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"	4879
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4668
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4669
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: 2025-12-05 10:32:05 -0500 (Fri, 05 Dec 2025)

EndedAt: 2025-12-05 10:37:36 -0500 (Fri, 05 Dec 2025)

EllapsedTime: 331.8 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_1.46.0.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 
 13.420   1.360  18.139

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

name	user	system	elapsed
AA2DACOR	0.003	0.003	0.014
AA3DMoRSE	0.001	0.002	0.004
AAACF	0.002	0.003	0.006
AABLOSUM100	0.001	0.003	0.006
AABLOSUM45	0.002	0.002	0.004
AABLOSUM50	0.002	0.002	0.004
AABLOSUM62	0.001	0.003	0.004
AABLOSUM80	0.002	0.002	0.003
AABurden	0.001	0.002	0.004
AACPSA	0.002	0.002	0.004
AAConn	0.001	0.003	0.014
AAConst	0.002	0.002	0.004
AADescAll	0.002	0.003	0.018
AAEdgeAdj	0.001	0.003	0.008
AAEigIdx	0.002	0.002	0.004
AAFGC	0.001	0.003	0.012
AAGETAWAY	0.002	0.002	0.004
AAGeom	0.002	0.002	0.004
AAInfo	0.001	0.002	0.004
AAMOE2D	0.001	0.002	0.004
AAMOE3D	0.002	0.002	0.004
AAMetaInfo	0.001	0.002	0.003
AAMolProp	0.002	0.002	0.004
AAPAM120	0.001	0.002	0.004
AAPAM250	0.002	0.002	0.003
AAPAM30	0.001	0.002	0.004
AAPAM40	0.002	0.002	0.004
AAPAM70	0.001	0.002	0.004
AARDF	0.002	0.002	0.003
AARandic	0.002	0.002	0.008
AATopo	0.001	0.002	0.004
AATopoChg	0.002	0.001	0.006
AAWHIM	0.001	0.002	0.003
AAWalk	0.001	0.001	0.003
AAindex	0.001	0.002	0.007
OptAA3d	0.001	0.000	0.001
acc	0.017	0.025	0.066
calcDrugFPSim	0.001	0.001	0.000
calcDrugMCSSim	0.007	0.007	0.024
calcParProtGOSim	0.000	0.001	0.001
calcParProtSeqSim	0.011	0.004	0.018
calcTwoProtGOSim	0.000	0.001	0.001
calcTwoProtSeqSim	0.003	0.001	0.005
checkProt	0.003	0.002	0.014
convMolFormat	0.001	0.001	0.003
extractDrugAIO	0.002	0.000	0.002
extractDrugALOGP	0.001	0.001	0.003
extractDrugAminoAcidCount	0.002	0.001	0.003
extractDrugApol	0.001	0.001	0.003
extractDrugAromaticAtomsCount	0.002	0.001	0.003
extractDrugAromaticBondsCount	0.001	0.000	0.003
extractDrugAtomCount	0.002	0.001	0.002
extractDrugAutocorrelationCharge	0.001	0.001	0.002
extractDrugAutocorrelationMass	0.001	0.001	0.003
extractDrugAutocorrelationPolarizability	0.002	0.001	0.002
extractDrugBCUT	0.001	0.001	0.002
extractDrugBPol	0.002	0.001	0.004
extractDrugBondCount	0.001	0.001	0.004
extractDrugCPSA	0.002	0.001	0.003
extractDrugCarbonTypes	0.001	0.001	0.003
extractDrugChiChain	0.002	0.001	0.004
extractDrugChiCluster	0.001	0.001	0.003
extractDrugChiPath	0.002	0.001	0.003
extractDrugChiPathCluster	0.001	0.001	0.002
extractDrugDescOB	0.022	0.013	0.085
extractDrugECI	0.003	0.001	0.003
extractDrugEstate	0.001	0.001	0.002
extractDrugEstateComplete	0.002	0.001	0.003
extractDrugExtended	0.002	0.001	0.002
extractDrugExtendedComplete	0.001	0.001	0.002
extractDrugFMF	0.001	0.001	0.002
extractDrugFragmentComplexity	0.002	0.001	0.002
extractDrugGraph	0.001	0.000	0.002
extractDrugGraphComplete	0.002	0.001	0.005
extractDrugGravitationalIndex	0.001	0.001	0.003
extractDrugHBondAcceptorCount	0.002	0.001	0.002
extractDrugHBondDonorCount	0.001	0.000	0.002
extractDrugHybridization	0.001	0.001	0.002
