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This page was generated on 2024-03-29 11:38:07 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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: 2024-03-27 14:05:05 -0400 (Wed, 27 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 -0400 (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
merida1macOS 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 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: 1.38.0
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: 2024-03-28 07:31:03 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 07:35:50 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 286.1 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 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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 
 13.178   0.972  13.561 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0030.0030.007
AA3DMoRSE0.0020.0020.004
AAACF0.0020.0020.003
AABLOSUM1000.0010.0020.004
AABLOSUM450.0020.0030.004
AABLOSUM500.0010.0030.004
AABLOSUM620.0020.0030.004
AABLOSUM800.0020.0020.004
AABurden0.0010.0020.004
AACPSA0.0020.0010.004
AAConn0.0010.0020.004
AAConst0.0020.0020.003
AADescAll0.0020.0020.004
AAEdgeAdj0.0010.0020.004
AAEigIdx0.0020.0020.004
AAFGC0.0010.0020.005
AAGETAWAY0.0020.0020.004
AAGeom0.0010.0020.004
AAInfo0.0020.0020.004
AAMOE2D0.0010.0030.004
AAMOE3D0.0010.0020.003
AAMetaInfo0.0020.0010.003
AAMolProp0.0020.0020.003
AAPAM1200.0010.0020.004
AAPAM2500.0020.0020.004
AAPAM300.0010.0020.003
AAPAM400.0020.0020.004
AAPAM700.0010.0020.004
AARDF0.0020.0020.004
AARandic0.0010.0020.004
AATopo0.0020.0020.004
AATopoChg0.0010.0020.004
AAWHIM0.0020.0020.003
AAWalk0.0020.0020.004
AAindex0.0020.0020.004
OptAA3d0.0010.0000.000
acc0.0170.0140.032
calcDrugFPSim0.0000.0000.001
calcDrugMCSSim0.0270.0070.036
calcParProtGOSim0.0000.0000.001
calcParProtSeqSim0.0100.0040.016
calcTwoProtGOSim0.0010.0010.001
calcTwoProtSeqSim0.0030.0010.005
checkProt0.0020.0010.004
convMolFormat0.0020.0010.003
extractDrugAIO0.0010.0000.002
extractDrugALOGP0.0010.0010.002
extractDrugAminoAcidCount0.0020.0010.002
extractDrugApol0.0010.0010.002
extractDrugAromaticAtomsCount0.0010.0010.002
extractDrugAromaticBondsCount0.0020.0000.002
extractDrugAtomCount0.0010.0010.002
extractDrugAutocorrelationCharge0.0010.0000.002
extractDrugAutocorrelationMass0.0020.0010.002
extractDrugAutocorrelationPolarizability0.0010.0000.002
extractDrugBCUT0.0010.0010.003
extractDrugBPol0.0020.0010.003
extractDrugBondCount0.0010.0010.003
extractDrugCPSA0.0010.0010.002
extractDrugCarbonTypes0.0020.0010.003
extractDrugChiChain0.0020.0010.003
extractDrugChiCluster0.0010.0010.002
extractDrugChiPath0.0010.0010.002
extractDrugChiPathCluster0.0020.0010.002
extractDrugDescOB0.0110.0070.017
extractDrugECI0.0010.0000.002
extractDrugEstate0.0020.0010.003
extractDrugEstateComplete0.0010.0010.002
extractDrugExtended0.0010.0010.002
extractDrugExtendedComplete0.0020.0010.002
extractDrugFMF0.0010.0010.002
extractDrugFragmentComplexity0.0010.0000.002
extractDrugGraph0.0010.0010.002
extractDrugGraphComplete0.0010.0010.002
