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This page was generated on 2023-06-06 11:00:39 -0000 (Tue, 06 Jun 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4366
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CHECK results for Rcpi on kunpeng2


To the developers/maintainers of the Rcpi package:
- 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 Troubleshooting Build Report for more information.

- Use the following Renviron settings to reproduce errors and warnings.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1625/2199HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.37.0  (landing page)
Nan Xiao
Snapshot Date: 2023-06-05 06:35:06 -0000 (Mon, 05 Jun 2023)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: devel
git_last_commit: bcb3ec7
git_last_commit_date: 2023-04-25 14:31:00 -0000 (Tue, 25 Apr 2023)
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

Summary

Package: Rcpi
Version: 1.37.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings Rcpi_1.37.0.tar.gz
StartedAt: 2023-06-06 04:58:02 -0000 (Tue, 06 Jun 2023)
EndedAt: 2023-06-06 05:00:38 -0000 (Tue, 06 Jun 2023)
EllapsedTime: 156.2 seconds
RetCode: 0
Status:   OK  
CheckDir: Rcpi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings Rcpi_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Rcpi.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.37.0’
* 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:
  .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 loading without being on the library search path ... 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 ...
  ‘Rcpi-quickref.Rmd’ using ‘UTF-8’... OK
  ‘Rcpi.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/Rcpi.Rcheck/00check.log’
for details.



