Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-11-02 11:41:08 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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

Package 1681/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.38.0  (landing page)
Nan Xiao
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: RELEASE_3_18
git_last_commit: e0262bf
git_last_commit_date: 2023-10-24 09:58:01 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

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.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: Rcpi
Version: 1.38.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings Rcpi_1.38.0.tar.gz
StartedAt: 2023-11-02 13:30:47 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 13:33:05 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 138.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Rcpi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings Rcpi_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Rcpi.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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
* using option ‘--no-vignettes’
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.38.0’
* 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 ‘testthat.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-3.18-bioc/meat/Rcpi.Rcheck/00check.log’
for details.



Installation output

Rcpi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL Rcpi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/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/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
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.

> library(testthat)
> library(Rcpi)

> 
> test_check("Rcpi")
[ FAIL 0 | WARN 0 | SKIP 5 | PASS 17 ]

══ Skipped tests (5) ═══════════════════════════════════════════════════════════
• rcdk cannot be loaded (5): 'test_extractDrugALOGP.R:2:5',
  'test_extractDrugECI.R:2:5', 'test_extractDrugRuleOfFive.R:2:5',
  'test_extractDrugTPSA.R:2:5', 'test_extractDrugXLogP.R:2:5'

[ FAIL 0 | WARN 0 | SKIP 5 | PASS 17 ]
> 
> proc.time()
   user  system elapsed 
  5.781   0.193   5.974 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0020.0000.002
AA3DMoRSE0.0010.0000.000
AAACF0.0010.0000.001
AABLOSUM1000.0000.0000.001
AABLOSUM450.0010.0000.001
AABLOSUM500.0010.0000.000
AABLOSUM620.0000.0000.001
AABLOSUM800.0010.0000.001
AABurden0.0010.0000.001
AACPSA0.0010.0000.001
AAConn0.0010.0000.001
AAConst0.0010.0000.001
AADescAll0.0000.0010.001
AAEdgeAdj0.0000.0000.001
AAEigIdx0.0000.0010.001
AAFGC0.0010.0000.001
AAGETAWAY0.0010.0000.000
AAGeom0.0000.0000.001
AAInfo0.0010.0000.001
AAMOE2D0.0010.0000.000
AAMOE3D0.0000.0000.001
AAMetaInfo0.0010.0000.001
AAMolProp0.0010.0000.000
AAPAM1200.0000.0000.001
AAPAM2500.0010.0000.001
AAPAM300.0010.0000.000
AAPAM400.0000.0000.001
AAPAM700.0010.0000.001
AARDF0.0010.0000.000
AARandic0.0000.0000.001
AATopo0.0010.0000.001
AATopoChg0.0010.0000.001
AAWHIM0.0000.0000.001
AAWalk0.0010.0000.001
AAindex0.0010.0000.001
OptAA3d000
acc0.0080.0040.012
calcDrugFPSim000
calcDrugMCSSim0.0180.0030.022
calcParProtGOSim000
calcParProtSeqSim0.0070.0000.009
calcTwoProtGOSim0.0000.0000.001
calcTwoProtSeqSim0.0020.0000.002
checkProt0.0010.0000.001
convMolFormat0.0010.0000.001
extractDrugAIO0.0010.0000.001
extractDrugALOGP0.0010.0000.001
extractDrugAminoAcidCount0.0010.0000.001
extractDrugApol0.0000.0000.001
extractDrugAromaticAtomsCount0.0010.0000.001
extractDrugAromaticBondsCount0.0010.0000.001
extractDrugAtomCount0.0010.0000.000
extractDrugAutocorrelationCharge0.0010.0000.001
