Multiple platform build/check report for BioC 3.20 - CHECK results for Rcpi on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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: 1.42.0

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_1.42.0.tar.gz

StartedAt: 2024-12-20 08:15:43 -0500 (Fri, 20 Dec 2024)

EndedAt: 2024-12-20 08:20:08 -0500 (Fri, 20 Dec 2024)

EllapsedTime: 265.3 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_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rcpi.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.42.0’
* 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/4.4-x86_64/Resources/library’
* installing *source* package ‘Rcpi’ ...
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 
 13.081   0.998  12.640

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

name	user	system	elapsed
AA2DACOR	0.003	0.003	0.006
AA3DMoRSE	0.001	0.002	0.004
AAACF	0.001	0.002	0.004
AABLOSUM100	0.002	0.002	0.004
AABLOSUM45	0.002	0.003	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	0.002	0.002	0.004
AAConst	0.002	0.002	0.004
AADescAll	0.002	0.002	0.004
AAEdgeAdj	0.001	0.001	0.004
AAEigIdx	0.002	0.002	0.004
AAFGC	0.001	0.002	0.004
AAGETAWAY	0.002	0.002	0.004
AAGeom	0.001	0.002	0.004
AAInfo	0.002	0.002	0.004
AAMOE2D	0.002	0.002	0.004
AAMOE3D	0.001	0.002	0.004
AAMetaInfo	0.002	0.002	0.003
AAMolProp	0.001	0.003	0.004
AAPAM120	0.002	0.003	0.005
AAPAM250	0.001	0.003	0.004
AAPAM30	0.002	0.003	0.004
AAPAM40	0.002	0.002	0.003
AAPAM70	0.002	0.002	0.004
AARDF	0.002	0.002	0.004
AARandic	0.001	0.002	0.003
AATopo	0.002	0.002	0.004
AATopoChg	0.002	0.002	0.004
AAWHIM	0.001	0.002	0.004
AAWalk	0.002	0.002	0.004
AAindex	0.001	0.002	0.003
OptAA3d	0	0	0
acc	0.017	0.016	0.033
calcDrugFPSim	0.000	0.001	0.001
calcDrugMCSSim	0.007	0.007	0.014
calcParProtGOSim	0.000	0.000	0.001
calcParProtSeqSim	0.011	0.004	0.016
calcTwoProtGOSim	0.000	0.000	0.001
calcTwoProtSeqSim	0.003	0.001	0.004
checkProt	0.003	0.002	0.004
convMolFormat	0.001	0.001	0.002
extractDrugAIO	0.002	0.001	0.003
extractDrugALOGP	0.001	0.001	0.003
extractDrugAminoAcidCount	0.002	0.001	0.003
extractDrugApol	0.001	0.001	0.003
extractDrugAromaticAtomsCount	0.002	0.000	0.002
extractDrugAromaticBondsCount	0.002	0.001	0.002
extractDrugAtomCount	0.001	0.001	0.002
extractDrugAutocorrelationCharge	0.002	0.001	0.002
extractDrugAutocorrelationMass	0.001	0.000	0.002
extractDrugAutocorrelationPolarizability	0.001	0.001	0.002
extractDrugBCUT	0.002	0.001	0.003
extractDrugBPol	0.001	0.001	0.003
extractDrugBondCount	0.002	0.001	0.002
extractDrugCPSA	0.001	0.001	0.002
extractDrugCarbonTypes	0.002	0.001	0.002
extractDrugChiChain	0.001	0.001	0.003
extractDrugChiCluster	0.002	0.001	0.003
extractDrugChiPath	0.001	0.000	0.002
extractDrugChiPathCluster	0.002	0.001	0.002
extractDrugDescOB	0.019	0.007	0.026
extractDrugECI	0.002	0.001	0.002
extractDrugEstate	0.001	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	0.001	0.001	0.002
extractDrugFragmentComplexity	0.002	0.000	0.002
extractDrugGraph	0.001	0.001	0.002
extractDrugGraphComplete	0.001	0.001	0.002
extractDrugGravitationalIndex	0.002	0.001	0.002
extractDrugHBondAcceptorCount	0.001	0.001	0.002
extractDrugHBondDonorCount	0.001	0.000	0.002
