Multiple platform build/check report for BioC 3.19 - CHECK results for Rcpi on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4763
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4500
merida1	macOS 12.7.5 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4530
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4480
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: 1.40.3

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_1.40.3.tar.gz

StartedAt: 2024-10-17 11:33:20 -0400 (Thu, 17 Oct 2024)

EndedAt: 2024-10-17 11:38:19 -0400 (Thu, 17 Oct 2024)

EllapsedTime: 299.1 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_1.40.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Rcpi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘1.40.3’
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 
 13.442   1.034  14.850

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

name	user	system	elapsed
AA2DACOR	0.003	0.003	0.007
AA3DMoRSE	0.002	0.002	0.007
AAACF	0.001	0.003	0.005
AABLOSUM100	0.001	0.002	0.005
AABLOSUM45	0.002	0.002	0.005
AABLOSUM50	0.002	0.002	0.004
AABLOSUM62	0.002	0.002	0.004
AABLOSUM80	0.001	0.002	0.004
AABurden	0.002	0.002	0.004
AACPSA	0.001	0.002	0.003
AAConn	0.002	0.002	0.004
AAConst	0.002	0.002	0.004
AADescAll	0.002	0.002	0.004
AAEdgeAdj	0.002	0.002	0.004
AAEigIdx	0.001	0.003	0.015
AAFGC	0.001	0.002	0.004
AAGETAWAY	0.002	0.002	0.008
AAGeom	0.002	0.002	0.005
AAInfo	0.002	0.002	0.009
AAMOE2D	0.001	0.002	0.004
AAMOE3D	0.002	0.002	0.004
AAMetaInfo	0.002	0.002	0.003
AAMolProp	0.001	0.002	0.004
AAPAM120	0.002	0.002	0.003
AAPAM250	0.001	0.002	0.004
AAPAM30	0.002	0.002	0.003
AAPAM40	0.002	0.002	0.004
AAPAM70	0.001	0.003	0.004
AARDF	0.002	0.002	0.003
AARandic	0.001	0.002	0.004
AATopo	0.002	0.002	0.004
AATopoChg	0.002	0.003	0.005
AAWHIM	0.002	0.002	0.004
AAWalk	0.001	0.002	0.004
AAindex	0.002	0.002	0.003
OptAA3d	0.000	0.001	0.002
acc	0.018	0.020	0.064
calcDrugFPSim	0.000	0.001	0.001
calcDrugMCSSim	0.006	0.007	0.015
calcParProtGOSim	0.001	0.001	0.001
calcParProtSeqSim	0.011	0.005	0.019
calcTwoProtGOSim	0.000	0.001	0.002
calcTwoProtSeqSim	0.004	0.002	0.005
checkProt	0.002	0.001	0.004
convMolFormat	0.002	0.002	0.005
extractDrugAIO	0.001	0.001	0.002
extractDrugALOGP	0.002	0.001	0.004
extractDrugAminoAcidCount	0.001	0.001	0.003
extractDrugApol	0.001	0.001	0.002
extractDrugAromaticAtomsCount	0.002	0.000	0.002
extractDrugAromaticBondsCount	0.001	0.001	0.004
extractDrugAtomCount	0.002	0.001	0.003
extractDrugAutocorrelationCharge	0.001	0.001	0.004
extractDrugAutocorrelationMass	0.002	0.001	0.003
extractDrugAutocorrelationPolarizability	0.002	0.001	0.004
extractDrugBCUT	0.001	0.001	0.002
extractDrugBPol	0.002	0.001	0.002
extractDrugBondCount	0.001	0.001	0.003
extractDrugCPSA	0.002	0.001	0.002
extractDrugCarbonTypes	0.001	0.001	0.003
extractDrugChiChain	0.002	0.001	0.004
extractDrugChiCluster	0.001	0.000	0.002
extractDrugChiPath	0.002	0.001	0.002
extractDrugChiPathCluster	0.001	0.001	0.002
extractDrugDescOB	0.020	0.009	0.056
extractDrugECI	0.002	0.000	0.003
extractDrugEstate	0.002	0.001	0.003
extractDrugEstateComplete	0.001	0.001	0.003
extractDrugExtended	0.002	0.001	0.002
extractDrugExtendedComplete	0.001	0.001	0.002
extractDrugFMF	0.002	0.001	0.003
extractDrugFragmentComplexity	0.001	0.001	0.002
extractDrugGraph	0.002	0.000	0.003
