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This page was generated on 2023-04-12 11:06:22 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for Rcpi on lconway


To the developers/maintainers of the Rcpi package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1615/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.34.0  (landing page)
Nan Xiao
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: RELEASE_3_16
git_last_commit: 84c1d63
git_last_commit_date: 2022-11-01 11:09:23 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Rcpi
Version: 1.34.0
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_1.34.0.tar.gz
StartedAt: 2023-04-10 22:07:30 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 22:09:35 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 124.8 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_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/Rcpi.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.34.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 R 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 ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.16-bioc/meat/Rcpi.Rcheck/00check.log’
for details.



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/4.2/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/runTests.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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.

> BiocGenerics:::testPackage('Rcpi')



RUNIT TEST PROTOCOL -- Mon Apr 10 22:09:21 2023 
*********************************************** 
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Rcpi RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  5.414   0.428   4.954 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0020.0010.004
AA3DMoRSE0.0010.0010.002
AAACF0.0010.0010.002
AABLOSUM1000.0010.0010.002
AABLOSUM450.0010.0010.002
AABLOSUM500.0000.0010.002
AABLOSUM620.0010.0010.002
AABLOSUM800.0010.0010.001
AABurden0.0010.0010.003
AACPSA0.0010.0010.002
AAConn0.0010.0010.002
AAConst0.0010.0010.002
AADescAll0.0010.0010.002
AAEdgeAdj0.0000.0010.002
AAEigIdx0.0010.0010.002
AAFGC0.0010.0010.002
AAGETAWAY0.0010.0000.002
AAGeom0.0010.0010.002
AAInfo0.0010.0010.002
AAMOE2D0.0010.0010.002
AAMOE3D0.0010.0010.001
AAMetaInfo0.0010.0010.001
AAMolProp0.0010.0020.002
AAPAM1200.0000.0010.002
AAPAM2500.0010.0010.002
AAPAM300.0010.0010.002
AAPAM400.0010.0010.002
AAPAM700.0010.0010.002
AARDF0.0000.0010.002
AARandic0.0000.0000.002
AATopo0.0010.0000.002
AATopoChg0.0010.0010.002
AAWHIM0.0010.0010.003
AAWalk0.0000.0010.001
AAindex0.0010.0010.002
OptAA3d0.0000.0000.001
acc0.0080.0070.015
calcDrugFPSim2.0570.3200.711
calcDrugMCSSim0.0190.0040.008
calcParProtGOSim0.0010.0000.000
calcParProtSeqSim0.0180.0030.009
calcTwoProtGOSim0.0000.0000.001
calcTwoProtSeqSim0.0020.0010.002
checkProt0.0010.0010.002
convMolFormat0.0000.0010.001
extractDrugAIO0.0000.0010.001
extractDrugALOGP0.0000.0000.001
extractDrugAminoAcidCount0.0000.0000.001
extractDrugApol0.0000.0000.001
extractDrugAromaticAtomsCount0.0000.0010.001
extractDrugAromaticBondsCount0.0000.0000.001
extractDrugAtomCount0.0000.0000.001
extractDrugAutocorrelationCharge0.0000.0000.001
extractDrugAutocorrelationMass0.0010.0000.000
extractDrugAutocorrelationPolarizability0.0010.0000.001
extractDrugBCUT0.0000.0010.001
extractDrugBPol0.0000.0000.001
extractDrugBondCount0.0000.0000.001
extractDrugCPSA0.0000.0000.001
extractDrugCarbonTypes0.0010.0000.000