Installation output

Rcpi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL Rcpi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-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 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 Jun  6 05:00:25 2023 
*********************************************** 
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 
  7.041   0.463   6.422 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0020.0000.003
AA3DMoRSE0.0010.0000.001
AAACF0.0000.0010.001
AABLOSUM1000.0000.0010.001
AABLOSUM450.0000.0000.001
AABLOSUM500.0010.0000.001
AABLOSUM620.0010.0000.001
AABLOSUM800.0010.0000.001
AABurden0.0010.0000.000
AACPSA0.0010.0000.001
AAConn0.0000.0000.001
AAConst0.0010.0000.001
AADescAll0.0010.0000.001
AAEdgeAdj0.0010.0000.001
AAEigIdx0.0010.0000.001
AAFGC0.0010.0000.001
AAGETAWAY0.0000.0010.001
AAGeom0.0000.0010.001
AAInfo0.0000.0000.001
AAMOE2D0.0010.0000.001
AAMOE3D0.0010.0000.001
AAMetaInfo0.0000.0010.000
AAMolProp0.0000.0010.001
AAPAM1200.0000.0010.000
AAPAM2500.0000.0010.001
AAPAM300.0000.0010.000
AAPAM400.0000.0010.001
AAPAM700.0000.0010.001
AARDF0.0000.0010.001
AARandic0.0010.0000.001
AATopo0.0010.0000.001
AATopoChg0.0000.0000.001
AAWHIM0.0000.0010.001
AAWalk0.0000.0010.001
AAindex0.0000.0000.001
OptAA3d000
acc0.0130.0000.013
calcDrugFPSim2.2760.2470.777
calcDrugMCSSim0.0050.0000.007
calcParProtGOSim000
calcParProtSeqSim0.0050.0030.011
calcTwoProtGOSim0.0010.0000.001
calcTwoProtSeqSim0.0020.0000.002
checkProt0.0010.0000.001
convMolFormat0.0010.0000.001
extractDrugAIO0.0000.0000.001
extractDrugALOGP0.0000.0010.001
extractDrugAminoAcidCount0.0000.0010.001
extractDrugApol0.0000.0000.001
extractDrugAromaticAtomsCount0.0010.0000.001
extractDrugAromaticBondsCount0.0010.0000.001
extractDrugAtomCount0.0010.0000.001
extractDrugAutocorrelationCharge0.0010.0000.001
extractDrugAutocorrelationMass0.0010.0000.001
extractDrugAutocorrelationPolarizability0.0010.0000.001
extractDrugBCUT0.0010.0000.001
extractDrugBPol0.0010.0000.001
extractDrugBondCount0.0010.0000.001
extractDrugCPSA0.0010.0000.001
extractDrugCarbonTypes0.0010.0000.001
extractDrugChiChain0.0010.0000.001
extractDrugChiCluster0.0020.0000.002
extractDrugChiPath0.0010.0000.001
extractDrugChiPathCluster0.0010.0000.001
extractDrugDescOB0.1160.0680.185
extractDrugECI0.0010.0000.001
extractDrugEstate0.0010.0000.001
extractDrugEstateComplete0.0010.0000.001
extractDrugExtended0.0010.0000.000
extractDrugExtendedComplete0.0000.0000.001
extractDrugFMF0.0010.0000.001
extractDrugFragmentComplexity0.0010.0000.001
extractDrugGraph0.0000.0000.001
extractDrugGraphComplete0.0000.0010.001
extractDrugGravitationalIndex0.0000.0020.001
extractDrugHBondAcceptorCount0.0010.0000.001
extractDrugHBondDonorCount0.0010.0000.001
extractDrugHybridization0.0010.0000.001
extractDrugHybridizationComplete0.0010.0000.001
extractDrugHybridizationRatio0.0010.0000.001
extractDrugIPMolecularLearning0.0010.0000.000
extractDrugKR0.0000.0000.001
extractDrugKRComplete0.0010.0000.001
extractDrugKappaShapeIndices0.0010.0000.001
extractDrugKierHallSmarts0.0010.0000.001
extractDrugLargestChain0.0010.0000.001
extractDrugLargestPiSystem0.0010.0000.001
extractDrugLengthOverBreadth0.0010.0000.000
extractDrugLongestAliphaticChain0.0000.0000.001
extractDrugMACCS0.0010.0000.001
extractDrugMACCSComplete0.0010.0000.001
extractDrugMDE0.0010.0000.001
extractDrugMannholdLogP0.0010.0000.000
extractDrugMomentOfInertia0.0010.0000.001
extractDrugOBFP20.3990.1970.596
extractDrugOBFP30.0060.0000.007
extractDrugOBFP40.0050.0000.006
extractDrugOBMACCS0.0060.0070.013
extractDrugPetitjeanNumber0.0010.0000.001
extractDrugPetitjeanShapeIndex0.0010.0000.001
extractDrugPubChem0.0010.0000.000
extractDrugPubChemComplete0.0010.0000.001
extractDrugRotatableBondsCount0.0010.0000.001
extractDrugRuleOfFive0.0000.0000.001
extractDrugShortestPath0.0010.0000.001
extractDrugShortestPathComplete0.0010.0000.001
extractDrugStandard0.0010.0000.001
extractDrugStandardComplete000
extractDrugTPSA0.0000.0000.001
extractDrugVABC0.0000.0010.001
extractDrugVAdjMa0.0000.0010.001
extractDrugWHIM0.0000.0010.000
extractDrugWeight0.0010.0000.001
extractDrugWeightedPath0.0010.0000.001
extractDrugWienerNumbers0.0010.0000.001
extractDrugXLogP0.0000.0010.000
extractDrugZagrebIndex0.0000.0010.001
extractPCMBLOSUM0.0090.0050.015
extractPCMDescScales0.0150.0000.015
extractPCMFAScales0.0150.0070.022
extractPCMMDSScales0.0140.0010.014
extractPCMPropScales0.0170.0000.017
extractPCMScales0.0350.0000.035
extractProtAAC0.0030.0000.003
extractProtAPAAC1.0890.1671.259
extractProtCTDC0.0040.0000.004
extractProtCTDD0.0050.0000.005
extractProtCTDT0.0020.0040.006
extractProtCTriad0.1230.0070.130
extractProtDC0.0050.0000.005
extractProtGeary0.1690.0080.178
extractProtMoran0.1730.0360.210
extractProtMoreauBroto0.1590.0040.163
extractProtPAAC0.5900.0360.628
extractProtPSSM0.0010.0000.001
extractProtPSSMAcc0.0010.0000.001
extractProtPSSMFeature0.0010.0000.001
extractProtQSO0.9890.0080.999
extractProtSOCN0.9930.0000.994
extractProtTC0.0160.0350.053
getCPI0.0040.0000.005
getDrug0.0000.0000.001
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI0.0010.0010.003
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem0.0010.0000.000
readFASTA0.0010.0000.002
readMolFromSDF0.0020.0000.002
readMolFromSmi0.0010.0000.001
readPDB0.9270.0000.931
searchDrug0.0020.0000.002
segProt0.0020.0000.003