Multiple platform build/check report for BioC 3.18 - CHECK results for Rcpi on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4676
palomino4	Windows Server 2022 Datacenter	x64	4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"	4414
merida1	macOS 12.7.1 Monterey	x86_64	4.3.3 (2024-02-29) -- "Angel Food Cake"	4437
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: 1.38.0

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_1.38.0.tar.gz

StartedAt: 2024-04-16 07:30:47 -0400 (Tue, 16 Apr 2024)

EndedAt: 2024-04-16 07:35:00 -0400 (Tue, 16 Apr 2024)

EllapsedTime: 253.3 seconds

RetCode: 0

Status: OK

CheckDir: Rcpi.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### 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_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/Rcpi.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 ‘1.38.0’
* 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 in ‘inst/doc’ ... 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-3.18-bioc/meat/Rcpi.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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 version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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 
 13.260   0.935  13.272

name	user	system	elapsed
AA2DACOR	0.003	0.002	0.005
AA3DMoRSE	0.002	0.002	0.004
AAACF	0.002	0.002	0.004
AABLOSUM100	0.002	0.003	0.004
AABLOSUM45	0.001	0.002	0.004
AABLOSUM50	0.002	0.002	0.003
AABLOSUM62	0.001	0.002	0.003
AABLOSUM80	0.002	0.002	0.004
AABurden	0.002	0.002	0.005
AACPSA	0.002	0.002	0.004
AAConn	0.001	0.002	0.004
AAConst	0.002	0.002	0.003
AADescAll	0.002	0.002	0.003
AAEdgeAdj	0.001	0.002	0.004
AAEigIdx	0.002	0.002	0.005
AAFGC	0.001	0.002	0.004
AAGETAWAY	0.002	0.002	0.004
AAGeom	0.001	0.002	0.004
AAInfo	0.002	0.003	0.004
AAMOE2D	0.001	0.002	0.003
AAMOE3D	0.002	0.002	0.004
AAMetaInfo	0.001	0.002	0.005
AAMolProp	0.002	0.003	0.004
AAPAM120	0.001	0.002	0.003
AAPAM250	0.002	0.003	0.004
AAPAM30	0.001	0.002	0.003
AAPAM40	0.001	0.002	0.004
AAPAM70	0.002	0.002	0.003
AARDF	0.001	0.002	0.004
AARandic	0.002	0.002	0.004
AATopo	0.002	0.002	0.004
AATopoChg	0.002	0.002	0.005
AAWHIM	0.002	0.002	0.004
AAWalk	0.001	0.002	0.003
AAindex	0.002	0.002	0.004
OptAA3d	0	0	0
acc	0.018	0.018	0.036
calcDrugFPSim	0.000	0.001	0.000
calcDrugMCSSim	0.027	0.007	0.038
calcParProtGOSim	0.001	0.000	0.001
calcParProtSeqSim	0.011	0.005	0.034
calcTwoProtGOSim	0.000	0.001	0.000
calcTwoProtSeqSim	0.004	0.002	0.005
checkProt	0.002	0.001	0.003
convMolFormat	0.001	0.001	0.003
extractDrugAIO	0.002	0.001	0.002
extractDrugALOGP	0.001	0.001	0.002
extractDrugAminoAcidCount	0.002	0.001	0.002
extractDrugApol	0.001	0.001	0.002
extractDrugAromaticAtomsCount	0.001	0.001	0.004
extractDrugAromaticBondsCount	0.002	0.001	0.002
extractDrugAtomCount	0.001	0.001	0.003
extractDrugAutocorrelationCharge	0.002	0.001	0.002
extractDrugAutocorrelationMass	0.001	0.000	0.002
extractDrugAutocorrelationPolarizability	0.001	0.001	0.003
extractDrugBCUT	0.002	0.001	0.002
extractDrugBPol	0.001	0.001	0.002
extractDrugBondCount	0.001	0.001	0.003
extractDrugCPSA	0.002	0.000	0.002
extractDrugCarbonTypes	0.001	0.001	0.002
extractDrugChiChain	0.001	0.001	0.003
extractDrugChiCluster	0.001	0.001	0.003
extractDrugChiPath	0.002	0.001	0.003
extractDrugChiPathCluster	0.001	0.001	0.002
extractDrugDescOB	0.010	0.006	0.021
extractDrugECI	0.001	0.000	0.002
extractDrugEstate	0.001	0.001	0.002
extractDrugEstateComplete	0.002	0.001	0.002
extractDrugExtended	0.002	0.001	0.002
extractDrugExtendedComplete	0.001	0.001	0.002
extractDrugFMF	0.001	0.001	0.003
extractDrugFragmentComplexity	0.002	0.001	0.004
