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	R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"	4676
palomino3	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences"	4414
merida1	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"	4441
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences"	4417
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*

Package: Rcpi

Version: 1.39.0

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_1.39.0.tar.gz

StartedAt: 2024-03-02 09:10:38 -0500 (Sat, 02 Mar 2024)

EndedAt: 2024-03-02 09:16:55 -0500 (Sat, 02 Mar 2024)

EllapsedTime: 376.1 seconds

RetCode: 0

Status: OK

CheckDir: Rcpi.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.39.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Rcpi.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.39.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 R 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/Rcpi.Rcheck/00check.log’
for details.

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rcpi
###
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* 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)


R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
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 
 12.683   1.109  43.337

name	user	system	elapsed
AA2DACOR	0.003	0.003	0.011
AA3DMoRSE	0.002	0.002	0.005
AAACF	0.002	0.003	0.003
AABLOSUM100	0.002	0.002	0.005
AABLOSUM45	0.002	0.002	0.004
AABLOSUM50	0.001	0.002	0.005
AABLOSUM62	0.002	0.002	0.004
AABLOSUM80	0.001	0.002	0.004
AABurden	0.002	0.001	0.003
AACPSA	0.001	0.002	0.004
AAConn	0.002	0.002	0.003
AAConst	0.001	0.003	0.004
AADescAll	0.002	0.003	0.005
AAEdgeAdj	0.002	0.002	0.006
AAEigIdx	0.001	0.002	0.004
AAFGC	0.002	0.002	0.004
AAGETAWAY	0.002	0.003	0.004
AAGeom	0.001	0.002	0.006
AAInfo	0.002	0.003	0.006
AAMOE2D	0.001	0.003	0.005
AAMOE3D	0.002	0.003	0.004
AAMetaInfo	0.001	0.003	0.006
AAMolProp	0.002	0.002	0.003
AAPAM120	0.001	0.002	0.006
AAPAM250	0.002	0.002	0.007
AAPAM30	0.002	0.002	0.005
AAPAM40	0.001	0.002	0.005
AAPAM70	0.002	0.002	0.004
AARDF	0.001	0.003	0.009
AARandic	0.002	0.002	0.005
AATopo	0.002	0.003	0.004
AATopoChg	0.001	0.003	0.005
AAWHIM	0.002	0.002	0.003
AAWalk	0.001	0.002	0.006
AAindex	0.002	0.002	0.004
OptAA3d	0.000	0.000	0.001
acc	0.017	0.018	0.039
calcDrugFPSim	0	0	0
calcDrugMCSSim	0.007	0.006	0.022
calcParProtGOSim	0.001	0.001	0.001
calcParProtSeqSim	0.011	0.004	0.024
calcTwoProtGOSim	0.000	0.001	0.001
calcTwoProtSeqSim	0.004	0.002	0.006
checkProt	0.002	0.001	0.004
convMolFormat	0.002	0.001	0.004
extractDrugAIO	0.001	0.001	0.003
extractDrugALOGP	0.001	0.001	0.003
extractDrugAminoAcidCount	0.002	0.001	0.002
extractDrugApol	0.001	0.001	0.002
extractDrugAromaticAtomsCount	0.001	0.001	0.004
extractDrugAromaticBondsCount	0.002	0.000	0.003
extractDrugAtomCount	0.001	0.001	0.002
extractDrugAutocorrelationCharge	0.001	0.001	0.002
extractDrugAutocorrelationMass	0.002	0.001	0.002
extractDrugAutocorrelationPolarizability	0.001	0.001	0.004
extractDrugBCUT	0.001	0.001	0.002
extractDrugBPol	0.002	0.001	0.002
extractDrugBondCount	0.001	0.001	0.005
extractDrugCPSA	0.001	0.001	0.003
extractDrugCarbonTypes	0.002	0.001	0.003
extractDrugChiChain	0.001	0.001	0.002
extractDrugChiCluster	0.001	0.000	0.002
extractDrugChiPath	0.002	0.001	0.004
extractDrugChiPathCluster	0.001	0.001	0.002
extractDrugDescOB	0.020	0.009	0.039
extractDrugECI	0.001	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	0.001	0.003
extractDrugFMF	0.001	0.001	0.002
