Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:37 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 machv2


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 1547/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.30.0  (landing page)
Nan Xiao
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: RELEASE_3_14
git_last_commit: d21a4c1
git_last_commit_date: 2021-10-26 12:12:30 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Rcpi
Version: 1.30.0
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_1.30.0.tar.gz
StartedAt: 2022-04-12 17:21:38 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 17:25:24 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 226.2 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_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/Rcpi.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.30.0’
* 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:
  .BBSoptions
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-3.14-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/4.1/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
** 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 4.1.3 (2022-03-10) -- "One Push-Up"
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 -- Tue Apr 12 17:25:08 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 
 10.522   0.690   9.579 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0040.0020.006
AA3DMoRSE0.0010.0020.003
AAACF0.0020.0020.004
AABLOSUM1000.0020.0020.003
AABLOSUM450.0010.0020.003
AABLOSUM500.0010.0020.002
AABLOSUM620.0020.0020.003
AABLOSUM800.0010.0020.003
AABurden0.0010.0010.002
AACPSA0.0010.0010.003
AAConn0.0010.0010.002
AAConst0.0010.0020.002
AADescAll0.0010.0020.002
AAEdgeAdj0.0020.0020.003
AAEigIdx0.0010.0010.002
AAFGC0.0020.0020.003
AAGETAWAY0.0010.0010.003
AAGeom0.0010.0010.002
AAInfo0.0010.0010.002
AAMOE2D0.0010.0010.003
AAMOE3D0.0010.0010.003
AAMetaInfo0.0020.0010.002
AAMolProp0.0010.0010.003
AAPAM1200.0010.0010.003
AAPAM2500.0020.0020.003
AAPAM300.0010.0020.003
AAPAM400.0020.0020.003
AAPAM700.0010.0020.003
AARDF0.0010.0010.003
AARandic0.0020.0020.003
AATopo0.0010.0010.001
AATopoChg0.0010.0020.003
AAWHIM0.0010.0010.002
AAWalk0.0010.0020.003
AAindex0.0020.0020.003
OptAA3d0.0000.0000.001
acc0.0150.0170.115
calcDrugFPSim3.1920.2151.040
calcDrugMCSSim0.0290.0050.021
calcParProtGOSim0.0000.0000.001
calcParProtSeqSim0.0070.0020.009
calcTwoProtGOSim0.0000.0010.000
calcTwoProtSeqSim0.0020.0010.003
checkProt0.0010.0000.002
convMolFormat0.0010.0000.002
extractDrugAIO0.0010.0000.002
extractDrugALOGP0.0000.0000.001
extractDrugAminoAcidCount0.0000.0010.001
extractDrugApol0.0010.0000.000
extractDrugAromaticAtomsCount0.0010.0010.001
extractDrugAromaticBondsCount0.0010.0000.000
extractDrugAtomCount0.0010.0000.001
extractDrugAutocorrelationCharge0.0000.0010.002
extractDrugAutocorrelationMass0.0010.0010.001
extractDrugAutocorrelationPolarizability0.0010.0010.001
extractDrugBCUT0.0000.0000.001
extractDrugBPol0.0010.0000.001
extractDrugBondCount0.0010.0010.001
extractDrugCPSA0.0010.0010.001
extractDrugCarbonTypes0.0000.0010.002
extractDrugChiChain0.0010.0010.002
extractDrugChiCluster0.0010.0010.001
extractDrugChiPath0.0010.0010.001
extractDrugChiPathCluster0.0000.0000.001
extractDrugDescOB0.0090.0050.014
extractDrugECI0.0010.0010.002
