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This page was generated on 2025-09-22 12:03 -0400 (Mon, 22 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4814
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4603
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4547
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4553
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 1711/2333HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.45.0  (landing page)
Nan Xiao
Snapshot Date: 2025-09-21 13:45 -0400 (Sun, 21 Sep 2025)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: devel
git_last_commit: dba81ab
git_last_commit_date: 2025-04-15 10:29:42 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  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 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 1.45.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Rcpi_1.45.0.tar.gz
StartedAt: 2025-09-22 03:20:51 -0400 (Mon, 22 Sep 2025)
EndedAt: 2025-09-22 03:22:45 -0400 (Mon, 22 Sep 2025)
EllapsedTime: 114.2 seconds
RetCode: 0
Status:   OK  
CheckDir: Rcpi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings Rcpi_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/Rcpi.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.45.0’
* 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-3.22-bioc/R/bin/R CMD INSTALL Rcpi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘Rcpi’ ...
** this is package ‘Rcpi’ version ‘1.45.0’
** 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 version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 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 
  4.258   0.288   4.535 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0020.0000.001
AA3DMoRSE0.0000.0000.001
AAACF0.0000.0000.001
AABLOSUM1000.0000.0000.001
AABLOSUM450.0000.0000.001
AABLOSUM500.0000.0000.001
AABLOSUM620.0000.0000.001
AABLOSUM80000
AABurden000
AACPSA0.0000.0010.000
AAConn000
AAConst0.0010.0000.000
AADescAll0.0010.0000.000
AAEdgeAdj0.0010.0000.000
AAEigIdx0.0000.0000.001
AAFGC0.0010.0000.001
AAGETAWAY0.0010.0000.001
AAGeom0.0010.0000.001
AAInfo0.0010.0000.001
AAMOE2D0.0010.0000.001
AAMOE3D0.0000.0000.001
AAMetaInfo0.0000.0000.001
AAMolProp000
AAPAM120000
AAPAM2500.0000.0010.000
AAPAM30000
AAPAM400.0010.0000.000
AAPAM700.0010.0000.000
AARDF0.0000.0000.001
AARandic0.0010.0000.001
AATopo0.0010.0000.001
AATopoChg0.0010.0000.001
AAWHIM0.0010.0000.001
AAWalk0.0010.0000.001
AAindex0.0000.0000.001
OptAA3d000
acc0.0050.0020.007
calcDrugFPSim0.0000.0000.001
calcDrugMCSSim0.0020.0070.009
calcParProtGOSim000
calcParProtSeqSim0.0050.0010.005
calcTwoProtGOSim000
calcTwoProtSeqSim0.0020.0000.002
checkProt0.0010.0000.001
convMolFormat0.0000.0000.001
extractDrugAIO0.0000.0000.001
extractDrugALOGP0.0000.0000.001
extractDrugAminoAcidCount0.0010.0000.001
extractDrugApol0.0010.0000.001
extractDrugAromaticAtomsCount0.0010.0000.001
extractDrugAromaticBondsCount0.0010.0000.001
extractDrugAtomCount0.0010.0000.001
extractDrugAutocorrelationCharge0.0010.0000.001
extractDrugAutocorrelationMass0.0010.0000.001
extractDrugAutocorrelationPolarizability0.0010.0000.001
extractDrugBCUT0.0010.0000.000
extractDrugBPol0.0010.0000.000
extractDrugBondCount0.0010.0000.000
extractDrugCPSA0.0010.0000.000
extractDrugCarbonTypes000
extractDrugChiChain000
extractDrugChiCluster000
extractDrugChiPath000
extractDrugChiPathCluster0.0000.0000.001
extractDrugDescOB0.0100.0070.017
extractDrugECI000
extractDrugEstate000
extractDrugEstateComplete000
extractDrugExtended000
extractDrugExtendedComplete000
extractDrugFMF000
extractDrugFragmentComplexity000
extractDrugGraph0.0000.0010.001
extractDrugGraphComplete0.0010.0000.001
extractDrugGravitationalIndex0.0010.0000.001
extractDrugHBondAcceptorCount0.0010.0000.001
extractDrugHBondDonorCount0.0010.0000.001
extractDrugHybridization0.0010.0000.001
extractDrugHybridizationComplete0.0010.0000.001
extractDrugHybridizationRatio0.0010.0000.001
extractDrugIPMolecularLearning0.0010.0000.001
extractDrugKR0.0010.0000.001
extractDrugKRComplete0.0010.0000.001
extractDrugKappaShapeIndices0.0010.0000.000
extractDrugKierHallSmarts0.0010.0000.000
extractDrugLargestChain000
extractDrugLargestPiSystem000
extractDrugLengthOverBreadth000
extractDrugLongestAliphaticChain000
extractDrugMACCS000
extractDrugMACCSComplete000
extractDrugMDE0.0000.0000.001
extractDrugMannholdLogP0.0010.0000.001
extractDrugMomentOfInertia0.0010.0000.001
extractDrugOBFP20.0800.0060.086
extractDrugOBFP30.0050.0060.010
extractDrugOBFP40.0140.0060.020
extractDrugOBMACCS0.0100.0050.015
extractDrugPetitjeanNumber0.0010.0000.001
extractDrugPetitjeanShapeIndex000
extractDrugPubChem0.0010.0000.000
extractDrugPubChemComplete0.0010.0000.001
extractDrugRotatableBondsCount0.0010.0000.000
extractDrugRuleOfFive0.0010.0000.000
extractDrugShortestPath000
extractDrugShortestPathComplete000
extractDrugStandard000
extractDrugStandardComplete000
extractDrugTPSA000
extractDrugVABC000
extractDrugVAdjMa000
extractDrugWHIM000
extractDrugWeight000
extractDrugWeightedPath0.0000.0000.001
extractDrugWienerNumbers0.0010.0000.001
extractDrugXLogP0.0010.0000.001
extractDrugZagrebIndex0.0010.0000.001
extractPCMBLOSUM0.0090.0000.009
extractPCMDescScales0.010.000.01
extractPCMFAScales0.0130.0010.013
extractPCMMDSScales0.0080.0000.008
extractPCMPropScales0.0160.0000.016
extractPCMScales0.0110.0020.013
extractProtAAC0.0010.0010.002
extractProtAPAAC0.7110.0020.713
extractProtCTDC0.0020.0000.003
extractProtCTDD0.0040.0000.004
extractProtCTDT0.0030.0010.005
extractProtCTriad0.0710.0060.077
extractProtDC0.0010.0020.003
extractProtGeary0.0970.0030.100
extractProtMoran0.1000.0010.101
extractProtMoreauBroto0.0920.0010.092
extractProtPAAC0.3420.0020.343
extractProtPSSM0.0010.0000.001
extractProtPSSMAcc0.0010.0000.001
extractProtPSSMFeature0.0010.0000.001
extractProtQSO0.6010.0030.603
extractProtSOCN0.5940.0010.594
extractProtTC0.0190.0090.028
getCPI0.0020.0000.003
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI0.0010.0010.002
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt0.0000.0000.001
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA0.0010.0000.001
readMolFromSDF0.0020.0000.002
readMolFromSmi0.0010.0000.001
readPDB1.0320.0011.033
searchDrug0.0020.0000.001
segProt0.0020.0000.001