Multiple platform build/check report for BioC 3.21 - CHECK results for Rcpi on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4833
merida1	macOS 12.7.6 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4614
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4555
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4586
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 merida1

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: 1.44.0

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_1.44.0.tar.gz

StartedAt: 2025-10-14 08:53:46 -0400 (Tue, 14 Oct 2025)

EndedAt: 2025-10-14 08:58:19 -0400 (Tue, 14 Oct 2025)

EllapsedTime: 272.7 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_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Rcpi.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.44.0’
* 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-x86_64/Resources/library’
* installing *source* package ‘Rcpi’ ...
** this is package ‘Rcpi’ version ‘1.44.0’
** 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 RC (2025-06-05 r88288) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 
 12.909   0.967  13.380

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

name	user	system	elapsed
AA2DACOR	0.003	0.002	0.006
AA3DMoRSE	0.001	0.002	0.003
AAACF	0.001	0.003	0.004
AABLOSUM100	0.002	0.002	0.003
AABLOSUM45	0.001	0.002	0.003
AABLOSUM50	0.001	0.002	0.003
AABLOSUM62	0.002	0.001	0.003
AABLOSUM80	0.001	0.002	0.004
AABurden	0.001	0.001	0.003
AACPSA	0.001	0.001	0.002
AAConn	0.001	0.002	0.003
AAConst	0.002	0.002	0.003
AADescAll	0.002	0.002	0.003
AAEdgeAdj	0.001	0.001	0.003
AAEigIdx	0.001	0.002	0.003
AAFGC	0.002	0.002	0.004
AAGETAWAY	0.001	0.002	0.003
AAGeom	0.002	0.002	0.004
AAInfo	0.001	0.002	0.003
AAMOE2D	0.001	0.002	0.003
AAMOE3D	0.001	0.001	0.003
AAMetaInfo	0.001	0.001	0.002
AAMolProp	0.002	0.002	0.003
AAPAM120	0.001	0.002	0.004
AAPAM250	0.002	0.002	0.003
AAPAM30	0.002	0.002	0.003
AAPAM40	0.001	0.002	0.003
AAPAM70	0.002	0.002	0.004
AARDF	0.002	0.002	0.003
AARandic	0.001	0.002	0.003
AATopo	0.002	0.001	0.003
AATopoChg	0.001	0.002	0.003
AAWHIM	0.001	0.002	0.004
AAWalk	0.002	0.002	0.002
AAindex	0.001	0.002	0.004
OptAA3d	0.000	0.001	0.001
acc	0.018	0.017	0.034
calcDrugFPSim	0.000	0.000	0.001
calcDrugMCSSim	0.007	0.006	0.013
calcParProtGOSim	0.000	0.000	0.001
calcParProtSeqSim	0.011	0.004	0.015
calcTwoProtGOSim	0.000	0.001	0.001
calcTwoProtSeqSim	0.003	0.001	0.004
checkProt	0.002	0.002	0.004
convMolFormat	0.002	0.001	0.002
extractDrugAIO	0.001	0.001	0.002
extractDrugALOGP	0.001	0.001	0.003
extractDrugAminoAcidCount	0.002	0.000	0.002
extractDrugApol	0.001	0.001	0.003
extractDrugAromaticAtomsCount	0.002	0.000	0.002
extractDrugAromaticBondsCount	0.001	0.001	0.002
extractDrugAtomCount	0.002	0.000	0.002
extractDrugAutocorrelationCharge	0.001	0.001	0.003
extractDrugAutocorrelationMass	0.002	0.001	0.002
extractDrugAutocorrelationPolarizability	0.001	0.001	0.003
extractDrugBCUT	0.001	0.001	0.002
extractDrugBPol	0.002	0.001	0.002
extractDrugBondCount	0.001	0.001	0.002
extractDrugCPSA	0.002	0.001	0.002
extractDrugCarbonTypes	0.001	0.001	0.002
extractDrugChiChain	0.002	0.001	0.002
extractDrugChiCluster	0.001	0.001	0.002
extractDrugChiPath	0.002	0.001	0.002
extractDrugChiPathCluster	0.001	0.001	0.002
extractDrugDescOB	0.011	0.006	0.018
extractDrugECI	0.001	0.001	0.002
extractDrugEstate	0.002	0.001	0.002
extractDrugEstateComplete	0.001	0.000	0.002
extractDrugExtended	0.002	0.001	0.002
extractDrugExtendedComplete	0.001	0.000	0.002