extractDrugChiChain0.0000.0000.001
extractDrugChiCluster0.0000.0000.001
extractDrugChiPath000
extractDrugChiPathCluster0.0010.0000.001
extractDrugDescOB0.0060.0040.010
extractDrugECI0.0010.0010.001
extractDrugEstate000
extractDrugEstateComplete0.0000.0000.001
extractDrugExtended0.0000.0000.001
extractDrugExtendedComplete0.0000.0010.000
extractDrugFMF0.0000.0000.001
extractDrugFragmentComplexity0.0010.0000.001
extractDrugGraph0.0000.0010.001
extractDrugGraphComplete0.0000.0010.001
extractDrugGravitationalIndex000
extractDrugHBondAcceptorCount0.0000.0000.001
extractDrugHBondDonorCount0.0000.0010.001
extractDrugHybridization0.0000.0000.001
extractDrugHybridizationComplete0.0000.0000.001
extractDrugHybridizationRatio0.0000.0000.001
extractDrugIPMolecularLearning0.0000.0000.001
extractDrugKR0.0010.0010.000
extractDrugKRComplete0.0010.0000.001
extractDrugKappaShapeIndices0.0000.0000.001
extractDrugKierHallSmarts0.0000.0010.001
extractDrugLargestChain0.0000.0000.001
extractDrugLargestPiSystem0.0000.0000.001
extractDrugLengthOverBreadth0.0000.0010.001
extractDrugLongestAliphaticChain0.0010.0000.001
extractDrugMACCS0.0010.0000.001
extractDrugMACCSComplete000
extractDrugMDE0.0010.0010.001
extractDrugMannholdLogP0.0010.0000.001
extractDrugMomentOfInertia0.0010.0000.001
extractDrugOBFP20.0180.0090.026
extractDrugOBFP30.0070.0030.011
extractDrugOBFP40.0070.0030.010
extractDrugOBMACCS0.0070.0030.010
extractDrugPetitjeanNumber0.0010.0000.000
extractDrugPetitjeanShapeIndex0.0010.0000.001
extractDrugPubChem0.0010.0000.001
extractDrugPubChemComplete0.0000.0000.001
extractDrugRotatableBondsCount0.0000.0010.001
extractDrugRuleOfFive0.0000.0000.001
extractDrugShortestPath000
extractDrugShortestPathComplete0.0000.0000.001
extractDrugStandard0.0000.0000.001
extractDrugStandardComplete0.0000.0000.001
extractDrugTPSA0.0010.0010.001
extractDrugVABC0.0010.0000.001
extractDrugVAdjMa0.0010.0000.001
extractDrugWHIM0.0010.0000.001
extractDrugWeight0.0000.0010.001
extractDrugWeightedPath000
extractDrugWienerNumbers0.0010.0000.001
extractDrugXLogP0.0010.0010.001
extractDrugZagrebIndex0.0010.0000.000
extractPCMBLOSUM0.0090.0020.011
extractPCMDescScales0.0250.0060.032
extractPCMFAScales0.0130.0030.015
extractPCMMDSScales0.0070.0020.009
extractPCMPropScales0.0110.0020.012
extractPCMScales0.0110.0020.014
extractProtAAC0.0020.0000.003
extractProtAPAAC1.0190.0721.096
extractProtCTDC0.0020.0010.003
extractProtCTDD0.0040.0020.006
extractProtCTDT0.0050.0010.006
extractProtCTriad0.0860.0130.100
extractProtDC0.0030.0040.006
extractProtGeary0.0930.0090.103
extractProtMoran0.1000.0090.109
extractProtMoreauBroto0.1140.0100.125
extractProtPAAC0.3280.0090.338
extractProtPSSM0.0010.0010.002
extractProtPSSMAcc0.0000.0010.001
extractProtPSSMFeature0.0010.0000.001
extractProtQSO0.5760.0230.601
extractProtSOCN0.5950.0100.609
extractProtTC0.0290.0920.122
getCPI0.0020.0020.003
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt0.0010.0000.000
getMolFromCAS000
getMolFromChEMBL0.0000.0000.001
getMolFromDrugBank0.0000.0000.001
getMolFromKEGG0.0000.0010.000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI0.0010.0010.004
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank0.0010.0010.001
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA0.0010.0000.001
readMolFromSDF0.0010.0000.002
readMolFromSmi000
readPDB0.6460.0060.654
searchDrug0.0010.0000.001
segProt0.0020.0000.002