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This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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: 2024-11-19 13:40 -0500 (Tue, 19 Nov 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)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / 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: 1.42.0
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_1.42.0.tar.gz
StartedAt: 2024-11-20 01:40:51 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 01:46:46 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 355.2 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_1.42.0.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: x86_64-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 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 ‘1.42.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-x86_64/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: 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 
  5.288   0.553  14.526 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0020.0010.003
AA3DMoRSE0.0000.0010.001
AAACF0.0010.0010.002
AABLOSUM1000.0010.0010.001
AABLOSUM450.0010.0010.002
AABLOSUM500.0000.0010.002
AABLOSUM620.0010.0010.002
AABLOSUM800.0010.0000.002
AABurden0.0010.0000.002
AACPSA0.0000.0010.001
AAConn0.0000.0010.001
AAConst0.0010.0010.002
AADescAll0.0010.0010.002
AAEdgeAdj0.0010.0010.002
AAEigIdx0.0000.0010.001
AAFGC0.0000.0010.002
AAGETAWAY0.0010.0000.002
AAGeom0.0010.0000.001
AAInfo0.0010.0010.002
AAMOE2D0.0000.0010.002
AAMOE3D0.0000.0010.001
AAMetaInfo0.0010.0000.002
AAMolProp0.0010.0010.002
AAPAM1200.0010.0010.002
AAPAM2500.0000.0010.002
AAPAM300.0010.0010.002
AAPAM400.0010.0010.002
AAPAM700.0010.0010.001
AARDF0.0000.0010.001
AARandic0.0010.0010.001
AATopo0.0010.0010.002
AATopoChg0.0010.0000.001
AAWHIM0.0000.0010.002
AAWalk0.0000.0010.001
AAindex0.0000.0010.002
OptAA3d000
acc0.0060.0040.010
calcDrugFPSim000
calcDrugMCSSim0.0040.0030.064
calcParProtGOSim0.0010.0000.000
calcParProtSeqSim0.0060.0030.111
calcTwoProtGOSim000
calcTwoProtSeqSim0.0010.0010.002
checkProt0.0010.0000.002
convMolFormat0.0010.0000.001
extractDrugAIO0.0000.0010.001
extractDrugALOGP0.0010.0010.002
extractDrugAminoAcidCount0.0010.0000.001
extractDrugApol0.0010.0000.001
extractDrugAromaticAtomsCount0.0000.0010.001
extractDrugAromaticBondsCount0.0000.0000.001
extractDrugAtomCount0.0010.0000.001
extractDrugAutocorrelationCharge0.0010.0000.001
extractDrugAutocorrelationMass0.0010.0010.001
extractDrugAutocorrelationPolarizability0.0000.0000.001
extractDrugBCUT0.0000.0000.001
extractDrugBPol0.0000.0000.001
extractDrugBondCount0.0010.0010.001
extractDrugCPSA0.0010.0000.001
extractDrugCarbonTypes0.0000.0000.001
extractDrugChiChain0.0000.0010.001
extractDrugChiCluster0.0000.0010.001
extractDrugChiPath0.0010.0000.002
extractDrugChiPathCluster0.0010.0000.001
extractDrugDescOB0.0110.0040.107
extractDrugECI0.0010.0000.001
extractDrugEstate0.0010.0010.001
extractDrugEstateComplete0.0000.0000.001
extractDrugExtended0.0000.0000.001
extractDrugExtendedComplete0.0010.0000.001
extractDrugFMF0.0010.0010.001
extractDrugFragmentComplexity0.0010.0000.001
extractDrugGraph0.0010.0000.002
extractDrugGraphComplete0.0000.0000.001
extractDrugGravitationalIndex0.0000.0000.001
extractDrugHBondAcceptorCount0.0010.0010.001
extractDrugHBondDonorCount0.0010.0010.001
extractDrugHybridization0.0010.0000.001
extractDrugHybridizationComplete0.0010.0000.002
extractDrugHybridizationRatio0.0010.0000.001
extractDrugIPMolecularLearning0.0010.0000.001
extractDrugKR0.0010.0010.001
extractDrugKRComplete0.0000.0000.001
extractDrugKappaShapeIndices0.0000.0000.001
extractDrugKierHallSmarts0.0010.0000.001
extractDrugLargestChain0.0010.0010.001
extractDrugLargestPiSystem0.0010.0010.001
extractDrugLengthOverBreadth0.0000.0010.002
extractDrugLongestAliphaticChain0.0010.0000.001
extractDrugMACCS0.0010.0000.001
extractDrugMACCSComplete0.0010.0000.001
extractDrugMDE0.0000.0000.001
extractDrugMannholdLogP0.0000.0010.001
extractDrugMomentOfInertia0.0010.0010.001
extractDrugOBFP20.0050.0020.007
extractDrugOBFP30.0090.0030.012
extractDrugOBFP40.0060.0020.008
extractDrugOBMACCS0.0060.0030.009
extractDrugPetitjeanNumber0.0000.0000.001
extractDrugPetitjeanShapeIndex0.0010.0000.001
extractDrugPubChem0.0010.0010.001
extractDrugPubChemComplete0.0010.0010.001
extractDrugRotatableBondsCount0.0010.0000.002
extractDrugRuleOfFive0.0000.0000.001
extractDrugShortestPath0.0010.0000.001
extractDrugShortestPathComplete0.0010.0010.001
extractDrugStandard0.0010.0000.001
extractDrugStandardComplete0.0010.0000.001
extractDrugTPSA0.0000.0000.001
extractDrugVABC0.0000.0010.001
extractDrugVAdjMa0.0010.0000.001
extractDrugWHIM0.0010.0000.002
extractDrugWeight0.0010.0000.001
extractDrugWeightedPath0.0000.0000.001
extractDrugWienerNumbers0.0000.0010.001
extractDrugXLogP0.0000.0010.001
extractDrugZagrebIndex0.0010.0000.001
extractPCMBLOSUM0.0710.0050.076
extractPCMDescScales0.0090.0010.010
extractPCMFAScales0.0120.0030.014
extractPCMMDSScales0.0070.0020.009
extractPCMPropScales0.0090.0020.010
extractPCMScales0.0180.0030.020
extractProtAAC0.0020.0010.002
extractProtAPAAC0.5690.0180.684
extractProtCTDC0.0030.0020.004
extractProtCTDD0.0030.0010.004
extractProtCTDT0.0040.0010.005
extractProtCTriad0.0640.0100.073
extractProtDC0.0030.0040.006
extractProtGeary0.0890.0080.097
extractProtMoran0.0800.0080.088
extractProtMoreauBroto0.0820.0070.088
extractProtPAAC0.2820.0060.288
extractProtPSSM0.0010.0010.001
extractProtPSSMAcc0.0010.0000.001
extractProtPSSMFeature0.0010.0000.002
extractProtQSO0.4950.0090.550
extractProtSOCN0.4800.0060.487
extractProtTC0.0240.0630.087
getCPI0.0020.0010.003
getDrug0.0010.0000.001
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank0.0000.0000.001
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI0.0010.0020.003
getProt000
getSeqFromKEGG0.0000.0010.000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG0.0000.0010.000
getSmiFromPubChem000
readFASTA0.0010.0000.002
readMolFromSDF0.0020.0010.002
readMolFromSmi0.0010.0000.001
readPDB0.5360.0050.671
searchDrug0.0010.0010.002
segProt0.0010.0020.003