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This page was generated on 2024-07-23 11:42 -0400 (Tue, 23 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4688
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4280
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4455
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4404
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 1659/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.41.1  (landing page)
Nan Xiao
Snapshot Date: 2024-07-22 14:00 -0400 (Mon, 22 Jul 2024)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: devel
git_last_commit: d311940
git_last_commit_date: 2024-07-20 23:14:10 -0400 (Sat, 20 Jul 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 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: 1.41.1
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_1.41.1.tar.gz
StartedAt: 2024-07-23 00:06:32 -0400 (Tue, 23 Jul 2024)
EndedAt: 2024-07-23 00:07:17 -0400 (Tue, 23 Jul 2024)
EllapsedTime: 45.5 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_1.41.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Rcpi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.41.1’
* 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-arm64/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: 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 
  2.300   0.205   2.108 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0010.0010.002
AA3DMoRSE0.0010.0010.001
AAACF0.0010.0010.001
AABLOSUM100000
AABLOSUM45000
AABLOSUM500.0000.0010.001
AABLOSUM620.0000.0000.001
AABLOSUM800.0000.0010.001
AABurden0.0000.0010.001
AACPSA0.0010.0000.001
AAConn0.0000.0010.001
AAConst0.0000.0000.001
AADescAll0.0000.0010.000
AAEdgeAdj000
AAEigIdx0.0000.0010.001
AAFGC0.0000.0000.001
AAGETAWAY0.0010.0010.000
AAGeom000
AAInfo0.0000.0010.001
AAMOE2D0.0000.0000.001
AAMOE3D0.0000.0010.001
AAMetaInfo000
AAMolProp0.0000.0010.001
AAPAM1200.0010.0000.001
AAPAM2500.0000.0010.000
AAPAM300.0000.0000.001
AAPAM400.0000.0010.001
AAPAM70000
AARDF0.0000.0000.001
AARandic0.0000.0000.001
AATopo0.0010.0000.001
AATopoChg0.0000.0010.001
AAWHIM000
AAWalk0.0000.0010.001
AAindex0.0000.0000.001
OptAA3d000
acc0.0030.0020.005
calcDrugFPSim000
calcDrugMCSSim0.0060.0010.008
calcParProtGOSim000
calcParProtSeqSim0.0020.0000.003
calcTwoProtGOSim0.0010.0000.000
calcTwoProtSeqSim0.0000.0000.001
checkProt0.0010.0000.001
convMolFormat0.0000.0010.000
extractDrugAIO0.0000.0000.001
extractDrugALOGP000
extractDrugAminoAcidCount0.0000.0000.001
extractDrugApol0.0000.0010.000
extractDrugAromaticAtomsCount0.0000.0000.001
extractDrugAromaticBondsCount0.0010.0000.000
extractDrugAtomCount0.0000.0000.001
extractDrugAutocorrelationCharge000
extractDrugAutocorrelationMass0.0000.0000.001
extractDrugAutocorrelationPolarizability000
extractDrugBCUT0.0000.0000.001
extractDrugBPol000
extractDrugBondCount0.0010.0000.001
extractDrugCPSA000
extractDrugCarbonTypes0.0000.0000.001
extractDrugChiChain000
extractDrugChiCluster0.0010.0000.001
extractDrugChiPath000
extractDrugChiPathCluster0.0000.0000.001
extractDrugDescOB0.0020.0010.002
extractDrugECI000
extractDrugEstate0.0010.0000.000
extractDrugEstateComplete000
extractDrugExtended000
extractDrugExtendedComplete0.0000.0000.001
extractDrugFMF0.0010.0000.000
extractDrugFragmentComplexity0.0000.0000.001
extractDrugGraph000
extractDrugGraphComplete0.0000.0000.001
extractDrugGravitationalIndex000
extractDrugHBondAcceptorCount0.0000.0000.001
extractDrugHBondDonorCount000
extractDrugHybridization0.0010.0000.001
extractDrugHybridizationComplete000
extractDrugHybridizationRatio0.0000.0010.000
extractDrugIPMolecularLearning000
extractDrugKR000
extractDrugKRComplete000
extractDrugKappaShapeIndices000
extractDrugKierHallSmarts0.0010.0010.000
extractDrugLargestChain000
extractDrugLargestPiSystem000
extractDrugLengthOverBreadth000
extractDrugLongestAliphaticChain0.0010.0000.001
extractDrugMACCS0.0000.0010.000
extractDrugMACCSComplete0.0000.0000.001
extractDrugMDE000
extractDrugMannholdLogP0.0000.0000.001
extractDrugMomentOfInertia000
extractDrugOBFP20.0020.0010.002
extractDrugOBFP30.0040.0010.005
extractDrugOBFP40.0010.0010.003
extractDrugOBMACCS0.0040.0010.004
extractDrugPetitjeanNumber000
extractDrugPetitjeanShapeIndex0.0010.0010.001
extractDrugPubChem000
extractDrugPubChemComplete000
extractDrugRotatableBondsCount000
extractDrugRuleOfFive000
extractDrugShortestPath000
extractDrugShortestPathComplete000
extractDrugStandard0.0010.0000.001
extractDrugStandardComplete000
extractDrugTPSA0.0000.0010.000
extractDrugVABC000
extractDrugVAdjMa0.0000.0000.001
extractDrugWHIM000
extractDrugWeight0.0000.0000.001
extractDrugWeightedPath0.0000.0010.000
extractDrugWienerNumbers0.0000.0000.001
extractDrugXLogP000
extractDrugZagrebIndex0.0010.0000.001
extractPCMBLOSUM0.0030.0010.004
extractPCMDescScales0.0040.0010.004
extractPCMFAScales0.0050.0010.006
extractPCMMDSScales0.0030.0010.004
extractPCMPropScales0.0340.0020.036
extractPCMScales0.0050.0010.006
extractProtAAC0.0010.0000.000
extractProtAPAAC0.2550.0100.268
extractProtCTDC0.0010.0000.001
extractProtCTDD0.0010.0000.002
extractProtCTDT0.0020.0010.002
extractProtCTriad0.0280.0050.033
extractProtDC0.0010.0020.003
extractProtGeary0.0370.0030.040
extractProtMoran0.0370.0030.040
extractProtMoreauBroto0.0330.0020.035
extractProtPAAC0.1170.0020.119
extractProtPSSM0.0010.0000.000
extractProtPSSMAcc000
extractProtPSSMFeature0.0010.0000.001
extractProtQSO0.2060.0040.211
extractProtSOCN0.2020.0030.205
extractProtTC0.0100.0290.038
getCPI0.0010.0000.001
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI0.0010.0010.001
getProt000
getSeqFromKEGG0.0000.0000.001
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA0.0000.0000.001
readMolFromSDF0.0010.0010.001
readMolFromSmi000
readPDB0.2450.0020.247
searchDrug0.0010.0000.001
segProt0.0000.0010.001