Back to Multiple platform build/check report for BioC 3.17:   simplified   long
ABCDEFGHIJKLMNOPQ[R]STUVWXYZ

This page was generated on 2023-10-16 11:37:25 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1651/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rcpi 1.36.1  (landing page)
Nan Xiao
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/Rcpi
git_branch: RELEASE_3_17
git_last_commit: 14c427d
git_last_commit_date: 2023-06-27 01:30:50 -0400 (Tue, 27 Jun 2023)
nebbiolo1Linux (Ubuntu 22.04.2 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 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for Rcpi on merida1


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.

raw results


Summary

Package: Rcpi
Version: 1.36.1
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_1.36.1.tar.gz
StartedAt: 2023-10-16 05:51:44 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 05:56:55 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 311.5 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_1.36.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/Rcpi.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.36.1’
* 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 ‘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
  ‘/Users/biocbuild/bbs-3.17-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/4.3-x86_64/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
*** 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: x86_64-apple-darwin20 (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 0 | PASS 22 ]
> 
> proc.time()
   user  system elapsed 
 13.331   0.926  16.046 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0040.0030.006
AA3DMoRSE0.0020.0020.004
AAACF0.0020.0030.004
AABLOSUM1000.0010.0030.007
AABLOSUM450.0020.0020.005
AABLOSUM500.0010.0020.005
AABLOSUM620.0020.0020.003
AABLOSUM800.0020.0030.008
AABurden0.0010.0020.004
AACPSA0.0020.0020.004
AAConn0.0010.0020.004
AAConst0.0020.0020.003
AADescAll0.0010.0020.004
AAEdgeAdj0.0020.0020.004
AAEigIdx0.0010.0020.005
AAFGC0.0020.0020.003
AAGETAWAY0.0010.0030.005
AAGeom0.0020.0020.004
AAInfo0.0010.0020.003
AAMOE2D0.0020.0020.004
AAMOE3D0.0010.0020.007
AAMetaInfo0.0020.0020.004
AAMolProp0.0010.0020.006
AAPAM1200.0020.0030.006
AAPAM2500.0010.0030.004
AAPAM300.0020.0020.006
AAPAM400.0010.0020.004
AAPAM700.0020.0020.005
AARDF0.0020.0020.005
AARandic0.0010.0020.004
AATopo0.0020.0020.005
AATopoChg0.0010.0020.005
AAWHIM0.0020.0030.008
AAWalk0.0010.0020.004
AAindex0.0020.0020.005
OptAA3d0.0000.0010.001
acc0.0170.0170.045
calcDrugFPSim0.0000.0010.000
calcDrugMCSSim0.0250.0090.041
calcParProtGOSim0.0000.0010.001
calcParProtSeqSim0.0110.0040.021
calcTwoProtGOSim0.0010.0010.001
calcTwoProtSeqSim0.0040.0020.005
checkProt0.0020.0010.004
convMolFormat0.0010.0010.003
extractDrugAIO0.0020.0010.005
extractDrugALOGP0.0010.0000.003
extractDrugAminoAcidCount0.0010.0010.003
extractDrugApol0.0020.0000.004
extractDrugAromaticAtomsCount0.0010.0010.002
extractDrugAromaticBondsCount0.0020.0010.004
extractDrugAtomCount0.0010.0010.002
extractDrugAutocorrelationCharge0.0010.0010.002
extractDrugAutocorrelationMass0.0020.0010.004
extractDrugAutocorrelationPolarizability0.0010.0010.002
extractDrugBCUT0.0010.0010.002
extractDrugBPol0.0020.0010.002
extractDrugBondCount0.0020.0010.002
extractDrugCPSA0.0010.0010.006
extractDrugCarbonTypes0.0020.0010.004
extractDrugChiChain0.0010.0010.003
