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"	4615
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"	4610
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4598
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4668
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: 2025-11-18 12:42:01 -0500 (Tue, 18 Nov 2025)

EndedAt: 2025-11-18 12:46:26 -0500 (Tue, 18 Nov 2025)

EllapsedTime: 264.3 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 Patched (2025-11-05 r88990)
* 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 Patched (2025-11-05 r88990) -- "[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 
 13.159   1.022  12.553

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

name	user	system	elapsed
AA2DACOR	0.002	0.002	0.005
AA3DMoRSE	0.001	0.002	0.004
AAACF	0.001	0.002	0.004
AABLOSUM100	0.002	0.002	0.004
AABLOSUM45	0.001	0.003	0.003
AABLOSUM50	0.002	0.002	0.004
AABLOSUM62	0.001	0.002	0.004
AABLOSUM80	0.002	0.002	0.004
AABurden	0.001	0.002	0.004
AACPSA	0.002	0.002	0.003
AAConn	0.001	0.003	0.005
AAConst	0.002	0.002	0.004
AADescAll	0.001	0.002	0.004
AAEdgeAdj	0.001	0.002	0.003
AAEigIdx	0.002	0.002	0.003
AAFGC	0.001	0.002	0.004
AAGETAWAY	0.002	0.002	0.005
AAGeom	0.001	0.002	0.003
AAInfo	0.002	0.002	0.003
AAMOE2D	0.001	0.002	0.004
AAMOE3D	0.001	0.002	0.005
AAMetaInfo	0.002	0.002	0.004
AAMolProp	0.001	0.002	0.003
AAPAM120	0.001	0.001	0.002
AAPAM250	0.002	0.002	0.003
AAPAM30	0.001	0.002	0.003
AAPAM40	0.001	0.002	0.004
AAPAM70	0.002	0.002	0.004
AARDF	0.001	0.003	0.005
AARandic	0.002	0.002	0.003
AATopo	0.001	0.002	0.004
AATopoChg	0.002	0.002	0.004
AAWHIM	0.001	0.002	0.005
AAWalk	0.002	0.002	0.005
AAindex	0.001	0.002	0.004
OptAA3d	0.000	0.000	0.001
acc	0.017	0.014	0.031
calcDrugFPSim	0	0	0
calcDrugMCSSim	0.007	0.006	0.015
calcParProtGOSim	0.000	0.001	0.001
calcParProtSeqSim	0.011	0.005	0.017
calcTwoProtGOSim	0.000	0.001	0.001
calcTwoProtSeqSim	0.003	0.002	0.005
checkProt	0.003	0.001	0.003
convMolFormat	0.002	0.001	0.003
extractDrugAIO	0.001	0.001	0.003
extractDrugALOGP	0.002	0.001	0.002
extractDrugAminoAcidCount	0.001	0.001	0.002
extractDrugApol	0.001	0.000	0.002
extractDrugAromaticAtomsCount	0.002	0.001	0.003
extractDrugAromaticBondsCount	0.002	0.000	0.002
extractDrugAtomCount	0.001	0.001	0.002
extractDrugAutocorrelationCharge	0.002	0.000	0.002
extractDrugAutocorrelationMass	0.002	0.001	0.002
extractDrugAutocorrelationPolarizability	0.001	0.001	0.003
extractDrugBCUT	0.002	0.001	0.002
extractDrugBPol	0.001	0.001	0.002
extractDrugBondCount	0.002	0.001	0.003
extractDrugCPSA	0.001	0.000	0.002
extractDrugCarbonTypes	0.001	0.001	0.003
extractDrugChiChain	0.002	0.001	0.003
extractDrugChiCluster	0.001	0.001	0.003
extractDrugChiPath	0.002	0.000	0.002
extractDrugChiPathCluster	0.002	0.001	0.002
extractDrugDescOB	0.021	0.009	0.032
extractDrugECI	0.002	0.000	0.003
extractDrugEstate	0.001	0.001	0.003
extractDrugEstateComplete	0.002	0.001	0.003
extractDrugExtended	0.001	0.001	0.003
extractDrugExtendedComplete	0.002	0.001	0.002
extractDrugFMF	0.001	0.001	0.002
extractDrugFragmentComplexity	0.001	0.000	0.002
extractDrugGraph	0.002	0.001	0.002
extractDrugGraphComplete	0.001	0.000	0.002
extractDrugGravitationalIndex	0.001	0.001	0.002
