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This page was generated on 2025-02-01 11:45 -0500 (Sat, 01 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4704
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4467
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4478
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4431
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 1681/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.43.0  (landing page)
Nan Xiao
Snapshot Date: 2025-01-31 13:40 -0500 (Fri, 31 Jan 2025)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: devel
git_last_commit: 88f2c1f
git_last_commit_date: 2024-10-29 09:50:50 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for Rcpi on kjohnson3

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: 1.43.0
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_1.43.0.tar.gz
StartedAt: 2025-01-31 20:55:49 -0500 (Fri, 31 Jan 2025)
EndedAt: 2025-01-31 20:56:37 -0500 (Fri, 31 Jan 2025)
EllapsedTime: 47.8 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_1.43.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Rcpi.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.43.0’
* 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/4.5-arm64/Resources/library’
* installing *source* package ‘Rcpi’ ...
** this is package ‘Rcpi’ version ‘1.43.0’
** 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 Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 
  2.378   0.255   2.189 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0010.0010.001
AA3DMoRSE0.0010.0010.001
AAACF0.0000.0010.001
AABLOSUM1000.0000.0010.001
AABLOSUM450.0000.0000.001
AABLOSUM500.0010.0000.001
AABLOSUM620.0000.0010.001
AABLOSUM800.0000.0000.001
AABurden0.0000.0000.001
AACPSA0.0000.0010.001
AAConn0.0000.0010.001
AAConst0.0000.0000.001
AADescAll0.0010.0000.001
AAEdgeAdj0.0000.0010.001
AAEigIdx0.0000.0000.001
AAFGC0.0000.0010.001
AAGETAWAY0.0000.0010.001
AAGeom0.0000.0010.001
AAInfo0.0000.0000.001
AAMOE2D0.0010.0000.001
AAMOE3D0.0000.0010.001
AAMetaInfo0.0000.0010.001
AAMolProp0.0010.0010.001
AAPAM1200.0000.0010.001
AAPAM2500.0000.0000.001
AAPAM300.0000.0010.001
AAPAM400.0000.0010.000
AAPAM700.0000.0010.000
AARDF000
AARandic0.0010.0010.001
AATopo0.0000.0010.001
AATopoChg0.0000.0010.001
AAWHIM0.0010.0010.002
AAWalk0.0000.0010.001
AAindex0.0000.0000.001
OptAA3d000
acc0.0100.0020.012
calcDrugFPSim0.0010.0000.000
calcDrugMCSSim0.0010.0010.003
calcParProtGOSim000
calcParProtSeqSim0.0020.0010.004
calcTwoProtGOSim0.0000.0010.000
calcTwoProtSeqSim0.0010.0000.000
checkProt000
convMolFormat0.0010.0010.001
extractDrugAIO000
extractDrugALOGP000
extractDrugAminoAcidCount000
extractDrugApol000
extractDrugAromaticAtomsCount0.0000.0000.001
extractDrugAromaticBondsCount000
extractDrugAtomCount0.0010.0010.001
extractDrugAutocorrelationCharge000
extractDrugAutocorrelationMass000
extractDrugAutocorrelationPolarizability0.0000.0010.001
extractDrugBCUT000
extractDrugBPol0.0000.0000.001
extractDrugBondCount000
extractDrugCPSA0.0000.0000.001
extractDrugCarbonTypes000
extractDrugChiChain000
extractDrugChiCluster0.0000.0000.001
extractDrugChiPath000
extractDrugChiPathCluster000
extractDrugDescOB0.0020.0010.003
extractDrugECI000
extractDrugEstate000
extractDrugEstateComplete0.0000.0000.001
extractDrugExtended0.0010.0000.001
extractDrugExtendedComplete000
extractDrugFMF0.0000.0000.001
extractDrugFragmentComplexity0.0000.0010.000
extractDrugGraph0.0000.0000.001
extractDrugGraphComplete000
extractDrugGravitationalIndex000
extractDrugHBondAcceptorCount0.0010.0000.001
extractDrugHBondDonorCount000
extractDrugHybridization0.0000.0000.001
extractDrugHybridizationComplete0.0000.0010.000
extractDrugHybridizationRatio0.0010.0000.001
extractDrugIPMolecularLearning000
extractDrugKR000
extractDrugKRComplete0.0000.0000.001
extractDrugKappaShapeIndices000
extractDrugKierHallSmarts0.0000.0000.001
extractDrugLargestChain0.0000.0010.000
extractDrugLargestPiSystem0.0010.0000.000
extractDrugLengthOverBreadth000
extractDrugLongestAliphaticChain000
extractDrugMACCS0.0000.0000.001
extractDrugMACCSComplete000
extractDrugMDE0.0000.0000.001
extractDrugMannholdLogP0.0000.0010.000
extractDrugMomentOfInertia0.0010.0000.000
extractDrugOBFP20.0040.0020.006
extractDrugOBFP30.0020.0010.003
extractDrugOBFP40.0370.0020.039
extractDrugOBMACCS0.0020.0010.003
extractDrugPetitjeanNumber0.0010.0000.000
extractDrugPetitjeanShapeIndex0.0000.0000.001
extractDrugPubChem0.0000.0010.000
extractDrugPubChemComplete000
extractDrugRotatableBondsCount0.0000.0000.001
extractDrugRuleOfFive0.0000.0010.000
extractDrugShortestPath0.0000.0000.001
extractDrugShortestPathComplete0.0010.0000.000
extractDrugStandard0.0000.0000.001
extractDrugStandardComplete000
extractDrugTPSA0.0010.0000.000
extractDrugVABC0.0000.0010.001
extractDrugVAdjMa000
extractDrugWHIM000
extractDrugWeight0.0010.0000.001
extractDrugWeightedPath000
extractDrugWienerNumbers0.0000.0000.001
extractDrugXLogP0.0010.0000.000
extractDrugZagrebIndex0.0000.0010.000
extractPCMBLOSUM0.0030.0000.004
extractPCMDescScales0.0030.0000.004
extractPCMFAScales0.0100.0020.013
extractPCMMDSScales0.0030.0010.004
extractPCMPropScales0.0040.0000.004
extractPCMScales0.0050.0020.007
extractProtAAC0.0000.0000.001
extractProtAPAAC0.2480.0070.268
extractProtCTDC0.0010.0010.001
extractProtCTDD0.0020.0000.002
extractProtCTDT0.0010.0010.002
extractProtCTriad0.0280.0030.031
extractProtDC0.0010.0010.002
extractProtGeary0.0370.0040.040
extractProtMoran0.1750.0030.181
extractProtMoreauBroto0.0310.0050.035
extractProtPAAC0.1110.0040.115
extractProtPSSM0.0000.0000.001
extractProtPSSMAcc0.0000.0000.001
extractProtPSSMFeature000
extractProtQSO0.1980.0050.203
extractProtSOCN0.1910.0030.197
extractProtTC0.0100.0260.036
getCPI0.0010.0010.002
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem0.0000.0000.001
getPDBFromRCSBPDB000
getPPI0.0000.0000.001
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA0.0000.0010.001
readMolFromSDF0.0010.0000.001
readMolFromSmi000
readPDB0.2420.0010.243
searchDrug0.0010.0000.001
segProt0.0000.0010.001