Multiple platform build/check report for BioC 3.22 - CHECK results for Rcpi on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4883
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4673
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4607
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4671
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: 1.46.0

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_1.46.0.tar.gz

StartedAt: 2025-12-19 09:50:24 -0500 (Fri, 19 Dec 2025)

EndedAt: 2025-12-19 09:55:37 -0500 (Fri, 19 Dec 2025)

EllapsedTime: 312.9 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_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/Rcpi.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘1.46.0’
* 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 ‘1.46.0’
** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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 
 13.097   1.066  14.196

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

name	user	system	elapsed
AA2DACOR	0.003	0.002	0.008
AA3DMoRSE	0.001	0.002	0.004
AAACF	0.002	0.002	0.006
AABLOSUM100	0.001	0.003	0.004
AABLOSUM45	0.001	0.002	0.004
AABLOSUM50	0.002	0.003	0.005
AABLOSUM62	0.001	0.003	0.004
AABLOSUM80	0.002	0.003	0.008
AABurden	0.001	0.002	0.003
AACPSA	0.002	0.003	0.006
AAConn	0.001	0.002	0.004
AAConst	0.002	0.002	0.006
AADescAll	0.001	0.002	0.003
AAEdgeAdj	0.001	0.002	0.006
AAEigIdx	0.002	0.002	0.004
AAFGC	0.001	0.002	0.007
AAGETAWAY	0.002	0.002	0.004
AAGeom	0.001	0.002	0.005
AAInfo	0.002	0.003	0.004
AAMOE2D	0.001	0.002	0.006
AAMOE3D	0.002	0.002	0.004
AAMetaInfo	0.001	0.002	0.004
AAMolProp	0.001	0.002	0.003
AAPAM120	0.002	0.002	0.004
AAPAM250	0.001	0.002	0.004
AAPAM30	0.001	0.002	0.007
AAPAM40	0.002	0.002	0.003
AAPAM70	0.001	0.002	0.004
AARDF	0.002	0.002	0.003
AARandic	0.001	0.003	0.004
AATopo	0.001	0.002	0.004
AATopoChg	0.002	0.002	0.009
AAWHIM	0.001	0.002	0.004
AAWalk	0.002	0.002	0.006
AAindex	0.001	0.002	0.004
OptAA3d	0.000	0.001	0.000
acc	0.017	0.016	0.037
calcDrugFPSim	0.000	0.000	0.001
calcDrugMCSSim	0.007	0.006	0.017
calcParProtGOSim	0.000	0.000	0.001
calcParProtSeqSim	0.011	0.004	0.017
calcTwoProtGOSim	0.000	0.001	0.001
calcTwoProtSeqSim	0.003	0.002	0.005
checkProt	0.003	0.001	0.004
convMolFormat	0.002	0.001	0.003
extractDrugAIO	0.001	0.001	0.004
extractDrugALOGP	0.002	0.001	0.002
extractDrugAminoAcidCount	0.001	0.001	0.002
extractDrugApol	0.002	0.000	0.003
extractDrugAromaticAtomsCount	0.001	0.001	0.003
extractDrugAromaticBondsCount	0.001	0.000	0.002
extractDrugAtomCount	0.002	0.001	0.002
extractDrugAutocorrelationCharge	0.001	0.000	0.003
extractDrugAutocorrelationMass	0.002	0.001	0.006
extractDrugAutocorrelationPolarizability	0.001	0.000	0.003
extractDrugBCUT	0.001	0.001	0.002
extractDrugBPol	0.002	0.000	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	0.003
extractDrugChiCluster	0.001	0.001	0.002
extractDrugChiPath	0.002	0.000	0.002
extractDrugChiPathCluster	0.002	0.001	0.003
extractDrugDescOB	0.022	0.008	0.032
extractDrugECI	0.001	0.001	0.003
extractDrugEstate	0.002	0.001	0.002
extractDrugEstateComplete	0.001	0.001	0.005
extractDrugExtended	0.002	0.001	0.002
extractDrugExtendedComplete	0.002	0.001	0.003
extractDrugFMF	0.001	0.001	0.002
extractDrugFragmentComplexity	0.002	0.000	0.003
extractDrugGraph	0.001	0.001	0.003
extractDrugGraphComplete	0.002	0.001	0.004
