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This page was generated on 2024-03-04 11:37:44 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
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 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 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 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for Rcpi on lconway


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: 1.38.0
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_1.38.0.tar.gz
StartedAt: 2024-03-03 22:50:57 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 22:53:28 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 150.9 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_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/Rcpi.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* 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 12.7.1
* 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 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-3.18-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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
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 
  7.742   0.703   7.368 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0020.0020.004
AA3DMoRSE0.0010.0020.003
AAACF0.0010.0010.002
AABLOSUM1000.0010.0010.003
AABLOSUM450.0010.0010.002
AABLOSUM500.0010.0020.002
AABLOSUM620.0010.0010.003
AABLOSUM800.0010.0010.002
AABurden0.0010.0010.002
AACPSA0.0010.0020.003
AAConn0.0010.0010.002
AAConst0.0010.0010.002
AADescAll0.0010.0000.002
AAEdgeAdj0.0000.0010.001
AAEigIdx0.0010.0010.002
AAFGC0.0010.0010.001
AAGETAWAY0.0010.0000.001
AAGeom0.0010.0010.001
AAInfo0.0010.0010.001
AAMOE2D0.0010.0010.002
AAMOE3D0.0000.0010.002
AAMetaInfo0.0000.0010.001
AAMolProp0.0010.0010.002
AAPAM1200.0010.0010.002
AAPAM2500.0010.0020.002
AAPAM300.0010.0010.002
AAPAM400.0000.0010.002
AAPAM700.0010.0020.003
AARDF0.0010.0020.002
AARandic0.0010.0010.002
AATopo0.0010.0020.003
AATopoChg0.0010.0020.002
AAWHIM0.0010.0010.002
AAWalk0.0010.0010.003
AAindex0.0010.0010.002
OptAA3d000
acc0.0090.0060.014
calcDrugFPSim000
calcDrugMCSSim0.0200.0040.026
calcParProtGOSim0.0000.0000.001
calcParProtSeqSim0.0070.0040.012
calcTwoProtGOSim0.0000.0000.001
calcTwoProtSeqSim0.0020.0020.003
checkProt0.0020.0010.002
convMolFormat0.0010.0010.002
extractDrugAIO0.0010.0010.001
extractDrugALOGP0.0010.0010.002
extractDrugAminoAcidCount0.0000.0010.001
extractDrugApol0.0010.0010.002
extractDrugAromaticAtomsCount0.0010.0010.001
extractDrugAromaticBondsCount0.0010.0010.002
extractDrugAtomCount0.0010.0010.001
extractDrugAutocorrelationCharge0.0010.0010.001
extractDrugAutocorrelationMass0.0010.0010.001
extractDrugAutocorrelationPolarizability0.0000.0010.001
extractDrugBCUT0.0010.0000.001
extractDrugBPol0.0010.0000.001
extractDrugBondCount0.0010.0010.001
extractDrugCPSA0.0010.0010.001
extractDrugCarbonTypes0.0010.0010.002
extractDrugChiChain0.0010.0010.001
extractDrugChiCluster0.0000.0010.001
extractDrugChiPath0.0000.0000.001
extractDrugChiPathCluster0.0000.0010.001
extractDrugDescOB0.0060.0030.010
extractDrugECI0.0010.0000.001
extractDrugEstate0.0000.0010.001
extractDrugEstateComplete0.0010.0000.001
extractDrugExtended0.0010.0000.001
extractDrugExtendedComplete0.0010.0010.001
extractDrugFMF0.0010.0010.002
extractDrugFragmentComplexity0.0000.0010.001
extractDrugGraph0.0010.0000.001
extractDrugGraphComplete0.0010.0000.001
extractDrugGravitationalIndex0.0010.0000.001
extractDrugHBondAcceptorCount0.0010.0000.001
extractDrugHBondDonorCount0.0010.0010.001
extractDrugHybridization0.0010.0010.001
extractDrugHybridizationComplete0.0010.0010.002
extractDrugHybridizationRatio0.0000.0010.001
extractDrugIPMolecularLearning0.0010.0010.001
extractDrugKR0.0010.0010.002
extractDrugKRComplete0.0010.0010.001
extractDrugKappaShapeIndices0.0010.0010.002
extractDrugKierHallSmarts0.0010.0010.001
extractDrugLargestChain0.0000.0010.002
extractDrugLargestPiSystem0.0010.0010.002
extractDrugLengthOverBreadth0.0010.0010.002
extractDrugLongestAliphaticChain0.0000.0000.001
extractDrugMACCS0.0010.0010.001
extractDrugMACCSComplete0.0010.0010.001
extractDrugMDE0.0010.0010.001
extractDrugMannholdLogP0.0010.0000.001
extractDrugMomentOfInertia0.0010.0000.001
extractDrugOBFP20.0140.0070.020
extractDrugOBFP30.0060.0040.011
extractDrugOBFP40.0880.0070.098
extractDrugOBMACCS0.0070.0040.011
extractDrugPetitjeanNumber0.0010.0010.002
extractDrugPetitjeanShapeIndex0.0010.0010.001
extractDrugPubChem0.0010.0010.002
extractDrugPubChemComplete0.0010.0010.001
extractDrugRotatableBondsCount0.0010.0010.002
extractDrugRuleOfFive0.0010.0010.001
extractDrugShortestPath0.0010.0010.002
extractDrugShortestPathComplete0.0000.0010.001
extractDrugStandard0.0010.0000.001
extractDrugStandardComplete0.0010.0000.002
extractDrugTPSA0.0010.0000.001
extractDrugVABC0.0010.0000.002
extractDrugVAdjMa0.0000.0000.001
extractDrugWHIM0.0010.0010.001
extractDrugWeight0.0000.0010.001
extractDrugWeightedPath0.0010.0010.001
extractDrugWienerNumbers0.0010.0010.001
extractDrugXLogP0.0010.0010.001
extractDrugZagrebIndex0.0010.0010.001
extractPCMBLOSUM0.0100.0020.013
extractPCMDescScales0.0120.0020.015
extractPCMFAScales0.0260.0070.033
extractPCMMDSScales0.0080.0020.010
extractPCMPropScales0.0110.0010.013
extractPCMScales0.0170.0030.021
extractProtAAC0.0020.0010.003
extractProtAPAAC0.7660.0290.801
extractProtCTDC0.0030.0010.004
extractProtCTDD0.0040.0010.005
extractProtCTDT0.0050.0010.007
extractProtCTriad0.0930.0150.110
extractProtDC0.0040.0070.010
extractProtGeary0.1240.0130.138
extractProtMoran0.1340.0120.147
extractProtMoreauBroto0.1280.0110.140
extractProtPAAC0.4180.0120.435
extractProtPSSM0.0020.0010.002
extractProtPSSMAcc0.0020.0000.002
extractProtPSSMFeature0.0010.0000.001
extractProtQSO0.7750.0160.800
extractProtSOCN0.7700.0150.793
extractProtTC0.0360.0860.122
getCPI0.0030.0010.004
getDrug0.0000.0010.000
getFASTAFromKEGG0.0000.0000.001
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem000
getPDBFromRCSBPDB000
getPPI0.0020.0020.005
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt0.0010.0000.000
getSmiFromChEMBL000
getSmiFromDrugBank0.0000.0010.000
getSmiFromKEGG000
getSmiFromPubChem0.0000.0000.001
readFASTA0.0020.0010.002
readMolFromSDF0.0030.0020.004
readMolFromSmi0.0010.0010.001
readPDB0.7980.0160.824
searchDrug0.0010.0010.003
segProt0.0020.0010.003