Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:06:37 -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 palomino3


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: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rcpi.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Rcpi_1.32.1.tar.gz
StartedAt: 2022-06-24 04:02:34 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 04:05:08 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 154.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Rcpi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rcpi.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Rcpi_1.32.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/Rcpi.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (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 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
  'F:/biocbuild/bbs-3.15-bioc/meat/Rcpi.Rcheck/00check.log'
for details.



Installation output

Rcpi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Rcpi
###
##############################################################################
##############################################################################


* installing to library 'F:/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 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 04:04:51 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 
   6.23    0.68    6.21 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR000
AA3DMoRSE0.010.000.01
AAACF000
AABLOSUM1000.000.010.02
AABLOSUM45000
AABLOSUM50000
AABLOSUM620.000.020.01
AABLOSUM80000
AABurden000
AACPSA000
AAConn0.000.010.02
AAConst000
AADescAll000
AAEdgeAdj0.000.000.01
AAEigIdx000
AAFGC000
AAGETAWAY000
AAGeom0.000.020.02
AAInfo000
AAMOE2D000
AAMOE3D000
AAMetaInfo0.020.000.01
AAMolProp000
AAPAM120000
AAPAM2500.000.010.02
AAPAM30000
AAPAM40000
AAPAM700.000.020.02
AARDF000
AARandic000
AATopo000
AATopoChg000
AAWHIM000
AAWalk0.000.010.02
AAindex000
OptAA3d000
acc0.000.020.01
calcDrugFPSim1.810.141.83
calcDrugMCSSim000
calcParProtGOSim000
calcParProtSeqSim0.030.000.02
calcTwoProtGOSim000
calcTwoProtSeqSim000
checkProt000
convMolFormat000
extractDrugAIO000
extractDrugALOGP0.030.010.01
extractDrugAminoAcidCount000
extractDrugApol000
extractDrugAromaticAtomsCount000
extractDrugAromaticBondsCount000
extractDrugAtomCount000
extractDrugAutocorrelationCharge000
extractDrugAutocorrelationMass000
extractDrugAutocorrelationPolarizability000
extractDrugBCUT000
extractDrugBPol000
extractDrugBondCount000
extractDrugCPSA000
extractDrugCarbonTypes000
extractDrugChiChain000
extractDrugChiCluster000
extractDrugChiPath000
extractDrugChiPathCluster000
extractDrugDescOB0.010.000.02
extractDrugECI000
extractDrugEstate000
extractDrugEstateComplete000
extractDrugExtended000
extractDrugExtendedComplete000
extractDrugFMF000
extractDrugFragmentComplexity000
extractDrugGraph000
extractDrugGraphComplete000
extractDrugGravitationalIndex000
extractDrugHBondAcceptorCount000
extractDrugHBondDonorCount000
extractDrugHybridization000
extractDrugHybridizationComplete000
extractDrugHybridizationRatio000
extractDrugIPMolecularLearning000
extractDrugKR000
extractDrugKRComplete000
extractDrugKappaShapeIndices000
extractDrugKierHallSmarts000
extractDrugLargestChain000
extractDrugLargestPiSystem000
extractDrugLengthOverBreadth000
extractDrugLongestAliphaticChain000
extractDrugMACCS0.000.010.02
extractDrugMACCSComplete000
extractDrugMDE000
extractDrugMannholdLogP000
extractDrugMomentOfInertia000
extractDrugOBFP2000
extractDrugOBFP30.100.000.09
extractDrugOBFP40.010.000.02
extractDrugOBMACCS0.020.000.01
extractDrugPetitjeanNumber000
extractDrugPetitjeanShapeIndex000
extractDrugPubChem000
extractDrugPubChemComplete000
extractDrugRotatableBondsCount000
extractDrugRuleOfFive0.000.020.02
extractDrugShortestPath000
extractDrugShortestPathComplete000
extractDrugStandard000
extractDrugStandardComplete000
extractDrugTPSA000
extractDrugVABC000
extractDrugVAdjMa000
extractDrugWHIM000
extractDrugWeight0.010.000.01
extractDrugWeightedPath000
extractDrugWienerNumbers000
extractDrugXLogP000
extractDrugZagrebIndex000
extractPCMBLOSUM0.020.000.02
extractPCMDescScales0.020.000.01
extractPCMFAScales0.030.000.03
extractPCMMDSScales0.010.000.02
extractPCMPropScales0.000.020.02
extractPCMScales0.020.000.01
extractProtAAC000
extractProtAPAAC0.650.030.69
extractProtCTDC000
extractProtCTDD000
extractProtCTDT0.020.000.01
extractProtCTriad0.090.000.10
extractProtDC000
extractProtGeary0.110.000.11
extractProtMoran0.100.010.11
extractProtMoreauBroto0.090.000.09
extractProtPAAC0.380.000.38
extractProtPSSM0.010.000.01
extractProtPSSMAcc000
extractProtPSSMFeature000
extractProtQSO0.50.00.5
extractProtSOCN0.770.000.77
extractProtTC0.090.050.14
getCPI000
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI000
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA000
readMolFromSDF000
readMolFromSmi000
readPDB0.970.001.21
searchDrug000
segProt000