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"	4746
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4493
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4517
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4469
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4394
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: 2025-01-21 08:51:36 -0500 (Tue, 21 Jan 2025)

EndedAt: 2025-01-21 08:56:05 -0500 (Tue, 21 Jan 2025)

EllapsedTime: 268.6 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 
 13.223   1.036  13.149

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

name	user	system	elapsed
AA2DACOR	0.004	0.002	0.006
AA3DMoRSE	0.002	0.002	0.004
AAACF	0.002	0.003	0.005
AABLOSUM100	0.001	0.002	0.004
AABLOSUM45	0.002	0.002	0.003
AABLOSUM50	0.001	0.002	0.005
AABLOSUM62	0.002	0.002	0.004
AABLOSUM80	0.001	0.002	0.004
AABurden	0.002	0.002	0.004
AACPSA	0.002	0.002	0.003
AAConn	0.001	0.002	0.004
AAConst	0.002	0.002	0.004
AADescAll	0.001	0.002	0.003
AAEdgeAdj	0.002	0.002	0.004
AAEigIdx	0.001	0.002	0.004
AAFGC	0.002	0.002	0.003
AAGETAWAY	0.001	0.002	0.003
AAGeom	0.002	0.002	0.004
AAInfo	0.001	0.002	0.004
AAMOE2D	0.002	0.002	0.004
AAMOE3D	0.001	0.002	0.004
AAMetaInfo	0.002	0.003	0.004
AAMolProp	0.002	0.002	0.004
AAPAM120	0.001	0.002	0.004
AAPAM250	0.002	0.002	0.005
AAPAM30	0.001	0.002	0.004
AAPAM40	0.002	0.002	0.004
AAPAM70	0.002	0.002	0.004
AARDF	0.001	0.002	0.004
AARandic	0.002	0.002	0.003
AATopo	0.001	0.002	0.003
AATopoChg	0.002	0.002	0.004
AAWHIM	0.002	0.002	0.005
AAWalk	0.002	0.002	0.003
AAindex	0.001	0.002	0.004
OptAA3d	0.000	0.001	0.001
acc	0.018	0.016	0.034
calcDrugFPSim	0	0	0
calcDrugMCSSim	0.006	0.006	0.013
calcParProtGOSim	0.001	0.000	0.000
calcParProtSeqSim	0.010	0.004	0.015
calcTwoProtGOSim	0.000	0.001	0.001
calcTwoProtSeqSim	0.004	0.002	0.005
checkProt	0.002	0.001	0.004
convMolFormat	0.002	0.001	0.002
extractDrugAIO	0.001	0.001	0.002
extractDrugALOGP	0.001	0.001	0.002
extractDrugAminoAcidCount	0.002	0.001	0.003
extractDrugApol	0.001	0.001	0.002
extractDrugAromaticAtomsCount	0.002	0.001	0.002
extractDrugAromaticBondsCount	0.001	0.001	0.002
extractDrugAtomCount	0.001	0.000	0.002
extractDrugAutocorrelationCharge	0.002	0.001	0.002
extractDrugAutocorrelationMass	0.001	0.001	0.002
extractDrugAutocorrelationPolarizability	0.002	0.001	0.003
extractDrugBCUT	0.001	0.001	0.002
extractDrugBPol	0.001	0.001	0.002
extractDrugBondCount	0.002	0.001	0.002
extractDrugCPSA	0.001	0.000	0.002
extractDrugCarbonTypes	0.001	0.001	0.002
extractDrugChiChain	0.002	0.000	0.003
extractDrugChiCluster	0.001	0.001	0.003
extractDrugChiPath	0.001	0.000	0.002
extractDrugChiPathCluster	0.002	0.001	0.003
extractDrugDescOB	0.020	0.008	0.047
extractDrugECI	0.002	0.001	0.003
extractDrugEstate	0.002	0.001	0.002
extractDrugEstateComplete	0.001	0.001	0.002
extractDrugExtended	0.001	0.001	0.002
extractDrugExtendedComplete	0.002	0.000	0.002
extractDrugFMF	0.001	0.001	0.002
extractDrugFragmentComplexity	0.002	0.001	0.002
extractDrugGraph	0.001	0.001	0.003
extractDrugGraphComplete	0.001	0.001	0.002
