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"	4882
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: 2025-12-12 10:09:25 -0500 (Fri, 12 Dec 2025)

EndedAt: 2025-12-12 10:14:11 -0500 (Fri, 12 Dec 2025)

EllapsedTime: 286.5 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_1.46.0.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 
 13.129   1.021  13.682

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

name	user	system	elapsed
AA2DACOR	0.002	0.002	0.007
AA3DMoRSE	0.001	0.003	0.003
AAACF	0.002	0.002	0.004
AABLOSUM100	0.001	0.002	0.004
AABLOSUM45	0.002	0.002	0.004
AABLOSUM50	0.001	0.002	0.004
AABLOSUM62	0.002	0.002	0.004
AABLOSUM80	0.002	0.002	0.004
AABurden	0.001	0.002	0.003
AACPSA	0.002	0.002	0.004
AAConn	0.001	0.002	0.006
AAConst	0.002	0.003	0.005
AADescAll	0.002	0.001	0.005
AAEdgeAdj	0.001	0.002	0.004
AAEigIdx	0.002	0.002	0.004
AAFGC	0.001	0.002	0.003
AAGETAWAY	0.001	0.002	0.005
AAGeom	0.002	0.002	0.005
AAInfo	0.001	0.002	0.005
AAMOE2D	0.002	0.003	0.004
AAMOE3D	0.001	0.003	0.004
AAMetaInfo	0.002	0.001	0.003
AAMolProp	0.001	0.002	0.003
AAPAM120	0.002	0.002	0.004
AAPAM250	0.001	0.002	0.004
AAPAM30	0.002	0.002	0.004
AAPAM40	0.001	0.002	0.003
AAPAM70	0.002	0.002	0.005
AARDF	0.001	0.002	0.004
AARandic	0.002	0.002	0.004
AATopo	0.001	0.002	0.003
AATopoChg	0.001	0.002	0.004
AAWHIM	0.002	0.002	0.004
AAWalk	0.001	0.002	0.004
AAindex	0.002	0.002	0.003
OptAA3d	0.000	0.000	0.001
acc	0.018	0.017	0.036
calcDrugFPSim	0.000	0.000	0.001
calcDrugMCSSim	0.007	0.006	0.015
calcParProtGOSim	0.000	0.000	0.001
calcParProtSeqSim	0.011	0.005	0.018
calcTwoProtGOSim	0.000	0.001	0.001
calcTwoProtSeqSim	0.004	0.001	0.005
checkProt	0.003	0.001	0.004
convMolFormat	0.001	0.001	0.002
extractDrugAIO	0.002	0.001	0.004
extractDrugALOGP	0.001	0.000	0.002
extractDrugAminoAcidCount	0.002	0.001	0.004
extractDrugApol	0.001	0.000	0.002
extractDrugAromaticAtomsCount	0.001	0.001	0.002
extractDrugAromaticBondsCount	0.002	0.001	0.002
extractDrugAtomCount	0.001	0.001	0.002
extractDrugAutocorrelationCharge	0.002	0.001	0.003
extractDrugAutocorrelationMass	0.001	0.001	0.003
extractDrugAutocorrelationPolarizability	0.002	0.000	0.002
extractDrugBCUT	0.001	0.001	0.004
extractDrugBPol	0.001	0.000	0.002
extractDrugBondCount	0.002	0.001	0.002
extractDrugCPSA	0.001	0.001	0.003
extractDrugCarbonTypes	0.002	0.001	0.002
extractDrugChiChain	0.001	0.000	0.002
extractDrugChiCluster	0.002	0.001	0.003
extractDrugChiPath	0.002	0.000	0.002
extractDrugChiPathCluster	0.001	0.001	0.002
extractDrugDescOB	0.022	0.008	0.036
extractDrugECI	0.002	0.001	0.002
extractDrugEstate	0.002	0.000	0.002
extractDrugEstateComplete	0.001	0.001	0.002
extractDrugExtended	0.002	0.000	0.002
extractDrugExtendedComplete	0.001	0.001	0.002
extractDrugFMF	0.002	0.000	0.003
extractDrugFragmentComplexity	0.001	0.001	0.002
extractDrugGraph	0.002	0.000	0.002
extractDrugGraphComplete	0.001	0.001	0.003
extractDrugGravitationalIndex	0.002	0.001	0.003
extractDrugHBondAcceptorCount	0.001	0.001	0.003
extractDrugHBondDonorCount	0.002	0.001	0.002
extractDrugHybridization	0.001	0.001	0.003
extractDrugHybridizationComplete	0.002	0.001	0.003
extractDrugHybridizationRatio	0.001	0.001	0.002
