Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:08:02 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 merida1


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 1.32.1  (landing page)
Nan Xiao
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: RELEASE_3_15
git_last_commit: e8428d2
git_last_commit_date: 2022-05-07 20:47:44 -0400 (Sat, 07 May 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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    NA  

Summary

Package: Rcpi
Version: 1.32.1
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_1.32.1.tar.gz
StartedAt: 2022-06-24 07:22:54 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 07:26:59 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 244.9 seconds
RetCode: 0
Status:   OK  
CheckDir: Rcpi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.32.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/Rcpi.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.32.1’
* 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-3.15-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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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 -- Fri Jun 24 07:26:43 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 
 11.457   0.604  10.503 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0040.0020.005
AA3DMoRSE0.0010.0010.003
AAACF0.0020.0010.002
AABLOSUM1000.0010.0020.003
AABLOSUM450.0010.0010.003
AABLOSUM500.0020.0020.003
AABLOSUM620.0010.0010.003
AABLOSUM800.0010.0010.003
AABurden0.0020.0020.003
AACPSA0.0010.0010.003
AAConn0.0020.0010.003
AAConst0.0010.0020.003
AADescAll0.0010.0010.002
AAEdgeAdj0.0020.0010.003
AAEigIdx0.0010.0020.003
AAFGC0.0010.0010.003
AAGETAWAY0.0020.0010.003
AAGeom0.0010.0010.003
AAInfo0.0020.0020.003
AAMOE2D0.0010.0020.003
AAMOE3D0.0020.0010.002
AAMetaInfo0.0010.0020.003
AAMolProp0.0020.0010.003
AAPAM1200.0020.0010.002
AAPAM2500.0010.0020.003
AAPAM300.0020.0010.003
AAPAM400.0020.0010.003
AAPAM700.0010.0020.002
AARDF0.0020.0010.003
AARandic0.0010.0010.003
AATopo0.0020.0020.003
AATopoChg0.0010.0020.003
AAWHIM0.0020.0010.003
AAWalk0.0010.0010.003
AAindex0.0020.0010.003
OptAA3d0.0000.0010.001
acc0.0150.0060.021
calcDrugFPSim3.5460.2121.077
calcDrugMCSSim0.0050.0030.008
calcParProtGOSim0.0000.0000.001
calcParProtSeqSim0.0070.0020.012
calcTwoProtGOSim000
calcTwoProtSeqSim0.0020.0010.002
checkProt0.0020.0010.002
convMolFormat0.0010.0000.001
extractDrugAIO0.0010.0000.001
extractDrugALOGP0.0010.0010.001
extractDrugAminoAcidCount0.0010.0000.001
extractDrugApol0.0010.0000.001
extractDrugAromaticAtomsCount0.0010.0000.001
extractDrugAromaticBondsCount0.0010.0000.001
extractDrugAtomCount0.0010.0010.001
extractDrugAutocorrelationCharge0.0010.0000.002
extractDrugAutocorrelationMass0.0010.0010.001
extractDrugAutocorrelationPolarizability0.0000.0000.001
extractDrugBCUT000
extractDrugBPol0.0010.0000.001
extractDrugBondCount0.0010.0010.001
extractDrugCPSA0.0010.0000.001
extractDrugCarbonTypes0.0010.0000.001
extractDrugChiChain0.0010.0000.001
extractDrugChiCluster0.0000.0000.001
extractDrugChiPath0.0010.0010.002
extractDrugChiPathCluster0.0010.0000.001
extractDrugDescOB0.0190.0060.026
