Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2025-04-22 13:16 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
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 1717/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.44.0  (landing page)
Nan Xiao
Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: RELEASE_3_21
git_last_commit: a5056ba
git_last_commit_date: 2025-04-15 10:29:42 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'Biostrings' which is only available as a source package that needs compilation
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for Rcpi on lconway

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: 1.44.0
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_1.44.0.tar.gz
StartedAt: 2025-04-21 22:56:19 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 22:58:44 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 144.2 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_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/Rcpi.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.44.0’
* 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-x86_64/Resources/library’
* installing *source* package ‘Rcpi’ ...
** this is package ‘Rcpi’ version ‘1.44.0’
** 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 
  6.948   0.654   6.674 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0020.0010.003
AA3DMoRSE0.0010.0020.002
AAACF0.0010.0020.003
AABLOSUM1000.0010.0000.002
AABLOSUM450.0010.0010.001
AABLOSUM500.0010.0010.001
AABLOSUM620.0010.0010.002
AABLOSUM800.0000.0020.002
AABurden0.0010.0010.002
AACPSA0.0010.0010.002
AAConn0.0010.0020.002
AAConst0.0010.0010.002
AADescAll0.0010.0010.002
AAEdgeAdj0.0010.0010.002
AAEigIdx0.0010.0010.002
AAFGC0.0000.0020.002
AAGETAWAY0.0010.0020.003
AAGeom0.0010.0020.002
AAInfo0.0010.0020.002
AAMOE2D0.0010.0010.003
AAMOE3D0.0010.0010.002
AAMetaInfo0.0010.0010.002
AAMolProp0.0010.0010.002
AAPAM1200.0010.0010.002
AAPAM2500.0010.0020.002
AAPAM300.0010.0010.003
AAPAM400.0000.0010.002
AAPAM700.0010.0010.002
AARDF0.0010.0020.002
AARandic0.0010.0010.002
AATopo0.0010.0010.002
AATopoChg0.0010.0010.003
AAWHIM0.0010.0010.001
AAWalk0.0000.0010.001
AAindex0.0000.0000.001
OptAA3d0.0000.0000.001
acc0.0090.0080.016
calcDrugFPSim000
calcDrugMCSSim0.0050.0040.011
calcParProtGOSim000
calcParProtSeqSim0.0060.0030.010
calcTwoProtGOSim0.0000.0010.000
calcTwoProtSeqSim0.0020.0010.004
checkProt0.0020.0010.002
convMolFormat0.0010.0010.002
extractDrugAIO0.0010.0000.001
extractDrugALOGP0.0010.0010.001
extractDrugAminoAcidCount0.0000.0010.001
extractDrugApol0.0010.0010.001
extractDrugAromaticAtomsCount0.0010.0010.002
extractDrugAromaticBondsCount0.0010.0010.001
extractDrugAtomCount0.0010.0010.002
extractDrugAutocorrelationCharge0.0010.0010.001
extractDrugAutocorrelationMass0.0000.0010.001
extractDrugAutocorrelationPolarizability0.0010.0010.002
extractDrugBCUT0.0010.0010.001
extractDrugBPol0.0000.0010.002
extractDrugBondCount0.0010.0010.001
extractDrugCPSA0.0000.0010.002
extractDrugCarbonTypes0.0010.0010.001
extractDrugChiChain0.0010.0010.001
extractDrugChiCluster0.0010.0010.002
extractDrugChiPath0.0010.0010.001
extractDrugChiPathCluster0.0000.0010.001
extractDrugDescOB0.0060.0040.011
extractDrugECI0.0010.0010.001