extractDrugIPMolecularLearning	0.002	0.001	0.002
extractDrugKR	0.001	0.001	0.002
extractDrugKRComplete	0.001	0.001	0.002
extractDrugKappaShapeIndices	0.002	0.001	0.002
extractDrugKierHallSmarts	0.002	0.000	0.004
extractDrugLargestChain	0.001	0.001	0.002
extractDrugLargestPiSystem	0.002	0.001	0.002
extractDrugLengthOverBreadth	0.001	0.000	0.002
extractDrugLongestAliphaticChain	0.002	0.001	0.002
extractDrugMACCS	0.001	0.001	0.003
extractDrugMACCSComplete	0.002	0.001	0.003
extractDrugMDE	0.002	0.001	0.003
extractDrugMannholdLogP	0.001	0.001	0.002
extractDrugMomentOfInertia	0.002	0.001	0.003
extractDrugOBFP2	0.011	0.006	0.019
extractDrugOBFP3	0.018	0.008	0.029
extractDrugOBFP4	0.012	0.006	0.019
extractDrugOBMACCS	0.101	0.009	0.124
extractDrugPetitjeanNumber	0.001	0.000	0.002
extractDrugPetitjeanShapeIndex	0.002	0.001	0.002
extractDrugPubChem	0.002	0.001	0.003
extractDrugPubChemComplete	0.001	0.001	0.003
extractDrugRotatableBondsCount	0.002	0.001	0.002
extractDrugRuleOfFive	0.001	0.001	0.002
extractDrugShortestPath	0.002	0.001	0.002
extractDrugShortestPathComplete	0.001	0.001	0.002
extractDrugStandard	0.001	0.001	0.002
extractDrugStandardComplete	0.002	0.001	0.002
extractDrugTPSA	0.001	0.001	0.002
extractDrugVABC	0.002	0.001	0.002
extractDrugVAdjMa	0.001	0.000	0.002
extractDrugWHIM	0.001	0.001	0.002
extractDrugWeight	0.002	0.000	0.003
extractDrugWeightedPath	0.001	0.001	0.002
extractDrugWienerNumbers	0.001	0.001	0.002
extractDrugXLogP	0.002	0.000	0.002
extractDrugZagrebIndex	0.002	0.001	0.002
extractPCMBLOSUM	0.017	0.005	0.021
extractPCMDescScales	0.021	0.004	0.025
extractPCMFAScales	0.028	0.007	0.040
extractPCMMDSScales	0.018	0.006	0.024
extractPCMPropScales	0.031	0.006	0.039
extractPCMScales	0.030	0.005	0.040
extractProtAAC	0.003	0.002	0.006
extractProtAPAAC	1.760	0.056	2.000
extractProtCTDC	0.004	0.002	0.006
extractProtCTDD	0.008	0.005	0.014
extractProtCTDT	0.008	0.002	0.013
extractProtCTriad	0.194	0.024	0.259
extractProtDC	0.007	0.013	0.021
extractProtGeary	0.297	0.026	0.346
extractProtMoran	0.293	0.023	0.335
extractProtMoreauBroto	0.274	0.021	0.307
extractProtPAAC	1.150	0.019	1.282
extractProtPSSM	0.002	0.001	0.004
extractProtPSSMAcc	0.002	0.001	0.003
extractProtPSSMFeature	0.002	0.001	0.003
extractProtQSO	2.216	0.029	2.412
extractProtSOCN	2.128	0.018	2.361
extractProtTC	0.086	0.243	0.400
getCPI	0.005	0.004	0.008
getDrug	0.001	0.001	0.001
getFASTAFromKEGG	0.001	0.001	0.001
getFASTAFromUniProt	0.001	0.001	0.001
getMolFromCAS	0.000	0.001	0.000
getMolFromChEMBL	0.000	0.001	0.000
getMolFromDrugBank	0.000	0.001	0.000
getMolFromKEGG	0.000	0.001	0.000
getMolFromPubChem	0.000	0.001	0.000
getPDBFromRCSBPDB	0.000	0.001	0.001
getPPI	0.006	0.005	0.011
getProt	0.000	0.001	0.001
getSeqFromKEGG	0.000	0.001	0.000
getSeqFromRCSBPDB	0.000	0.001	0.000
getSeqFromUniProt	0.001	0.000	0.001
getSmiFromChEMBL	0.001	0.000	0.001
getSmiFromDrugBank	0.000	0.000	0.001
getSmiFromKEGG	0.000	0.000	0.001
getSmiFromPubChem	0	0	0
readFASTA	0.002	0.001	0.004
readMolFromSDF	0.004	0.002	0.006
readMolFromSmi	0.001	0.001	0.003
readPDB	1.610	0.014	1.888
searchDrug	0.003	0.001	0.005
segProt	0.003	0.003	0.007