extractDrugHBondAcceptorCount	0.002	0.001	0.002
extractDrugHBondDonorCount	0.002	0.000	0.002
extractDrugHybridization	0.001	0.001	0.003
extractDrugHybridizationComplete	0.002	0.001	0.002
extractDrugHybridizationRatio	0.001	0.001	0.002
extractDrugIPMolecularLearning	0.002	0.001	0.002
extractDrugKR	0.001	0.000	0.002
extractDrugKRComplete	0.002	0.001	0.002
extractDrugKappaShapeIndices	0.001	0.001	0.003
extractDrugKierHallSmarts	0.002	0.000	0.003
extractDrugLargestChain	0.001	0.001	0.003
extractDrugLargestPiSystem	0.002	0.001	0.002
extractDrugLengthOverBreadth	0.001	0.000	0.002
extractDrugLongestAliphaticChain	0.002	0.001	0.002
extractDrugMACCS	0.001	0.000	0.002
extractDrugMACCSComplete	0.001	0.001	0.002
extractDrugMDE	0.001	0.000	0.002
extractDrugMannholdLogP	0.001	0.001	0.002
extractDrugMomentOfInertia	0.002	0.000	0.002
extractDrugOBFP2	0.011	0.005	0.016
extractDrugOBFP3	0.018	0.010	0.028
extractDrugOBFP4	0.011	0.006	0.016
extractDrugOBMACCS	0.107	0.009	0.119
extractDrugPetitjeanNumber	0.001	0.001	0.002
extractDrugPetitjeanShapeIndex	0.002	0.001	0.002
extractDrugPubChem	0.001	0.001	0.002
extractDrugPubChemComplete	0.001	0.001	0.002
extractDrugRotatableBondsCount	0.002	0.000	0.003
extractDrugRuleOfFive	0.001	0.001	0.002
extractDrugShortestPath	0.002	0.001	0.002
extractDrugShortestPathComplete	0.001	0.001	0.002
extractDrugStandard	0.002	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	0.001	0.002
extractDrugWHIM	0.002	0.001	0.002
extractDrugWeight	0.001	0.001	0.002
extractDrugWeightedPath	0.001	0.001	0.002
extractDrugWienerNumbers	0.002	0.001	0.002
extractDrugXLogP	0.002	0.001	0.002
extractDrugZagrebIndex	0.001	0.001	0.002
extractPCMBLOSUM	0.017	0.003	0.020
extractPCMDescScales	0.020	0.004	0.024
extractPCMFAScales	0.028	0.006	0.036
extractPCMMDSScales	0.017	0.005	0.023
extractPCMPropScales	0.030	0.004	0.035
extractPCMScales	0.030	0.005	0.036
extractProtAAC	0.004	0.001	0.005
extractProtAPAAC	1.815	0.056	1.903
extractProtCTDC	0.004	0.002	0.006
extractProtCTDD	0.008	0.005	0.013
extractProtCTDT	0.009	0.002	0.012
extractProtCTriad	0.188	0.027	0.218
extractProtDC	0.007	0.011	0.019
extractProtGeary	0.292	0.026	0.322
extractProtMoran	0.294	0.022	0.331
extractProtMoreauBroto	0.276	0.021	0.299
extractProtPAAC	1.170	0.016	1.197
extractProtPSSM	0.002	0.000	0.003
extractProtPSSMAcc	0.002	0.001	0.002
extractProtPSSMFeature	0.002	0.000	0.003
extractProtQSO	2.142	0.024	2.198
extractProtSOCN	2.131	0.017	2.160
extractProtTC	0.087	0.242	0.331
getCPI	0.005	0.004	0.009
getDrug	0.000	0.000	0.001
getFASTAFromKEGG	0.001	0.000	0.000
getFASTAFromUniProt	0.000	0.001	0.001
getMolFromCAS	0.000	0.001	0.001
getMolFromChEMBL	0.000	0.001	0.001
getMolFromDrugBank	0	0	0
getMolFromKEGG	0	0	0
getMolFromPubChem	0.000	0.000	0.001
getPDBFromRCSBPDB	0.001	0.000	0.000
getPPI	0.006	0.005	0.021
getProt	0	0	0
getSeqFromKEGG	0	0	0
getSeqFromRCSBPDB	0	0	0
getSeqFromUniProt	0.000	0.000	0.001
getSmiFromChEMBL	0.000	0.000	0.001
getSmiFromDrugBank	0.000	0.000	0.001
getSmiFromKEGG	0.000	0.000	0.001
getSmiFromPubChem	0.001	0.000	0.001
readFASTA	0.003	0.001	0.004
readMolFromSDF	0.004	0.002	0.006
readMolFromSmi	0.001	0.000	0.003
readPDB	1.558	0.011	1.606
searchDrug	0.002	0.002	0.004
segProt	0.004	0.004	0.009