSim0.0010.0010.001
checkProt000
convMolFormat0.0010.0000.001
extractDrugAIO000
extractDrugALOGP0.0000.0000.001
extractDrugAminoAcidCount000
extractDrugApol0.0010.0010.000
extractDrugAromaticAtomsCount000
extractDrugAromaticBondsCount000
extractDrugAtomCount0.0000.0000.001
extractDrugAutocorrelationCharge000
extractDrugAutocorrelationMass0.0000.0000.001
extractDrugAutocorrelationPolarizability0.0000.0010.000
extractDrugBCUT0.0010.0000.000
extractDrugBPol000
extractDrugBondCount000
extractDrugCPSA0.0000.0000.001
extractDrugCarbonTypes0.0010.0000.000
extractDrugChiChain0.0000.0000.001
extractDrugChiCluster0.0000.0010.000
extractDrugChiPath000
extractDrugChiPathCluster000
extractDrugDescOB0.0040.0010.006
extractDrugECI0.0010.0000.000
extractDrugEstate0.0000.0010.001
extractDrugEstateComplete000
extractDrugExtended0.0000.0000.001
extractDrugExtendedComplete0.0010.0000.000
extractDrugFMF000
extractDrugFragmentComplexity000
extractDrugGraph0.0000.0010.000
extractDrugGraphComplete0.0000.0000.001
extractDrugGravitationalIndex000
extractDrugHBondAcceptorCount0.0000.0000.001
extractDrugHBondDonorCount0.0010.0000.000
extractDrugHybridization000
extractDrugHybridizationComplete000
extractDrugHybridizationRatio000
extractDrugIPMolecularLearning0.0010.0000.001
extractDrugKR000
extractDrugKRComplete0.0000.0000.001
extractDrugKappaShapeIndices000
extractDrugKierHallSmarts0.0010.0000.000
extractDrugLargestChain0.0000.0010.000
extractDrugLargestPiSystem000
extractDrugLengthOverBreadth0.0000.0000.001
extractDrugLongestAliphaticChain000
extractDrugMACCS000
extractDrugMACCSComplete000
extractDrugMDE000
extractDrugMannholdLogP0.0000.0000.001
extractDrugMomentOfInertia000
extractDrugOBFP20.0020.0010.003
extractDrugOBFP30.0030.0010.004
extractDrugOBFP40.0020.0010.002
extractDrugOBMACCS0.0310.0020.033
extractDrugPetitjeanNumber0.0010.0000.001
extractDrugPetitjeanShapeIndex000
extractDrugPubChem0.0000.0000.001
extractDrugPubChemComplete000
extractDrugRotatableBondsCount000
extractDrugRuleOfFive000
extractDrugShortestPath000
extractDrugShortestPathComplete0.0010.0000.000
extractDrugStandard000
extractDrugStandardComplete0.0000.0000.001
extractDrugTPSA000
extractDrugVABC0.0010.0010.000
extractDrugVAdjMa000
extractDrugWHIM000
extractDrugWeight000
extractDrugWeightedPath000
extractDrugWienerNumbers0.0000.0000.001
extractDrugXLogP000
extractDrugZagrebIndex000
extractPCMBLOSUM0.0030.0000.003
extractPCMDescScales0.0030.0010.004
extractPCMFAScales0.0050.0010.005
extractPCMMDSScales0.0020.0000.003
extractPCMPropScales0.0080.0010.009
extractPCMScales0.0050.0010.005
extractProtAAC0.0010.0010.001
extractProtAPAAC0.2280.0040.232
extractProtCTDC0.0010.0000.001
extractProtCTDD0.0010.0000.002
extractProtCTDT0.0010.0010.002
extractProtCTriad0.0280.0020.030
extractProtDC0.0010.0020.002
extractProtGeary0.0380.0020.040
extractProtMoran0.1570.0020.159
extractProtMoreauBroto0.0270.0020.030
extractProtPAAC0.0950.0050.100
extractProtPSSM0.0000.0000.001
extractProtPSSMAcc0.0010.0000.000
extractProtPSSMFeature0.0000.0010.001
extractProtQSO0.1940.0030.198
extractProtSOCN0.1880.0020.191
extractProtTC0.0090.0220.031
getCPI0.0010.0000.001
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt0.0000.0010.000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem0.0000.0000.001
getPDBFromRCSBPDB000
getPPI0.0010.0010.001
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG0.0000.0000.001
getSmiFromPubChem000
readFASTA000
readMolFromSDF0.0010.0000.000
readMolFromSmi000
readPDB0.2380.0010.239
searchDrug0.0000.0010.000
segProt0.0010.0000.001