extractDrugFragmentComplexity	0.001	0.001	0.005
extractDrugGraph	0.002	0.000	0.004
extractDrugGraphComplete	0.001	0.001	0.003
extractDrugGravitationalIndex	0.002	0.001	0.002
extractDrugHBondAcceptorCount	0.001	0.001	0.003
extractDrugHBondDonorCount	0.001	0.001	0.003
extractDrugHybridization	0.002	0.001	0.004
extractDrugHybridizationComplete	0.001	0.001	0.002
extractDrugHybridizationRatio	0.001	0.000	0.002
extractDrugIPMolecularLearning	0.002	0.001	0.002
extractDrugKR	0.001	0.001	0.006
extractDrugKRComplete	0.002	0.001	0.002
extractDrugKappaShapeIndices	0.001	0.001	0.004
extractDrugKierHallSmarts	0.002	0.001	0.003
extractDrugLargestChain	0.001	0.001	0.002
extractDrugLargestPiSystem	0.002	0.001	0.003
extractDrugLengthOverBreadth	0.001	0.001	0.004
extractDrugLongestAliphaticChain	0.002	0.001	0.004
extractDrugMACCS	0.002	0.000	0.002
extractDrugMACCSComplete	0.001	0.001	0.002
extractDrugMDE	0.001	0.000	0.002
extractDrugMannholdLogP	0.002	0.001	0.002
extractDrugMomentOfInertia	0.002	0.000	0.002
extractDrugOBFP2	0.010	0.007	0.018
extractDrugOBFP3	0.018	0.006	0.027
extractDrugOBFP4	0.010	0.006	0.019
extractDrugOBMACCS	0.107	0.011	0.150
extractDrugPetitjeanNumber	0.001	0.000	0.003
extractDrugPetitjeanShapeIndex	0.002	0.001	0.002
extractDrugPubChem	0.001	0.001	0.002
extractDrugPubChemComplete	0.002	0.000	0.003
extractDrugRotatableBondsCount	0.001	0.001	0.002
extractDrugRuleOfFive	0.002	0.000	0.002
extractDrugShortestPath	0.001	0.001	0.004
extractDrugShortestPathComplete	0.002	0.000	0.002
extractDrugStandard	0.001	0.001	0.002
extractDrugStandardComplete	0.001	0.000	0.002
extractDrugTPSA	0.002	0.001	0.002
extractDrugVABC	0.001	0.001	0.004
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	0.001	0.001	0.003
extractDrugXLogP	0.002	0.000	0.002
extractDrugZagrebIndex	0.001	0.001	0.004
extractPCMBLOSUM	0.017	0.003	0.024
extractPCMDescScales	0.020	0.003	0.026
extractPCMFAScales	0.030	0.008	0.047
extractPCMMDSScales	0.018	0.005	0.028
extractPCMPropScales	0.029	0.004	0.039
extractPCMScales	0.030	0.005	0.044
extractProtAAC	0.004	0.002	0.006
extractProtAPAAC	1.715	0.065	2.180
extractProtCTDC	0.005	0.001	0.006
extractProtCTDD	0.008	0.004	0.015
extractProtCTDT	0.009	0.002	0.011
extractProtCTriad	0.189	0.025	0.256
extractProtDC	0.008	0.013	0.026
extractProtGeary	0.299	0.026	0.418
extractProtMoran	0.290	0.027	0.434
extractProtMoreauBroto	0.292	0.024	0.417
extractProtPAAC	1.189	0.023	1.693
extractProtPSSM	0.001	0.001	0.003
extractProtPSSMAcc	0.002	0.001	0.003
extractProtPSSMFeature	0.002	0.001	0.003
extractProtQSO	2.168	0.041	2.931
extractProtSOCN	2.115	0.027	2.796
extractProtTC	0.086	0.246	0.450
getCPI	0.005	0.003	0.008
getDrug	0	0	0
getFASTAFromKEGG	0.001	0.001	0.001
getFASTAFromUniProt	0.000	0.001	0.001
getMolFromCAS	0.000	0.001	0.000
getMolFromChEMBL	0	0	0
getMolFromDrugBank	0.000	0.001	0.000
getMolFromKEGG	0.000	0.001	0.000
getMolFromPubChem	0.000	0.001	0.000
getPDBFromRCSBPDB	0.001	0.001	0.001
getPPI	0.005	0.005	0.013
getProt	0.000	0.000	0.001
getSeqFromKEGG	0.000	0.000	0.001
getSeqFromRCSBPDB	0.000	0.001	0.001
getSeqFromUniProt	0.000	0.001	0.000
getSmiFromChEMBL	0.000	0.000	0.001
getSmiFromDrugBank	0.001	0.000	0.001
getSmiFromKEGG	0	0	0
getSmiFromPubChem	0	0	0
readFASTA	0.002	0.001	0.003
readMolFromSDF	0.003	0.002	0.008
readMolFromSmi	0.002	0.001	0.002
readPDB	1.488	0.019	1.948
searchDrug	0.003	0.002	0.008
segProt	0.004	0.004	0.012

CHECK results for Rcpi on merida1

Summary

Command output

Installation output

Tests output

Example timings