extractDrugGravitationalIndex0.0020.0010.002
extractDrugHBondAcceptorCount0.0010.0000.002
extractDrugHBondDonorCount0.0010.0010.002
extractDrugHybridization0.0020.0000.002
extractDrugHybridizationComplete0.0010.0010.002
extractDrugHybridizationRatio0.0010.0010.003
extractDrugIPMolecularLearning0.0020.0010.002
extractDrugKR0.0010.0010.006
extractDrugKRComplete0.0020.0010.002
extractDrugKappaShapeIndices0.0020.0010.002
extractDrugKierHallSmarts0.0010.0000.002
extractDrugLargestChain0.0010.0010.002
extractDrugLargestPiSystem0.0020.0010.002
extractDrugLengthOverBreadth0.0010.0010.004
extractDrugLongestAliphaticChain0.0020.0010.002
extractDrugMACCS0.0010.0000.002
extractDrugMACCSComplete0.0010.0010.002
extractDrugMDE0.0020.0000.003
extractDrugMannholdLogP0.0010.0010.004
extractDrugMomentOfInertia0.0020.0010.003
extractDrugOBFP20.0180.0080.028
extractDrugOBFP30.0110.0060.017
extractDrugOBFP40.0960.0110.126
extractDrugOBMACCS0.0110.0040.015
extractDrugPetitjeanNumber0.0010.0010.002
extractDrugPetitjeanShapeIndex0.0010.0010.002
extractDrugPubChem0.0020.0010.003
extractDrugPubChemComplete0.0010.0010.002
extractDrugRotatableBondsCount0.0020.0010.003
extractDrugRuleOfFive0.0020.0010.003
extractDrugShortestPath0.0010.0000.002
extractDrugShortestPathComplete0.0010.0010.002
extractDrugStandard0.0020.0000.002
extractDrugStandardComplete0.0010.0010.002
extractDrugTPSA0.0010.0010.002
extractDrugVABC0.0010.0010.003
extractDrugVAdjMa0.0020.0010.003
extractDrugWHIM0.0010.0010.002
extractDrugWeight0.0010.0010.002
extractDrugWeightedPath0.0010.0010.002
extractDrugWienerNumbers0.0020.0010.002
extractDrugXLogP0.0010.0010.002
extractDrugZagrebIndex0.0010.0010.002
extractPCMBLOSUM0.0170.0040.021
extractPCMDescScales0.0200.0030.024
extractPCMFAScales0.0380.0100.050
extractPCMMDSScales0.0170.0060.024
extractPCMPropScales0.0200.0040.024
extractPCMScales0.0310.0070.038
extractProtAAC0.0030.0020.006
extractProtAPAAC1.7120.0591.995
extractProtCTDC0.0050.0020.009
extractProtCTDD0.0070.0050.013
extractProtCTDT0.0090.0030.011
extractProtCTriad0.1820.0270.220
extractProtDC0.0070.0140.022
extractProtGeary0.2750.0250.316
extractProtMoran0.2870.0260.334
extractProtMoreauBroto0.2770.0240.318
extractProtPAAC1.1060.0201.187
extractProtPSSM0.0020.0010.003
extractProtPSSMAcc0.0010.0010.003
extractProtPSSMFeature0.0020.0010.004
extractProtQSO2.0840.0352.335
extractProtSOCN2.0600.0212.270
extractProtTC0.0860.2340.354
getCPI0.0050.0040.008
getDrug0.0000.0010.000
getFASTAFromKEGG0.0000.0000.001
getFASTAFromUniProt0.0000.0000.001
getMolFromCAS0.0000.0000.001
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem0.0000.0000.001
getPDBFromRCSBPDB0.0000.0000.001
getPPI0.0050.0050.011
getProt0.0000.0010.000
getSeqFromKEGG0.0000.0010.000
getSeqFromRCSBPDB0.0000.0010.000
getSeqFromUniProt0.0000.0010.000
getSmiFromChEMBL0.0000.0010.000
getSmiFromDrugBank0.0000.0010.000
getSmiFromKEGG0.0010.0010.001
getSmiFromPubChem0.0000.0000.001
readFASTA0.0020.0010.003
readMolFromSDF0.0040.0020.006
readMolFromSmi0.0010.0010.002
readPDB1.5880.0181.760
searchDrug0.0030.0020.008
segProt0.0040.0030.013