extractDrugGraphComplete	0.002	0.001	0.002
extractDrugGravitationalIndex	0.002	0.001	0.003
extractDrugHBondAcceptorCount	0.001	0.001	0.002
extractDrugHBondDonorCount	0.001	0.001	0.003
extractDrugHybridization	0.001	0.001	0.002
extractDrugHybridizationComplete	0.002	0.001	0.002
extractDrugHybridizationRatio	0.001	0.001	0.003
extractDrugIPMolecularLearning	0.002	0.001	0.002
extractDrugKR	0.001	0.000	0.002
extractDrugKRComplete	0.002	0.001	0.003
extractDrugKappaShapeIndices	0.002	0.001	0.003
extractDrugKierHallSmarts	0.001	0.001	0.002
extractDrugLargestChain	0.001	0.001	0.002
extractDrugLargestPiSystem	0.002	0.001	0.003
extractDrugLengthOverBreadth	0.001	0.000	0.003
extractDrugLongestAliphaticChain	0.002	0.001	0.003
extractDrugMACCS	0.001	0.001	0.003
extractDrugMACCSComplete	0.002	0.000	0.002
extractDrugMDE	0.001	0.001	0.002
extractDrugMannholdLogP	0.002	0.001	0.002
extractDrugMomentOfInertia	0.001	0.000	0.003
extractDrugOBFP2	0.011	0.007	0.023
extractDrugOBFP3	0.011	0.003	0.014
extractDrugOBFP4	0.010	0.004	0.024
extractDrugOBMACCS	0.011	0.006	0.023
extractDrugPetitjeanNumber	0.002	0.001	0.003
extractDrugPetitjeanShapeIndex	0.001	0.001	0.010
extractDrugPubChem	0.002	0.001	0.010
extractDrugPubChemComplete	0.001	0.000	0.002
extractDrugRotatableBondsCount	0.002	0.001	0.002
extractDrugRuleOfFive	0.001	0.001	0.003
extractDrugShortestPath	0.002	0.001	0.002
extractDrugShortestPathComplete	0.001	0.001	0.002
extractDrugStandard	0.002	0.001	0.002
extractDrugStandardComplete	0.001	0.001	0.003
extractDrugTPSA	0.002	0.001	0.002
extractDrugVABC	0.001	0.000	0.002
extractDrugVAdjMa	0.002	0.001	0.002
extractDrugWHIM	0.001	0.001	0.003
extractDrugWeight	0.002	0.001	0.003
extractDrugWeightedPath	0.001	0.001	0.002
extractDrugWienerNumbers	0.002	0.001	0.003
extractDrugXLogP	0.001	0.001	0.002
extractDrugZagrebIndex	0.002	0.001	0.003
extractPCMBLOSUM	0.120	0.008	0.154
extractPCMDescScales	0.021	0.003	0.026
extractPCMFAScales	0.031	0.008	0.049
extractPCMMDSScales	0.018	0.005	0.030
extractPCMPropScales	0.021	0.003	0.030
extractPCMScales	0.042	0.007	0.055
extractProtAAC	0.003	0.001	0.008
extractProtAPAAC	1.838	0.056	2.225
extractProtCTDC	0.004	0.002	0.007
extractProtCTDD	0.008	0.006	0.017
extractProtCTDT	0.010	0.002	0.018
extractProtCTriad	0.196	0.025	0.313
extractProtDC	0.007	0.012	0.019
extractProtGeary	0.306	0.025	0.386
extractProtMoran	0.297	0.026	0.362
extractProtMoreauBroto	0.303	0.024	0.385
extractProtPAAC	1.242	0.021	1.453
extractProtPSSM	0.003	0.001	0.003
extractProtPSSMAcc	0.002	0.001	0.004
extractProtPSSMFeature	0.002	0.001	0.004
extractProtQSO	2.327	0.036	2.786
extractProtSOCN	2.267	0.020	2.571
extractProtTC	0.089	0.249	0.386
getCPI	0.005	0.004	0.009
getDrug	0	0	0
getFASTAFromKEGG	0	0	0
getFASTAFromUniProt	0	0	0
getMolFromCAS	0.001	0.000	0.000
getMolFromChEMBL	0.001	0.000	0.000
getMolFromDrugBank	0.000	0.000	0.001
getMolFromKEGG	0.000	0.000	0.001
getMolFromPubChem	0.000	0.000	0.001
getPDBFromRCSBPDB	0	0	0
getPPI	0.005	0.006	0.012
getProt	0.000	0.001	0.001
getSeqFromKEGG	0.000	0.000	0.001
getSeqFromRCSBPDB	0	0	0
getSeqFromUniProt	0	0	0
getSmiFromChEMBL	0	0	0
getSmiFromDrugBank	0	0	0
getSmiFromKEGG	0	0	0
getSmiFromPubChem	0.000	0.001	0.001
readFASTA	0.002	0.001	0.003
readMolFromSDF	0.004	0.002	0.006
readMolFromSmi	0.001	0.001	0.003
readPDB	1.538	0.014	1.815
searchDrug	0.003	0.001	0.004
segProt	0.004	0.004	0.008