extractDrugHybridization	0.002	0.001	0.003
extractDrugHybridizationComplete	0.001	0.000	0.003
extractDrugHybridizationRatio	0.002	0.001	0.003
extractDrugIPMolecularLearning	0.001	0.001	0.002
extractDrugKR	0.002	0.001	0.002
extractDrugKRComplete	0.001	0.001	0.002
extractDrugKappaShapeIndices	0.002	0.001	0.002
extractDrugKierHallSmarts	0.001	0.001	0.002
extractDrugLargestChain	0.002	0.000	0.002
extractDrugLargestPiSystem	0.001	0.001	0.002
extractDrugLengthOverBreadth	0.002	0.000	0.002
extractDrugLongestAliphaticChain	0.001	0.001	0.002
extractDrugMACCS	0.002	0.001	0.002
extractDrugMACCSComplete	0.001	0.000	0.003
extractDrugMDE	0.002	0.001	0.002
extractDrugMannholdLogP	0.001	0.000	0.002
extractDrugMomentOfInertia	0.002	0.001	0.002
extractDrugOBFP2	0.011	0.007	0.018
extractDrugOBFP3	0.020	0.009	0.029
extractDrugOBFP4	0.011	0.006	0.018
extractDrugOBMACCS	0.011	0.006	0.017
extractDrugPetitjeanNumber	0.001	0.001	0.002
extractDrugPetitjeanShapeIndex	0.002	0.001	0.003
extractDrugPubChem	0.001	0.000	0.002
extractDrugPubChemComplete	0.002	0.001	0.002
extractDrugRotatableBondsCount	0.001	0.001	0.002
extractDrugRuleOfFive	0.002	0.001	0.003
extractDrugShortestPath	0.002	0.001	0.003
extractDrugShortestPathComplete	0.001	0.000	0.002
extractDrugStandard	0.001	0.001	0.002
extractDrugStandardComplete	0.002	0.001	0.002
extractDrugTPSA	0.001	0.001	0.003
extractDrugVABC	0.002	0.000	0.002
extractDrugVAdjMa	0.002	0.001	0.002
extractDrugWHIM	0.001	0.000	0.002
extractDrugWeight	0.002	0.001	0.002
extractDrugWeightedPath	0.001	0.000	0.002
extractDrugWienerNumbers	0.001	0.001	0.003
extractDrugXLogP	0.002	0.000	0.002
extractDrugZagrebIndex	0.001	0.001	0.002
extractPCMBLOSUM	0.111	0.006	0.118
extractPCMDescScales	0.020	0.003	0.024
extractPCMFAScales	0.030	0.007	0.039
extractPCMMDSScales	0.018	0.006	0.024
extractPCMPropScales	0.020	0.004	0.025
extractPCMScales	0.044	0.007	0.053
extractProtAAC	0.004	0.002	0.006
extractProtAPAAC	1.814	0.047	1.881
extractProtCTDC	0.004	0.002	0.007
extractProtCTDD	0.008	0.005	0.014
extractProtCTDT	0.009	0.002	0.012
extractProtCTriad	0.191	0.023	0.218
extractProtDC	0.007	0.012	0.020
extractProtGeary	0.327	0.031	0.361
extractProtMoran	0.291	0.021	0.316
extractProtMoreauBroto	0.294	0.019	0.315
extractProtPAAC	1.212	0.011	1.246
extractProtPSSM	0.002	0.001	0.003
extractProtPSSMAcc	0.002	0.001	0.003
extractProtPSSMFeature	0.002	0.001	0.004
extractProtQSO	2.280	0.024	2.328
extractProtSOCN	2.253	0.017	2.292
extractProtTC	0.092	0.252	0.350
getCPI	0.005	0.004	0.008
getDrug	0.000	0.000	0.001
getFASTAFromKEGG	0	0	0
getFASTAFromUniProt	0	0	0
getMolFromCAS	0.001	0.000	0.000
getMolFromChEMBL	0.000	0.000	0.001
getMolFromDrugBank	0.000	0.000	0.001
getMolFromKEGG	0	0	0
getMolFromPubChem	0.000	0.000	0.001
getPDBFromRCSBPDB	0	0	0
getPPI	0.004	0.004	0.008
getProt	0.000	0.000	0.001
getSeqFromKEGG	0.000	0.000	0.001
getSeqFromRCSBPDB	0.001	0.000	0.001
getSeqFromUniProt	0.000	0.000	0.001
getSmiFromChEMBL	0.000	0.000	0.001
getSmiFromDrugBank	0.000	0.001	0.000
getSmiFromKEGG	0.000	0.001	0.000
getSmiFromPubChem	0.000	0.001	0.001
readFASTA	0.002	0.001	0.003
readMolFromSDF	0.004	0.002	0.006
readMolFromSmi	0.001	0.000	0.003
readPDB	1.609	0.009	1.673
searchDrug	0.003	0.001	0.004
segProt	0.004	0.004	0.008