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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1686/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.42.0  (landing page)
Nan Xiao
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: RELEASE_3_20
git_last_commit: c03a28c
git_last_commit_date: 2024-10-29 09:50:50 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for Rcpi on nebbiolo2

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: 1.42.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Rcpi_1.42.0.tar.gz
StartedAt: 2024-12-20 04:36:23 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 04:38:13 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 109.1 seconds
RetCode: 0
Status:   OK  
CheckDir: Rcpi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings Rcpi_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/Rcpi.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.42.0’
* 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 loading without being on the library search path ... 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

Rcpi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL Rcpi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 5 | PASS 17 ]

══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• {rcdk} is not installed (5): 'test_extractDrugALOGP.R:2:5',
  'test_extractDrugECI.R:2:5', 'test_extractDrugRuleOfFive.R:2:5',
  'test_extractDrugTPSA.R:2:5', 'test_extractDrugXLogP.R:2:5'

[ FAIL 0 | WARN 0 | SKIP 5 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
  4.028   0.288   4.306 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0010.0010.001
AA3DMoRSE0.0000.0010.001
AAACF0.0000.0010.000
AABLOSUM1000.0010.0000.000
AABLOSUM450.0010.0000.000
AABLOSUM500.0010.0000.000
AABLOSUM620.0010.0000.000
AABLOSUM800.0010.0000.000
AABurden0.0010.0000.000
AACPSA0.0010.0000.000
AAConn0.0000.0010.000
AAConst0.0000.0010.000
AADescAll000
AAEdgeAdj0.0000.0010.001
AAEigIdx0.0000.0010.001
AAFGC0.0000.0000.001
AAGETAWAY0.0000.0000.001
AAGeom0.0000.0000.001
AAInfo0.0000.0000.001
AAMOE2D0.0000.0000.001
AAMOE3D0.0000.0000.001
AAMetaInfo0.0000.0000.001
AAMolProp0.0010.0000.001
AAPAM1200.0010.0000.001
AAPAM2500.0010.0000.001
AAPAM300.0010.0000.001
AAPAM400.0010.0000.001
AAPAM700.0010.0000.001
AARDF0.0010.0000.001
AARandic0.0010.0000.001
AATopo0.0010.0000.001
AATopoChg0.0010.0000.001
AAWHIM0.0010.0000.001
AAWalk0.0000.0000.001
AAindex000
OptAA3d000
acc0.0060.0010.007
calcDrugFPSim000
calcDrugMCSSim0.0030.0070.009
calcParProtGOSim000
calcParProtSeqSim0.0050.0010.005
calcTwoProtGOSim000
calcTwoProtSeqSim0.0010.0000.001
checkProt0.0010.0000.001
convMolFormat0.0010.0000.001
extractDrugAIO0.0010.0000.001
extractDrugALOGP0.0000.0000.001
extractDrugAminoAcidCount0.0010.0010.001
extractDrugApol0.0000.0000.001
extractDrugAromaticAtomsCount0.0000.0000.001
extractDrugAromaticBondsCount0.0000.0000.001
extractDrugAtomCount000
extractDrugAutocorrelationCharge000
extractDrugAutocorrelationMass0.0010.0000.000
extractDrugAutocorrelationPolarizability0.0010.0000.000
extractDrugBCUT0.0010.0000.000
extractDrugBPol0.0010.0000.001
extractDrugBondCount0.0010.0000.001
extractDrugCPSA0.0010.0000.001