extractDrugGraph	0.001	0.001	0.002
extractDrugGraphComplete	0.002	0.001	0.003
extractDrugGravitationalIndex	0.001	0.001	0.003
extractDrugHBondAcceptorCount	0.002	0.000	0.003
extractDrugHBondDonorCount	0.001	0.001	0.003
extractDrugHybridization	0.001	0.001	0.003
extractDrugHybridizationComplete	0.002	0.001	0.002
extractDrugHybridizationRatio	0.001	0.001	0.002
extractDrugIPMolecularLearning	0.002	0.001	0.003
extractDrugKR	0.002	0.001	0.009
extractDrugKRComplete	0.002	0.001	0.003
extractDrugKappaShapeIndices	0.002	0.001	0.002
extractDrugKierHallSmarts	0.002	0.001	0.004
extractDrugLargestChain	0.001	0.001	0.008
extractDrugLargestPiSystem	0.002	0.001	0.002
extractDrugLengthOverBreadth	0.001	0.000	0.026
extractDrugLongestAliphaticChain	0.001	0.001	0.002
extractDrugMACCS	0.002	0.000	0.002
extractDrugMACCSComplete	0.001	0.001	0.003
extractDrugMDE	0.002	0.001	0.003
extractDrugMannholdLogP	0.001	0.001	0.002
extractDrugMomentOfInertia	0.001	0.001	0.002
extractDrugOBFP2	0.020	0.009	0.031
extractDrugOBFP3	0.010	0.006	0.016
extractDrugOBFP4	0.101	0.010	0.115
extractDrugOBMACCS	0.011	0.007	0.017
extractDrugPetitjeanNumber	0.001	0.001	0.002
extractDrugPetitjeanShapeIndex	0.002	0.001	0.002
extractDrugPubChem	0.001	0.001	0.002
extractDrugPubChemComplete	0.001	0.001	0.003
extractDrugRotatableBondsCount	0.002	0.001	0.002
extractDrugRuleOfFive	0.001	0.001	0.002
extractDrugShortestPath	0.001	0.000	0.002
extractDrugShortestPathComplete	0.002	0.001	0.002
extractDrugStandard	0.001	0.000	0.002
extractDrugStandardComplete	0.001	0.001	0.002
extractDrugTPSA	0.002	0.000	0.002
extractDrugVABC	0.001	0.001	0.002
extractDrugVAdjMa	0.002	0.001	0.002
extractDrugWHIM	0.001	0.001	0.003
extractDrugWeight	0.001	0.001	0.003
extractDrugWeightedPath	0.002	0.001	0.002
extractDrugWienerNumbers	0.001	0.000	0.002
extractDrugXLogP	0.002	0.001	0.002
extractDrugZagrebIndex	0.001	0.000	0.002
extractPCMBLOSUM	0.017	0.003	0.021
extractPCMDescScales	0.019	0.003	0.023
extractPCMFAScales	0.038	0.008	0.048
extractPCMMDSScales	0.016	0.004	0.022
extractPCMPropScales	0.020	0.003	0.023
extractPCMScales	0.030	0.006	0.037
extractProtAAC	0.004	0.002	0.006
extractProtAPAAC	1.728	0.061	1.865
extractProtCTDC	0.004	0.002	0.007
extractProtCTDD	0.008	0.005	0.013
extractProtCTDT	0.009	0.002	0.011
extractProtCTriad	0.186	0.022	0.219
extractProtDC	0.007	0.013	0.021
extractProtGeary	0.278	0.026	0.322
extractProtMoran	0.292	0.026	0.334
extractProtMoreauBroto	0.282	0.023	0.317
extractProtPAAC	1.093	0.017	1.139
extractProtPSSM	0.002	0.001	0.003
extractProtPSSMAcc	0.002	0.001	0.003
extractProtPSSMFeature	0.001	0.001	0.002
extractProtQSO	2.051	0.030	2.187
extractProtSOCN	2.023	0.019	2.232
extractProtTC	0.085	0.238	0.390
getCPI	0.004	0.003	0.007
getDrug	0.000	0.001	0.001
getFASTAFromKEGG	0.000	0.001	0.000
getFASTAFromUniProt	0.001	0.001	0.000
getMolFromCAS	0.001	0.001	0.000
getMolFromChEMBL	0.001	0.001	0.000
getMolFromDrugBank	0.001	0.001	0.001
getMolFromKEGG	0.001	0.001	0.001
getMolFromPubChem	0.001	0.001	0.001
getPDBFromRCSBPDB	0.001	0.001	0.001
getPPI	0.005	0.005	0.010
getProt	0.000	0.000	0.001
getSeqFromKEGG	0.000	0.000	0.001
getSeqFromRCSBPDB	0.000	0.000	0.001
getSeqFromUniProt	0.000	0.000	0.001
getSmiFromChEMBL	0.000	0.000	0.001
getSmiFromDrugBank	0.000	0.000	0.001
getSmiFromKEGG	0.000	0.000	0.001
getSmiFromPubChem	0.001	0.001	0.001
readFASTA	0.002	0.001	0.003
readMolFromSDF	0.004	0.002	0.006
readMolFromSmi	0.001	0.001	0.002
readPDB	1.538	0.013	1.589
searchDrug	0.002	0.002	0.004
segProt	0.004	0.004	0.007

CHECK results for Rcpi on merida1

Summary

Command output

Installation output

Tests output

Example timings