extractDrugEstate0.0010.0010.002
extractDrugEstateComplete0.0010.0010.001
extractDrugExtended0.0010.0010.001
extractDrugExtendedComplete0.0010.0000.002
extractDrugFMF0.0010.0010.002
extractDrugFragmentComplexity0.0010.0000.002
extractDrugGraph0.0010.0010.003
extractDrugGraphComplete0.0010.0000.000
extractDrugGravitationalIndex0.0010.0000.002
extractDrugHBondAcceptorCount0.0010.0000.001
extractDrugHBondDonorCount0.0010.0000.001
extractDrugHybridization0.0010.0000.002
extractDrugHybridizationComplete0.0010.0000.001
extractDrugHybridizationRatio0.0010.0000.001
extractDrugIPMolecularLearning0.0010.0010.001
extractDrugKR0.0010.0010.001
extractDrugKRComplete0.0000.0010.001
extractDrugKappaShapeIndices0.0010.0010.002
extractDrugKierHallSmarts0.0010.0010.001
extractDrugLargestChain0.0000.0010.001
extractDrugLargestPiSystem0.0010.0010.002
extractDrugLengthOverBreadth0.0010.0010.001
extractDrugLongestAliphaticChain0.0010.0000.001
extractDrugMACCS0.0000.0000.001
extractDrugMACCSComplete000
extractDrugMDE0.0000.0010.001
extractDrugMannholdLogP0.0000.0000.001
extractDrugMomentOfInertia0.0010.0000.001
extractDrugOBFP20.0220.0060.029
extractDrugOBFP30.0070.0040.010
extractDrugOBFP40.0060.0040.011
extractDrugOBMACCS0.0080.0040.011
extractDrugPetitjeanNumber0.0010.0000.001
extractDrugPetitjeanShapeIndex0.0000.0000.002
extractDrugPubChem0.0010.0000.001
extractDrugPubChemComplete0.0010.0000.001
extractDrugRotatableBondsCount0.0000.0000.001
extractDrugRuleOfFive0.0010.0000.001
extractDrugShortestPath0.0010.0010.001
extractDrugShortestPathComplete0.0010.0010.002
extractDrugStandard0.0010.0000.001
extractDrugStandardComplete0.0010.0010.001
extractDrugTPSA0.0000.0010.001
extractDrugVABC0.0010.0010.002
extractDrugVAdjMa0.0010.0000.002
extractDrugWHIM0.0010.0000.001
extractDrugWeight0.0000.0000.001
extractDrugWeightedPath0.0010.0000.002
extractDrugWienerNumbers0.0010.0000.000
extractDrugXLogP0.0010.0000.001
extractDrugZagrebIndex0.0010.0010.001
extractPCMBLOSUM0.0170.0070.024
extractPCMDescScales0.0110.0010.013
extractPCMFAScales0.0150.0040.019
extractPCMMDSScales0.0100.0030.013
extractPCMPropScales0.0100.0010.012
extractPCMScales0.0160.0030.018
extractProtAAC0.0020.0010.004
extractProtAPAAC0.9190.0330.962
extractProtCTDC0.0020.0010.004
extractProtCTDD0.0030.0020.005
extractProtCTDT0.0050.0010.006
extractProtCTriad0.0820.0110.093
extractProtDC0.0040.0070.011
extractProtGeary0.1170.0100.129
extractProtMoran0.1440.0140.162
extractProtMoreauBroto0.1130.0080.124
extractProtPAAC0.3580.0070.369
extractProtPSSM0.0020.0010.003
extractProtPSSMAcc0.0020.0010.003
extractProtPSSMFeature0.0010.0000.002
extractProtQSO0.7120.0130.735
extractProtSOCN0.7270.0160.755
extractProtTC0.0360.0900.127
getCPI0.0030.0020.005
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt0.0010.0000.000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG0.0010.0000.000
getMolFromPubChem000
getPDBFromRCSBPDB0.0010.0000.000
getPPI0.0030.0020.005
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB0.0000.0010.000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG0.0000.0010.000
getSmiFromPubChem000
readFASTA0.0010.0000.003
readMolFromSDF0.0020.0010.003
readMolFromSmi0.0010.0000.001
readPDB0.7680.0080.781
searchDrug0.0020.0010.003
segProt0.0020.0020.004