extractDrugGravitationalIndex	0.002	0.000	0.005
extractDrugHBondAcceptorCount	0.001	0.001	0.003
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	0.001	0.000	0.002
extractDrugKR	0.002	0.001	0.003
extractDrugKRComplete	0.001	0.001	0.003
extractDrugKappaShapeIndices	0.002	0.001	0.002
extractDrugKierHallSmarts	0.002	0.001	0.002
extractDrugLargestChain	0.001	0.001	0.003
extractDrugLargestPiSystem	0.002	0.001	0.003
extractDrugLengthOverBreadth	0.001	0.001	0.003
extractDrugLongestAliphaticChain	0.001	0.001	0.002
extractDrugMACCS	0.002	0.000	0.002
extractDrugMACCSComplete	0.001	0.001	0.002
extractDrugMDE	0.002	0.000	0.002
extractDrugMannholdLogP	0.001	0.001	0.003
extractDrugMomentOfInertia	0.001	0.001	0.002
extractDrugOBFP2	0.011	0.006	0.020
extractDrugOBFP3	0.018	0.009	0.028
extractDrugOBFP4	0.010	0.004	0.015
extractDrugOBMACCS	0.011	0.005	0.017
extractDrugPetitjeanNumber	0.002	0.001	0.002
extractDrugPetitjeanShapeIndex	0.001	0.001	0.002
extractDrugPubChem	0.002	0.000	0.002
extractDrugPubChemComplete	0.001	0.001	0.002
extractDrugRotatableBondsCount	0.001	0.001	0.003
extractDrugRuleOfFive	0.001	0.001	0.003
extractDrugShortestPath	0.002	0.001	0.002
extractDrugShortestPathComplete	0.001	0.001	0.003
extractDrugStandard	0.002	0.001	0.003
extractDrugStandardComplete	0.001	0.001	0.002
extractDrugTPSA	0.002	0.001	0.004
extractDrugVABC	0.001	0.001	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	0.001	0.002
extractDrugWienerNumbers	0.002	0.001	0.002
extractDrugXLogP	0.001	0.001	0.002
extractDrugZagrebIndex	0.002	0.001	0.002
extractPCMBLOSUM	0.105	0.007	0.116
extractPCMDescScales	0.020	0.003	0.029
extractPCMFAScales	0.030	0.007	0.039
extractPCMMDSScales	0.018	0.006	0.025
extractPCMPropScales	0.021	0.003	0.028
extractPCMScales	0.043	0.008	0.053
extractProtAAC	0.004	0.001	0.006
extractProtAPAAC	1.804	0.052	2.026
extractProtCTDC	0.004	0.001	0.005
extractProtCTDD	0.008	0.004	0.012
extractProtCTDT	0.009	0.002	0.011
extractProtCTriad	0.193	0.027	0.223
extractProtDC	0.008	0.014	0.023
extractProtGeary	0.306	0.029	0.349
extractProtMoran	0.298	0.023	0.341
extractProtMoreauBroto	0.300	0.020	0.355
extractProtPAAC	1.243	0.020	1.353
extractProtPSSM	0.002	0.001	0.003
extractProtPSSMAcc	0.001	0.001	0.003
extractProtPSSMFeature	0.002	0.001	0.003
extractProtQSO	2.271	0.029	2.434
extractProtSOCN	2.267	0.018	2.384
extractProtTC	0.090	0.245	0.349
getCPI	0.005	0.003	0.008
getDrug	0	0	0
getFASTAFromKEGG	0	0	0
getFASTAFromUniProt	0	0	0
getMolFromCAS	0	0	0
getMolFromChEMBL	0.000	0.000	0.001
getMolFromDrugBank	0.000	0.000	0.001
getMolFromKEGG	0.000	0.000	0.001
getMolFromPubChem	0.001	0.000	0.000
getPDBFromRCSBPDB	0.001	0.000	0.000
getPPI	0.005	0.005	0.010
getProt	0.000	0.001	0.000
getSeqFromKEGG	0.000	0.001	0.000
getSeqFromRCSBPDB	0.000	0.001	0.001
getSeqFromUniProt	0.001	0.001	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	0.003
readMolFromSDF	0.004	0.001	0.005
readMolFromSmi	0.001	0.001	0.003
readPDB	1.645	0.010	1.737
searchDrug	0.002	0.001	0.004
segProt	0.004	0.004	0.009