extractDrugEstate0.0010.0010.001
extractDrugEstateComplete0.0010.0010.000
extractDrugExtended0.0010.0000.001
extractDrugExtendedComplete0.0010.0010.002
extractDrugFMF0.0010.0000.001
extractDrugFragmentComplexity0.0010.0000.001
extractDrugGraph0.0000.0010.001
extractDrugGraphComplete0.0010.0010.001
extractDrugGravitationalIndex0.0000.0010.001
extractDrugHBondAcceptorCount0.0010.0000.001
extractDrugHBondDonorCount0.0010.0000.001
extractDrugHybridization0.0010.0000.001
extractDrugHybridizationComplete0.0010.0000.001
extractDrugHybridizationRatio0.0000.0000.002
extractDrugIPMolecularLearning0.0010.0000.001
extractDrugKR0.0010.0010.000
extractDrugKRComplete0.0010.0000.001
extractDrugKappaShapeIndices0.0010.0000.002
extractDrugKierHallSmarts0.0010.0000.001
extractDrugLargestChain0.0010.0000.001
extractDrugLargestPiSystem0.0010.0000.001
extractDrugLengthOverBreadth0.0000.0010.001
extractDrugLongestAliphaticChain000
extractDrugMACCS0.0000.0000.001
extractDrugMACCSComplete0.0000.0000.001
extractDrugMDE0.0000.0000.001
extractDrugMannholdLogP0.0000.0010.001
extractDrugMomentOfInertia0.0010.0000.001
extractDrugOBFP20.1160.0040.121
extractDrugOBFP30.3530.0050.359
extractDrugOBFP40.0070.0030.010
extractDrugOBMACCS0.0100.0050.014
extractDrugPetitjeanNumber0.0010.0010.001
extractDrugPetitjeanShapeIndex0.0010.0010.001
extractDrugPubChem0.0000.0010.001
extractDrugPubChemComplete0.0010.0010.002
extractDrugRotatableBondsCount0.0010.0010.001
extractDrugRuleOfFive0.0010.0010.001
extractDrugShortestPath0.0010.0010.001
extractDrugShortestPathComplete0.0010.0010.001
extractDrugStandard0.0000.0010.002
extractDrugStandardComplete0.0010.0000.001
extractDrugTPSA0.0010.0000.001
extractDrugVABC0.0010.0000.002
extractDrugVAdjMa0.0010.0000.002
extractDrugWHIM0.0010.0000.001
extractDrugWeight0.0010.0000.001
extractDrugWeightedPath0.0010.0000.001
extractDrugWienerNumbers0.0010.0000.001
extractDrugXLogP0.0010.0000.002
extractDrugZagrebIndex0.0010.0000.001
extractPCMBLOSUM0.0130.0010.014
extractPCMDescScales0.0140.0020.017
extractPCMFAScales0.0260.0050.031
extractPCMMDSScales0.0230.0060.030
extractPCMPropScales0.0190.0030.022
extractPCMScales0.0290.0030.032
extractProtAAC0.0030.0010.004
extractProtAPAAC1.6540.0891.750
extractProtCTDC0.0030.0010.005
extractProtCTDD0.0060.0030.009
extractProtCTDT0.0080.0010.009
extractProtCTriad0.1560.0170.174
extractProtDC0.0050.0080.013
extractProtGeary0.2220.0160.239
extractProtMoran0.2310.0160.248
extractProtMoreauBroto0.2380.0160.254
extractProtPAAC0.8150.0090.825
extractProtPSSM0.0020.0000.001
extractProtPSSMAcc0.0020.0000.002
extractProtPSSMFeature0.0010.0010.002
extractProtQSO1.6280.0561.684
extractProtSOCN1.5780.0111.591
extractProtTC0.0670.1710.239
getCPI0.0040.0020.007
getDrug000
getFASTAFromKEGG0.0000.0010.001
getFASTAFromUniProt0.0000.0010.001
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG0.0000.0000.001
getMolFromPubChem000
getPDBFromRCSBPDB0.0000.0000.001
getPPI0.0030.0030.007
getProt0.0010.0000.000
getSeqFromKEGG000
getSeqFromRCSBPDB0.0000.0010.001
getSeqFromUniProt0.0000.0000.001
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem0.0000.0000.001
readFASTA0.0020.0000.003
readMolFromSDF0.0030.0010.003
readMolFromSmi0.0010.0010.001
readPDB1.2670.0071.275
searchDrug0.0010.0010.002
segProt0.0040.0030.006