Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:45 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 nebbiolo1


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 1590/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.32.2  (landing page)
Nan Xiao
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: RELEASE_3_15
git_last_commit: 4c237e4
git_last_commit_date: 2022-07-17 23:35:52 -0400 (Sun, 17 Jul 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Rcpi
Version: 1.32.2
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings Rcpi_1.32.2.tar.gz
StartedAt: 2022-10-18 21:23:04 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 21:25:01 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 117.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Rcpi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings Rcpi_1.32.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/Rcpi.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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 ‘1.32.2’
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/Rcpi.Rcheck/00check.log’
for details.



Installation output

Rcpi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL Rcpi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 -- Tue Oct 18 21:24:55 2022 
*********************************************** 
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 
  6.701   0.322   5.576 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.1410.0000.142
AA3DMoRSE0.0020.0000.001
AAACF0.0020.0000.001
AABLOSUM1000.0010.0000.001
AABLOSUM450.0010.0000.001
AABLOSUM500.0010.0000.001
AABLOSUM620.0010.0000.001
AABLOSUM800.0010.0000.000
AABurden0.0010.0000.001
AACPSA0.0010.0000.001
AAConn0.0010.0000.001
AAConst0.0010.0000.001
AADescAll0.0010.0000.000
AAEdgeAdj0.0010.0000.001
AAEigIdx0.0010.0000.001
AAFGC0.0010.0000.000
AAGETAWAY0.0010.0000.001
AAGeom0.0000.0010.001
AAInfo0.0000.0010.000
AAMOE2D0.0000.0000.001
AAMOE3D0.0000.0010.001
AAMetaInfo0.0000.0010.000
AAMolProp0.0000.0000.001
AAPAM1200.0010.0000.001
AAPAM2500.0010.0000.000
AAPAM300.0010.0000.001
AAPAM400.0010.0000.001
AAPAM700.0010.0000.000
AARDF0.0010.0000.001
AARandic0.0010.0000.001
AATopo0.0010.0000.000
AATopoChg0.0010.0000.001
AAWHIM0.0010.0000.001
AAWalk0.0010.0000.000
AAindex0.0010.0000.001
OptAA3d000
acc0.0020.0110.014
calcDrugFPSim2.4640.1230.555
calcDrugMCSSim0.0210.0000.010
calcParProtGOSim0.0010.0000.001
calcParProtSeqSim0.0140.0000.007
calcTwoProtGOSim000
calcTwoProtSeqSim0.0020.0000.002
checkProt0.0050.0000.001
convMolFormat0.0010.0000.001
extractDrugAIO0.0010.0000.001
extractDrugALOGP0.0050.0000.001
extractDrugAminoAcidCount0.0010.0000.001
extractDrugApol0.0010.0000.001
extractDrugAromaticAtomsCount0.0010.0000.001
extractDrugAromaticBondsCount000
extractDrugAtomCount000
extractDrugAutocorrelationCharge000
extractDrugAutocorrelationMass0.0050.0000.001
extractDrugAutocorrelationPolarizability0.0010.0000.001
extractDrugBCUT0.0010.0000.001
extractDrugBPol0.0010.0000.001
extractDrugBondCount000
extractDrugCPSA000
extractDrugCarbonTypes0.0010.0000.001
extractDrugChiChain0.0050.0000.001
extractDrugChiCluster0.0010.0000.001
extractDrugChiPath0.0000.0000.001
extractDrugChiPathCluster000
extractDrugDescOB0.0310.0040.019
extractDrugECI0.0010.0000.001
extractDrugEstate0.0030.0000.000
extractDrugEstateComplete0.0000.0010.000
extractDrugExtended0.0000.0010.001
extractDrugExtendedComplete0.0000.0010.001
extractDrugFMF0.0000.0000.001
extractDrugFragmentComplexity0.0000.0000.001
extractDrugGraph000
extractDrugGraphComplete000
extractDrugGravitationalIndex0.0010.0000.001
extractDrugHBondAcceptorCount0.0010.0000.001
extractDrugHBondDonorCount0.0010.0000.001
extractDrugHybridization0.0000.0000.001
extractDrugHybridizationComplete000
extractDrugHybridizationRatio000
extractDrugIPMolecularLearning0.0000.0010.001
extractDrugKR0.0010.0000.001
extractDrugKRComplete0.0010.0000.001
extractDrugKappaShapeIndices0.0010.0000.001
extractDrugKierHallSmarts000
extractDrugLargestChain000
extractDrugLargestPiSystem000
extractDrugLengthOverBreadth0.0000.0010.000
extractDrugLongestAliphaticChain0.0010.0000.001
extractDrugMACCS0.0010.0000.001
extractDrugMACCSComplete0.0010.0000.001
extractDrugMDE0.0000.0000.001
extractDrugMannholdLogP000
extractDrugMomentOfInertia000
extractDrugOBFP20.0190.0080.027
extractDrugOBFP30.0060.0040.011
extractDrugOBFP40.3530.3150.668
extractDrugOBMACCS0.0060.0040.009
extractDrugPetitjeanNumber000
extractDrugPetitjeanShapeIndex0.0000.0010.001
extractDrugPubChem0.0000.0010.001
extractDrugPubChemComplete0.0000.0010.001
extractDrugRotatableBondsCount0.0000.0010.000
extractDrugRuleOfFive0.0000.0010.000
extractDrugShortestPath0.0000.0010.000
extractDrugShortestPathComplete000
extractDrugStandard000
extractDrugStandardComplete000
extractDrugTPSA0.0000.0000.001
extractDrugVABC0.0000.0000.001
extractDrugVAdjMa0.0000.0000.001
extractDrugWHIM0.0000.0000.001
extractDrugWeight0.0000.0010.001
extractDrugWeightedPath0.0000.0010.001
extractDrugWienerNumbers0.0000.0010.001
extractDrugXLogP0.0000.0010.001
extractDrugZagrebIndex0.0010.0000.000
extractPCMBLOSUM0.0090.0000.008
extractPCMDescScales0.0040.0040.009
extractPCMFAScales0.0140.0080.022
extractPCMMDSScales0.0080.0000.008
extractPCMPropScales0.0100.0000.009
extractPCMScales0.0130.0000.013
extractProtAAC0.0020.0000.002
extractProtAPAAC0.6560.0720.727
extractProtCTDC0.0030.0000.003
extractProtCTDD0.0030.0080.012
extractProtCTDT0.0040.0000.005
extractProtCTriad0.0620.0160.078
extractProtDC0.0050.0040.009
extractProtGeary0.0870.0160.102
extractProtMoran0.0900.0160.106
extractProtMoreauBroto0.0800.0110.090
extractProtPAAC0.3260.0040.329
extractProtPSSM0.0010.0000.001
extractProtPSSMAcc0.0000.0010.001
extractProtPSSMFeature0.0000.0010.001
extractProtQSO0.5390.0130.551
extractProtSOCN0.5760.0010.576
extractProtTC0.0210.1230.144
getCPI0.0010.0030.005
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt0.0010.0000.000
getMolFromCAS000
getMolFromChEMBL0.0000.0000.001
getMolFromDrugBank0.0000.0010.000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB0.0000.0000.001
getPPI0.0040.0000.005
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt0.0000.0010.000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG0.0000.0000.001
getSmiFromPubChem000
readFASTA0.0010.0000.001
readMolFromSDF0.0020.0000.002
readMolFromSmi0.0010.0000.001
readPDB0.7770.0070.785
searchDrug0.0010.0000.002
segProt0.0030.0000.003