extractDrugGravitationalIndex	0.001	0.000	0.002
extractDrugHBondAcceptorCount	0.001	0.001	0.004
extractDrugHBondDonorCount	0.002	0.001	0.002
extractDrugHybridization	0.001	0.001	0.002
extractDrugHybridizationComplete	0.002	0.001	0.002
extractDrugHybridizationRatio	0.002	0.000	0.002
extractDrugIPMolecularLearning	0.001	0.001	0.003
extractDrugKR	0.002	0.001	0.003
extractDrugKRComplete	0.001	0.001	0.003
extractDrugKappaShapeIndices	0.002	0.001	0.002
extractDrugKierHallSmarts	0.001	0.000	0.002
extractDrugLargestChain	0.002	0.001	0.005
extractDrugLargestPiSystem	0.001	0.000	0.002
extractDrugLengthOverBreadth	0.001	0.001	0.002
extractDrugLongestAliphaticChain	0.002	0.000	0.004
extractDrugMACCS	0.001	0.001	0.003
extractDrugMACCSComplete	0.001	0.001	0.002
extractDrugMDE	0.001	0.001	0.003
extractDrugMannholdLogP	0.002	0.001	0.003
extractDrugMomentOfInertia	0.001	0.000	0.002
extractDrugOBFP2	0.011	0.006	0.020
extractDrugOBFP3	0.019	0.009	0.032
extractDrugOBFP4	0.010	0.004	0.019
extractDrugOBMACCS	0.101	0.004	0.123
extractDrugPetitjeanNumber	0.002	0.001	0.002
extractDrugPetitjeanShapeIndex	0.001	0.001	0.003
extractDrugPubChem	0.002	0.001	0.005
extractDrugPubChemComplete	0.001	0.001	0.002
extractDrugRotatableBondsCount	0.002	0.001	0.005
extractDrugRuleOfFive	0.001	0.001	0.002
extractDrugShortestPath	0.002	0.001	0.004
extractDrugShortestPathComplete	0.001	0.001	0.002
extractDrugStandard	0.001	0.001	0.003
extractDrugStandardComplete	0.002	0.000	0.003
extractDrugTPSA	0.001	0.001	0.002
extractDrugVABC	0.002	0.001	0.003
extractDrugVAdjMa	0.001	0.001	0.002
extractDrugWHIM	0.001	0.001	0.002
extractDrugWeight	0.002	0.001	0.003
extractDrugWeightedPath	0.001	0.001	0.003
extractDrugWienerNumbers	0.002	0.001	0.003
extractDrugXLogP	0.001	0.001	0.004
extractDrugZagrebIndex	0.001	0.001	0.002
extractPCMBLOSUM	0.018	0.004	0.026
extractPCMDescScales	0.020	0.004	0.026
extractPCMFAScales	0.028	0.007	0.042
extractPCMMDSScales	0.017	0.005	0.025
extractPCMPropScales	0.031	0.005	0.042
extractPCMScales	0.031	0.006	0.045
extractProtAAC	0.003	0.002	0.006
extractProtAPAAC	1.758	0.051	1.936
extractProtCTDC	0.004	0.002	0.006
extractProtCTDD	0.007	0.005	0.013
extractProtCTDT	0.009	0.002	0.012
extractProtCTriad	0.187	0.026	0.218
extractProtDC	0.007	0.016	0.023
extractProtGeary	0.293	0.029	0.336
extractProtMoran	0.292	0.031	0.333
extractProtMoreauBroto	0.253	0.027	0.309
extractProtPAAC	1.122	0.025	1.180
extractProtPSSM	0.002	0.001	0.005
extractProtPSSMAcc	0.002	0.001	0.004
extractProtPSSMFeature	0.002	0.002	0.003
extractProtQSO	2.159	0.047	2.593
extractProtSOCN	2.108	0.029	2.201
extractProtTC	0.097	0.374	0.741
getCPI	0.006	0.007	0.021
getDrug	0.000	0.000	0.002
getFASTAFromKEGG	0.001	0.000	0.001
getFASTAFromUniProt	0.000	0.001	0.003
getMolFromCAS	0	0	0
getMolFromChEMBL	0.001	0.000	0.002
getMolFromDrugBank	0	0	0
getMolFromKEGG	0.000	0.001	0.001
getMolFromPubChem	0.001	0.001	0.001
getPDBFromRCSBPDB	0.000	0.001	0.001
getPPI	0.006	0.006	0.013
getProt	0.000	0.001	0.002
getSeqFromKEGG	0.000	0.001	0.001
getSeqFromRCSBPDB	0.000	0.001	0.000
getSeqFromUniProt	0.000	0.000	0.001
getSmiFromChEMBL	0.000	0.001	0.001
getSmiFromDrugBank	0.000	0.001	0.002
getSmiFromKEGG	0.000	0.001	0.000
getSmiFromPubChem	0.000	0.001	0.001
readFASTA	0.002	0.002	0.006
readMolFromSDF	0.004	0.001	0.009
readMolFromSmi	0.002	0.002	0.004
readPDB	1.467	0.024	3.506
searchDrug	0.003	0.001	0.018
segProt	0.003	0.005	0.008