Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:05:16 -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 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 1.32.1  (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: /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_1.32.1.tar.gz
StartedAt: 2022-06-23 21:35:01 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 21:36:56 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 115.3 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_1.32.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/Rcpi.Rcheck’
* using R version 4.2.0 (2022-04-22)
* 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 ‘1.32.1’
* 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
  ‘/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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
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 -- Thu Jun 23 21:36:50 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 
  6.237   0.341   5.274 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0020.0010.002
AA3DMoRSE000
AAACF0.0010.0000.001
AABLOSUM1000.0000.0010.001
AABLOSUM450.0000.0000.001
AABLOSUM500.0010.0000.001
AABLOSUM620.0010.0000.001
AABLOSUM800.0010.0000.001
AABurden0.0010.0000.001
AACPSA0.0010.0000.000
AAConn0.0000.0000.001
AAConst0.0000.0010.001
AADescAll0.0000.0010.001
AAEdgeAdj0.0010.0000.001
AAEigIdx0.0010.0000.000
AAFGC0.0010.0000.001
AAGETAWAY0.0000.0000.001
AAGeom0.0010.0000.001
AAInfo0.0010.0000.001
AAMOE2D0.0010.0000.000
AAMOE3D0.0010.0000.001
AAMetaInfo0.0010.0000.001
AAMolProp0.0000.0000.001
AAPAM1200.0000.0010.001
AAPAM2500.0000.0010.000
AAPAM300.0010.0000.001
AAPAM400.0000.0000.001
AAPAM700.0010.0000.001
AARDF0.0010.0000.001
AARandic0.0010.0000.000
AATopo0.0010.0000.001
AATopoChg0.0010.0000.001
AAWHIM0.0010.0000.000
AAWalk0.0000.0000.001
AAindex0.0000.0010.001
OptAA3d000
acc0.0050.0080.014
calcDrugFPSim2.5990.0820.579
calcDrugMCSSim0.0050.0040.009
calcParProtGOSim000
calcParProtSeqSim0.0060.0000.007
calcTwoProtGOSim0.0000.0010.000
calcTwoProtSeqSim0.0000.0020.003
checkProt0.0020.0000.002
convMolFormat0.0000.0020.002
extractDrugAIO0.0010.0000.001
extractDrugALOGP000
extractDrugAminoAcidCount000
extractDrugApol0.0000.0010.001
extractDrugAromaticAtomsCount0.0010.0000.001
extractDrugAromaticBondsCount0.0010.0000.001
extractDrugAtomCount0.0010.0000.001
extractDrugAutocorrelationCharge000
extractDrugAutocorrelationMass000
extractDrugAutocorrelationPolarizability000
extractDrugBCUT000
extractDrugBPol0.0000.0000.001
extractDrugBondCount0.0000.0000.001
extractDrugCPSA0.0010.0000.001
extractDrugCarbonTypes0.0010.0000.001
extractDrugChiChain0.0010.0000.001
extractDrugChiCluster0.0010.0000.000
extractDrugChiPath0.0010.0000.000
extractDrugChiPathCluster000
extractDrugDescOB0.0080.0110.019
extractDrugECI0.0010.0000.000
extractDrugEstate0.0000.0000.001
extractDrugEstateComplete0.0000.0000.001
extractDrugExtended0.0010.0000.000
extractDrugExtendedComplete0.0010.0000.001
extractDrugFMF0.0010.0000.001
extractDrugFragmentComplexity0.0000.0000.001
extractDrugGraph0.0000.0010.000
extractDrugGraphComplete0.0000.0010.000
extractDrugGravitationalIndex0.0010.0000.000
extractDrugHBondAcceptorCount0.0010.0000.001
extractDrugHBondDonorCount0.0010.0000.001
extractDrugHybridization0.0010.0000.001
extractDrugHybridizationComplete0.0000.0010.001
extractDrugHybridizationRatio0.0000.0000.001
extractDrugIPMolecularLearning000
extractDrugKR000
extractDrugKRComplete0.0010.0000.000
extractDrugKappaShapeIndices0.0010.0000.000
extractDrugKierHallSmarts0.0010.0000.001
extractDrugLargestChain0.0010.0000.001
extractDrugLargestPiSystem0.0010.0000.001
extractDrugLengthOverBreadth0.0000.0000.001
extractDrugLongestAliphaticChain0.0000.0000.001
extractDrugMACCS000
extractDrugMACCSComplete0.0010.0000.000
extractDrugMDE0.0010.0000.000
extractDrugMannholdLogP0.0000.0010.001
extractDrugMomentOfInertia0.0000.0000.001
extractDrugOBFP20.0150.0130.029
extractDrugOBFP30.0020.0080.010
extractDrugOBFP40.4480.0040.452
extractDrugOBMACCS0.0020.0080.010
extractDrugPetitjeanNumber0.0010.0000.000
extractDrugPetitjeanShapeIndex0.0000.0000.001
extractDrugPubChem0.0000.0000.001
extractDrugPubChemComplete0.0010.0000.001
extractDrugRotatableBondsCount0.0000.0010.001
extractDrugRuleOfFive0.0000.0010.000
extractDrugShortestPath0.0000.0000.001
extractDrugShortestPathComplete0.0010.0000.001
extractDrugStandard0.0010.0000.001
extractDrugStandardComplete0.0010.0000.000
extractDrugTPSA0.0010.0000.000
extractDrugVABC0.0010.0000.000
extractDrugVAdjMa0.0010.0000.000
extractDrugWHIM0.0010.0000.000
extractDrugWeight0.0000.0000.001
extractDrugWeightedPath0.0000.0000.001
extractDrugWienerNumbers0.0000.0000.001
extractDrugXLogP0.0010.0000.001
extractDrugZagrebIndex0.0010.0000.001
extractPCMBLOSUM0.0090.0000.009
extractPCMDescScales0.0140.0000.013
extractPCMFAScales0.3630.0120.374
extractPCMMDSScales0.0080.0000.008
extractPCMPropScales0.0100.0000.011
extractPCMScales0.0140.0000.014
extractProtAAC0.0000.0030.003
extractProtAPAAC0.7200.0290.750
extractProtCTDC0.0020.0000.002
extractProtCTDD0.0030.0040.005
extractProtCTDT0.0040.0000.004
extractProtCTriad0.0680.0120.080
extractProtDC0.0000.0090.009
extractProtGeary0.1040.0060.109
extractProtMoran0.0890.0080.097
extractProtMoreauBroto0.0830.0200.104
extractProtPAAC0.3320.0240.356
extractProtPSSM0.0010.0000.002
extractProtPSSMAcc0.0010.0000.001
extractProtPSSMFeature0.0010.0000.001
extractProtQSO0.5850.0890.673
extractProtSOCN0.5430.0030.546
extractProtTC0.0300.1130.143
getCPI0.0020.0040.006
getDrug0.0000.0000.001
getFASTAFromKEGG0.0010.0000.000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL0.0000.0000.001
getMolFromDrugBank0.0010.0000.000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB0.0000.0000.001
getPPI0.0000.0050.005
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem0.0000.0000.001
readFASTA0.0010.0000.002
readMolFromSDF0.0010.0010.002
readMolFromSmi0.0000.0010.001
readPDB0.8010.0080.808
searchDrug0.0020.0000.001
segProt0.0010.0020.003