extractDrugFMF	0.002	0.001	0.002
extractDrugFragmentComplexity	0.001	0.001	0.002
extractDrugGraph	0.002	0.001	0.002
extractDrugGraphComplete	0.001	0.001	0.002
extractDrugGravitationalIndex	0.001	0.001	0.002
extractDrugHBondAcceptorCount	0.002	0.001	0.002
extractDrugHBondDonorCount	0.001	0.001	0.002
extractDrugHybridization	0.001	0.000	0.003
extractDrugHybridizationComplete	0.002	0.001	0.002
extractDrugHybridizationRatio	0.001	0.000	0.002
extractDrugIPMolecularLearning	0.001	0.001	0.002
extractDrugKR	0.002	0.001	0.002
extractDrugKRComplete	0.001	0.001	0.002
extractDrugKappaShapeIndices	0.002	0.000	0.002
extractDrugKierHallSmarts	0.001	0.001	0.003
extractDrugLargestChain	0.001	0.001	0.002
extractDrugLargestPiSystem	0.002	0.000	0.002
extractDrugLengthOverBreadth	0.001	0.001	0.003
extractDrugLongestAliphaticChain	0.001	0.001	0.003
extractDrugMACCS	0.002	0.001	0.002
extractDrugMACCSComplete	0.001	0.001	0.002
extractDrugMDE	0.002	0.001	0.002
extractDrugMannholdLogP	0.001	0.001	0.003
extractDrugMomentOfInertia	0.002	0.001	0.003
extractDrugOBFP2	0.031	0.009	0.042
extractDrugOBFP3	0.010	0.004	0.013
extractDrugOBFP4	0.010	0.006	0.016
extractDrugOBMACCS	0.011	0.005	0.016
extractDrugPetitjeanNumber	0.001	0.001	0.002
extractDrugPetitjeanShapeIndex	0.002	0.000	0.002
extractDrugPubChem	0.002	0.001	0.002
extractDrugPubChemComplete	0.001	0.000	0.003
extractDrugRotatableBondsCount	0.001	0.001	0.003
extractDrugRuleOfFive	0.002	0.000	0.002
extractDrugShortestPath	0.001	0.001	0.002
extractDrugShortestPathComplete	0.001	0.001	0.002
extractDrugStandard	0.002	0.001	0.002
extractDrugStandardComplete	0.001	0.000	0.001
extractDrugTPSA	0.001	0.000	0.002
extractDrugVABC	0.002	0.001	0.002
extractDrugVAdjMa	0.001	0.001	0.002
extractDrugWHIM	0.001	0.001	0.002
extractDrugWeight	0.002	0.001	0.002
extractDrugWeightedPath	0.001	0.001	0.002
extractDrugWienerNumbers	0.001	0.001	0.002
extractDrugXLogP	0.002	0.001	0.003
extractDrugZagrebIndex	0.001	0.001	0.002
extractPCMBLOSUM	0.026	0.012	0.038
extractPCMDescScales	0.021	0.003	0.025
extractPCMFAScales	0.028	0.007	0.037
extractPCMMDSScales	0.017	0.005	0.023
extractPCMPropScales	0.020	0.004	0.024
extractPCMScales	0.031	0.007	0.038
extractProtAAC	0.004	0.002	0.006
extractProtAPAAC	1.903	0.064	1.977
extractProtCTDC	0.004	0.002	0.006
extractProtCTDD	0.008	0.004	0.012
extractProtCTDT	0.008	0.002	0.011
extractProtCTriad	0.186	0.022	0.208
extractProtDC	0.008	0.014	0.023
extractProtGeary	0.286	0.022	0.315
extractProtMoran	0.325	0.031	0.359
extractProtMoreauBroto	0.280	0.019	0.302
extractProtPAAC	1.161	0.014	1.185
extractProtPSSM	0.001	0.001	0.002
extractProtPSSMAcc	0.002	0.001	0.002
extractProtPSSMFeature	0.002	0.001	0.002
extractProtQSO	2.200	0.033	2.326
extractProtSOCN	2.165	0.023	2.279
extractProtTC	0.089	0.275	0.386
getCPI	0.005	0.004	0.009
getDrug	0	0	0
getFASTAFromKEGG	0.000	0.000	0.001
getFASTAFromUniProt	0.001	0.000	0.000
getMolFromCAS	0.001	0.000	0.000
getMolFromChEMBL	0	0	0
getMolFromDrugBank	0	0	0
getMolFromKEGG	0	0	0
getMolFromPubChem	0	0	0
getPDBFromRCSBPDB	0.000	0.000	0.003
getPPI	0.006	0.005	0.015
getProt	0.000	0.001	0.001
getSeqFromKEGG	0.000	0.000	0.001
getSeqFromRCSBPDB	0	0	0
getSeqFromUniProt	0.000	0.001	0.000
getSmiFromChEMBL	0.000	0.001	0.000
getSmiFromDrugBank	0.000	0.001	0.001
getSmiFromKEGG	0.000	0.001	0.001
getSmiFromPubChem	0.000	0.001	0.001
readFASTA	0.002	0.001	0.011
readMolFromSDF	0.004	0.002	0.009
readMolFromSmi	0.002	0.001	0.002
readPDB	1.755	0.012	1.921
searchDrug	0.002	0.001	0.004
segProt	0.004	0.004	0.007