extractDrugHybridizationComplete	0.001	0.001	0.002
extractDrugHybridizationRatio	0.001	0.000	0.002
extractDrugIPMolecularLearning	0.002	0.001	0.003
extractDrugKR	0.002	0.001	0.002
extractDrugKRComplete	0.001	0.001	0.005
extractDrugKappaShapeIndices	0.002	0.000	0.002
extractDrugKierHallSmarts	0.001	0.001	0.006
extractDrugLargestChain	0.001	0.001	0.002
extractDrugLargestPiSystem	0.002	0.001	0.002
extractDrugLengthOverBreadth	0.001	0.001	0.003
extractDrugLongestAliphaticChain	0.002	0.000	0.002
extractDrugMACCS	0.002	0.001	0.003
extractDrugMACCSComplete	0.001	0.000	0.003
extractDrugMDE	0.002	0.001	0.002
extractDrugMannholdLogP	0.001	0.001	0.003
extractDrugMomentOfInertia	0.001	0.001	0.003
extractDrugOBFP2	0.012	0.008	0.021
extractDrugOBFP3	0.018	0.008	0.040
extractDrugOBFP4	0.010	0.004	0.018
extractDrugOBMACCS	0.101	0.009	0.128
extractDrugPetitjeanNumber	0.002	0.001	0.003
extractDrugPetitjeanShapeIndex	0.001	0.001	0.003
extractDrugPubChem	0.002	0.000	0.002
extractDrugPubChemComplete	0.001	0.001	0.002
extractDrugRotatableBondsCount	0.001	0.001	0.002
extractDrugRuleOfFive	0.002	0.001	0.004
extractDrugShortestPath	0.001	0.001	0.003
extractDrugShortestPathComplete	0.001	0.001	0.002
extractDrugStandard	0.002	0.000	0.004
extractDrugStandardComplete	0.002	0.002	0.006
extractDrugTPSA	0.001	0.002	0.006
extractDrugVABC	0.002	0.001	0.002
extractDrugVAdjMa	0.002	0.000	0.002
extractDrugWHIM	0.001	0.000	0.003
extractDrugWeight	0.001	0.001	0.004
extractDrugWeightedPath	0.002	0.001	0.003
extractDrugWienerNumbers	0.001	0.001	0.002
extractDrugXLogP	0.002	0.001	0.003
extractDrugZagrebIndex	0.001	0.002	0.004
extractPCMBLOSUM	0.017	0.006	0.027
extractPCMDescScales	0.020	0.003	0.031
extractPCMFAScales	0.030	0.007	0.043
extractPCMMDSScales	0.017	0.005	0.024
extractPCMPropScales	0.031	0.003	0.042
extractPCMScales	0.030	0.005	0.050
extractProtAAC	0.004	0.002	0.006
extractProtAPAAC	1.747	0.058	2.331
extractProtCTDC	0.005	0.002	0.007
extractProtCTDD	0.008	0.005	0.017
extractProtCTDT	0.010	0.002	0.020
extractProtCTriad	0.198	0.026	0.312
extractProtDC	0.007	0.014	0.033
extractProtGeary	0.298	0.024	0.446
extractProtMoran	0.298	0.024	0.433
extractProtMoreauBroto	0.279	0.022	0.385
extractProtPAAC	1.156	0.016	1.480
extractProtPSSM	0.002	0.001	0.003
extractProtPSSMAcc	0.002	0.001	0.003
extractProtPSSMFeature	0.002	0.001	0.003
extractProtQSO	2.172	0.030	2.814
extractProtSOCN	2.161	0.021	2.775
extractProtTC	0.088	0.245	0.412
getCPI	0.005	0.004	0.010
getDrug	0.000	0.001	0.001
getFASTAFromKEGG	0.000	0.001	0.000
getFASTAFromUniProt	0.000	0.000	0.001
getMolFromCAS	0	0	0
getMolFromChEMBL	0	0	0
getMolFromDrugBank	0	0	0
getMolFromKEGG	0	0	0
getMolFromPubChem	0	0	0
getPDBFromRCSBPDB	0	0	0
getPPI	0.006	0.005	0.024
getProt	0.000	0.001	0.000
getSeqFromKEGG	0.000	0.001	0.001
getSeqFromRCSBPDB	0.000	0.001	0.000
getSeqFromUniProt	0.000	0.001	0.001
getSmiFromChEMBL	0.000	0.000	0.001
getSmiFromDrugBank	0.000	0.000	0.001
getSmiFromKEGG	0	0	0
getSmiFromPubChem	0	0	0
readFASTA	0.002	0.001	0.003
readMolFromSDF	0.004	0.002	0.006
readMolFromSmi	0.001	0.001	0.003
readPDB	1.626	0.017	2.174
searchDrug	0.003	0.002	0.008
segProt	0.004	0.007	0.048