extractDrugChiCluster0.0010.0010.002
extractDrugChiPath0.0020.0010.002
extractDrugChiPathCluster0.0010.0010.004
extractDrugDescOB0.0110.0060.022
extractDrugECI0.0010.0000.002
extractDrugEstate0.0010.0010.002
extractDrugEstateComplete0.0020.0010.002
extractDrugExtended0.0010.0010.004
extractDrugExtendedComplete0.0010.0000.002
extractDrugFMF0.0020.0010.002
extractDrugFragmentComplexity0.0010.0010.004
extractDrugGraph0.0020.0010.002
extractDrugGraphComplete0.0020.0010.002
extractDrugGravitationalIndex0.0010.0010.002
extractDrugHBondAcceptorCount0.0010.0010.002
extractDrugHBondDonorCount0.0020.0000.006
extractDrugHybridization0.0010.0010.003
extractDrugHybridizationComplete0.0020.0010.002
extractDrugHybridizationRatio0.0020.0010.004
extractDrugIPMolecularLearning0.0010.0010.002
extractDrugKR0.0020.0010.005
extractDrugKRComplete0.0010.0010.002
extractDrugKappaShapeIndices0.0010.0000.002
extractDrugKierHallSmarts0.0020.0010.006
extractDrugLargestChain0.0010.0000.002
extractDrugLargestPiSystem0.0010.0010.002
extractDrugLengthOverBreadth0.0020.0010.002
extractDrugLongestAliphaticChain0.0010.0010.002
extractDrugMACCS0.0010.0010.003
extractDrugMACCSComplete0.0020.0010.002
extractDrugMDE0.0010.0010.002
extractDrugMannholdLogP0.0010.0000.002
extractDrugMomentOfInertia0.0020.0010.004
extractDrugOBFP20.0180.0090.036
extractDrugOBFP30.0100.0040.016
extractDrugOBFP40.0100.0040.016
extractDrugOBMACCS0.1050.0070.148
extractDrugPetitjeanNumber0.0020.0010.002
extractDrugPetitjeanShapeIndex0.0010.0000.002
extractDrugPubChem0.0010.0010.005
extractDrugPubChemComplete0.0020.0010.003
extractDrugRotatableBondsCount0.0010.0000.010
extractDrugRuleOfFive0.0020.0010.002
extractDrugShortestPath0.0020.0000.002
extractDrugShortestPathComplete0.0020.0010.005
extractDrugStandard0.0010.0010.002
extractDrugStandardComplete0.0010.0000.002
extractDrugTPSA0.0020.0010.002
extractDrugVABC0.0010.0000.002
extractDrugVAdjMa0.0010.0000.002
extractDrugWHIM0.0010.0010.002
extractDrugWeight0.0010.0000.002
extractDrugWeightedPath0.0020.0010.004
extractDrugWienerNumbers0.0010.0010.003
extractDrugXLogP0.0010.0010.002
extractDrugZagrebIndex0.0010.0010.003
extractPCMBLOSUM0.0170.0030.026
extractPCMDescScales0.0210.0030.030
extractPCMFAScales0.0300.0060.049
extractPCMMDSScales0.0260.0060.041
extractPCMPropScales0.0210.0030.032
extractPCMScales0.0320.0050.048
extractProtAAC0.0040.0020.005
extractProtAPAAC1.7350.0722.827
extractProtCTDC0.0050.0020.006
extractProtCTDD0.0090.0070.026
extractProtCTDT0.0100.0030.018
extractProtCTriad0.1910.0260.397
extractProtDC0.0060.0110.023
extractProtGeary0.2950.0250.457
extractProtMoran0.2950.0280.440
extractProtMoreauBroto0.2800.0220.403
extractProtPAAC1.1360.0171.450
extractProtPSSM0.0020.0010.002
extractProtPSSMAcc0.0010.0010.004
extractProtPSSMFeature0.0020.0010.002
extractProtQSO2.0790.0282.649
extractProtSOCN2.0470.0182.590
extractProtTC0.0880.2360.387
getCPI0.0050.0030.008
getDrug0.0000.0000.001
getFASTAFromKEGG0.0000.0000.001
getFASTAFromUniProt0.0010.0000.000
getMolFromCAS0.0010.0000.000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI0.0050.0050.012
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL0.0000.0000.001
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem0.0000.0000.002
readFASTA0.0030.0010.004
readMolFromSDF0.0040.0020.009
readMolFromSmi0.0010.0000.003
readPDB1.5900.0152.046
searchDrug0.0030.0010.005
segProt0.0030.0030.007