extractDrugAutocorrelationMass0.0010.0000.001
extractDrugAutocorrelationPolarizability0.0010.0000.001
extractDrugBCUT0.0010.0000.001
extractDrugBPol000
extractDrugBondCount0.0010.0000.001
extractDrugCPSA0.0010.0000.001
extractDrugCarbonTypes0.0010.0000.000
extractDrugChiChain0.0010.0000.001
extractDrugChiCluster0.0010.0000.001
extractDrugChiPath0.0010.0000.001
extractDrugChiPathCluster0.0010.0000.001
extractDrugDescOB0.0100.0040.015
extractDrugECI0.0010.0000.002
extractDrugEstate0.0010.0000.001
extractDrugEstateComplete0.0010.0000.000
extractDrugExtended0.0010.0000.001
extractDrugExtendedComplete0.0010.0000.001
extractDrugFMF0.0010.0000.000
extractDrugFragmentComplexity0.0010.0000.001
extractDrugGraph0.0000.0000.001
extractDrugGraphComplete0.0010.0000.001
extractDrugGravitationalIndex0.0010.0000.001
extractDrugHBondAcceptorCount0.0010.0000.001
extractDrugHBondDonorCount0.0010.0000.001
extractDrugHybridization0.0010.0000.001
extractDrugHybridizationComplete0.0010.0000.001
extractDrugHybridizationRatio0.0010.0000.001
extractDrugIPMolecularLearning0.0000.0000.001
extractDrugKR0.0010.0000.000
extractDrugKRComplete0.0000.0010.001
extractDrugKappaShapeIndices0.0000.0010.001
extractDrugKierHallSmarts0.0000.0010.000
extractDrugLargestChain0.0010.0000.001
extractDrugLargestPiSystem0.0010.0000.001
extractDrugLengthOverBreadth0.0010.0000.001
extractDrugLongestAliphaticChain0.0010.0000.001
extractDrugMACCS0.0010.0000.001
extractDrugMACCSComplete0.0010.0000.001
extractDrugMDE0.0000.0010.001
extractDrugMannholdLogP0.0000.0010.000
extractDrugMomentOfInertia0.0000.0010.001
extractDrugOBFP20.0020.0030.006
extractDrugOBFP30.0960.0000.096
extractDrugOBFP40.0130.0000.014
extractDrugOBMACCS0.0010.0060.007
extractDrugPetitjeanNumber0.0000.0010.001
extractDrugPetitjeanShapeIndex0.0010.0000.001
extractDrugPubChem0.0010.0000.001
extractDrugPubChemComplete0.0010.0000.001
extractDrugRotatableBondsCount000
extractDrugRuleOfFive0.0010.0000.001
extractDrugShortestPath0.0010.0000.001
extractDrugShortestPathComplete0.0010.0000.001
extractDrugStandard0.0010.0000.000
extractDrugStandardComplete0.0010.0000.001
extractDrugTPSA0.0010.0000.001
extractDrugVABC0.0000.0010.001
extractDrugVAdjMa0.0000.0010.001
extractDrugWHIM0.0000.0010.001
extractDrugWeight0.0000.0000.001
extractDrugWeightedPath0.0010.0000.000
extractDrugWienerNumbers0.0010.0000.001
extractDrugXLogP0.0010.0000.001
extractDrugZagrebIndex0.0010.0000.001
extractPCMBLOSUM0.0220.0000.022
extractPCMDescScales0.0160.0000.016
extractPCMFAScales0.0210.0000.021
extractPCMMDSScales0.0100.0040.013
extractPCMPropScales0.0160.0000.016
extractPCMScales0.0240.0000.024
extractProtAAC0.0030.0000.002
extractProtAPAAC1.0870.0201.110
extractProtCTDC0.0030.0000.002
extractProtCTDD0.0040.0000.005
extractProtCTDT0.0050.0000.006
extractProtCTriad0.1290.0000.130
extractProtDC0.0010.0030.004
extractProtGeary0.1680.0280.195
extractProtMoran0.1720.0080.180
extractProtMoreauBroto0.1700.0040.173
extractProtPAAC0.5990.0000.599
extractProtPSSM0.0010.0000.001
extractProtPSSMAcc0.0010.0000.001
extractProtPSSMFeature0.0010.0000.001
extractProtQSO1.0190.0041.026
extractProtSOCN1.0060.0081.014
extractProtTC0.0180.0360.054
getCPI0.0010.0020.004
getDrug0.0000.0000.001
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem0.0000.0010.000
getPDBFromRCSBPDB000
getPPI0.0020.0010.003
getProt0.0000.0000.001
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank0.0000.0000.001
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA0.0020.0000.002
readMolFromSDF0.0030.0000.002
readMolFromSmi0.0000.0010.001
readPDB0.9320.0030.938
searchDrug0.0000.0010.002
segProt0.0010.0020.003