extractDrugCarbonTypes0.0010.0000.001
extractDrugChiChain0.0010.0000.001
extractDrugChiCluster0.0000.0000.001
extractDrugChiPath0.0000.0000.001
extractDrugChiPathCluster0.0000.0000.001
extractDrugDescOB0.0070.0080.016
extractDrugECI0.0000.0000.001
extractDrugEstate0.0000.0000.001
extractDrugEstateComplete000
extractDrugExtended000
extractDrugExtendedComplete0.0010.0000.000
extractDrugFMF0.0010.0000.000
extractDrugFragmentComplexity0.0010.0000.000
extractDrugGraph0.0010.0000.001
extractDrugGraphComplete0.0010.0000.001
extractDrugGravitationalIndex0.0010.0000.001
extractDrugHBondAcceptorCount0.0000.0000.001
extractDrugHBondDonorCount0.0000.0000.001
extractDrugHybridization0.0000.0000.001
extractDrugHybridizationComplete0.0000.0000.001
extractDrugHybridizationRatio000
extractDrugIPMolecularLearning0.0000.0010.000
extractDrugKR0.0010.0000.000
extractDrugKRComplete0.0010.0000.000
extractDrugKappaShapeIndices0.0010.0000.000
extractDrugKierHallSmarts0.0010.0000.001
extractDrugLargestChain0.0010.0000.001
extractDrugLargestPiSystem0.0010.0000.001
extractDrugLengthOverBreadth0.0000.0000.001
extractDrugLongestAliphaticChain0.0000.0000.001
extractDrugMACCS0.0000.0000.001
extractDrugMACCSComplete0.0000.0000.001
extractDrugMDE000
extractDrugMannholdLogP0.0010.0000.000
extractDrugMomentOfInertia0.0010.0000.000
extractDrugOBFP20.0070.0080.014
extractDrugOBFP30.0040.0060.009
extractDrugOBFP40.0790.0060.085
extractDrugOBMACCS0.0090.0060.014
extractDrugPetitjeanNumber0.0000.0010.001
extractDrugPetitjeanShapeIndex0.0010.0000.001
extractDrugPubChem0.0010.0000.001
extractDrugPubChemComplete0.0010.0000.001
extractDrugRotatableBondsCount0.0000.0000.001
extractDrugRuleOfFive0.0000.0000.001
extractDrugShortestPath0.0000.0000.001
extractDrugShortestPathComplete0.0000.0000.001
extractDrugStandard000
extractDrugStandardComplete0.0010.0000.000
extractDrugTPSA0.0010.0000.000
extractDrugVABC0.0000.0010.000
extractDrugVAdjMa0.0010.0000.000
extractDrugWHIM0.0010.0000.000
extractDrugWeight0.0000.0010.001
extractDrugWeightedPath0.0010.0000.001
extractDrugWienerNumbers0.0010.0000.001
extractDrugXLogP0.0010.0000.001
extractDrugZagrebIndex0.0000.0000.001
extractPCMBLOSUM0.0070.0010.008
extractPCMDescScales0.0090.0000.010
extractPCMFAScales0.0110.0020.013
extractPCMMDSScales0.0060.0020.007
extractPCMPropScales0.0170.0150.033
extractPCMScales0.0150.0000.015
extractProtAAC0.0020.0010.002
extractProtAPAAC0.6710.0330.705
extractProtCTDC0.0010.0010.003
extractProtCTDD0.0030.0000.004
extractProtCTDT0.0040.0000.004
extractProtCTriad0.0670.0120.079
extractProtDC0.0020.0010.003
extractProtGeary0.0940.0010.095
extractProtMoran0.0920.0020.094
extractProtMoreauBroto0.0860.0010.086
extractProtPAAC0.3320.0200.352
extractProtPSSM0.0010.0000.001
extractProtPSSMAcc0.0010.0000.001
extractProtPSSMFeature0.0000.0000.001
extractProtQSO0.5840.0030.587
extractProtSOCN0.5750.0000.575
extractProtTC0.0190.0090.029
getCPI0.0010.0000.002
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI0.0010.0010.002
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA0.0010.0000.001
readMolFromSDF0.0020.0000.002
readMolFromSmi0.0010.0000.001
readPDB0.7240.0040.728
searchDrug0.0010.0000.002
segProt0.0010.0000.001