extractDrugECI0.0010.0000.002
extractDrugEstate0.0010.0010.001
extractDrugEstateComplete0.0000.0000.001
extractDrugExtended0.0000.0000.001
extractDrugExtendedComplete0.0010.0000.001
extractDrugFMF0.0010.0000.001
extractDrugFragmentComplexity0.0010.0000.001
extractDrugGraph0.0010.0000.001
extractDrugGraphComplete0.0010.0010.001
extractDrugGravitationalIndex0.0010.0000.001
extractDrugHBondAcceptorCount0.0010.0000.001
extractDrugHBondDonorCount0.0010.0000.001
extractDrugHybridization0.0010.0000.001
extractDrugHybridizationComplete0.0010.0010.001
extractDrugHybridizationRatio0.0010.0000.001
extractDrugIPMolecularLearning0.0010.0000.001
extractDrugKR0.0010.0000.001
extractDrugKRComplete0.0000.0000.001
extractDrugKappaShapeIndices0.0010.0010.001
extractDrugKierHallSmarts0.0010.0000.001
extractDrugLargestChain0.0010.0000.001
extractDrugLargestPiSystem0.0010.0000.001
extractDrugLengthOverBreadth0.0010.0000.001
extractDrugLongestAliphaticChain0.0000.0010.001
extractDrugMACCS0.0010.0000.001
extractDrugMACCSComplete0.0010.0010.000
extractDrugMDE0.0010.0000.001
extractDrugMannholdLogP0.0010.0010.001
extractDrugMomentOfInertia0.0010.0000.001
extractDrugOBFP20.0090.0040.013
extractDrugOBFP30.0160.0040.020
extractDrugOBFP40.0090.0040.014
extractDrugOBMACCS0.0160.0060.021
extractDrugPetitjeanNumber0.0010.0010.002
extractDrugPetitjeanShapeIndex0.0010.0000.001
extractDrugPubChem0.0010.0010.001
extractDrugPubChemComplete0.0010.0000.001
extractDrugRotatableBondsCount0.0010.0000.001
extractDrugRuleOfFive0.0010.0010.001
extractDrugShortestPath0.0000.0000.001
extractDrugShortestPathComplete0.0010.0010.001
extractDrugStandard0.0010.0000.001
extractDrugStandardComplete0.0010.0000.001
extractDrugTPSA0.0010.0000.001
extractDrugVABC0.0010.0000.002
extractDrugVAdjMa0.0010.0010.001
extractDrugWHIM0.0010.0000.001
extractDrugWeight0.0010.0010.001
extractDrugWeightedPath0.0010.0000.001
extractDrugWienerNumbers0.0010.0010.001
extractDrugXLogP0.0010.0000.001
extractDrugZagrebIndex0.0010.0010.001
extractPCMBLOSUM0.0150.0020.017
extractPCMDescScales0.0180.0020.020
extractPCMFAScales0.0280.0050.033
extractPCMMDSScales0.0160.0030.019
extractPCMPropScales0.0300.0030.031
extractPCMScales0.0300.0030.032
extractProtAAC0.0030.0010.003
extractProtAPAAC1.4640.0361.499
extractProtCTDC0.0030.0010.005
extractProtCTDD0.0070.0020.008
extractProtCTDT0.0080.0010.009
extractProtCTriad0.1710.0180.188
extractProtDC0.0050.0040.009
extractProtGeary0.2610.0110.272
extractProtMoran0.2550.0110.267
extractProtMoreauBroto0.2430.0070.251
extractProtPAAC0.9740.0070.981
extractProtPSSM0.0010.0010.002
extractProtPSSMAcc0.0010.0000.002
extractProtPSSMFeature0.0020.0000.002
extractProtQSO1.8500.0121.864
extractProtSOCN1.8530.0141.869
extractProtTC0.0560.0680.125
getCPI0.0050.0010.005
getDrug0.0000.0010.001
getFASTAFromKEGG000
getFASTAFromUniProt0.0000.0000.001
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI0.0040.0010.006
getProt0.0000.0010.000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem0.0000.0000.001
readFASTA0.0010.0000.002
readMolFromSDF0.0030.0010.004
readMolFromSmi0.0010.0010.001
readPDB1.3430.0051.348
searchDrug0.0020.0010.003
segProt0.0020.0010.003