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This page was generated on 2024-04-18 11:32:16 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 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)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Rcpi on kjohnson1


To the developers/maintainers of the Rcpi package:
- 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: 2024-04-18 00:30:53 -0400 (Thu, 18 Apr 2024)
EndedAt: 2024-04-18 00:33:16 -0400 (Thu, 18 Apr 2024)
EllapsedTime: 142.2 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-mac-arm64/meat/Rcpi.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-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 Ventura 13.6.1
* 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-mac-arm64/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-arm64/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: aarch64-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 
  7.934   0.493   7.543 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0020.0020.005
AA3DMoRSE0.0000.0010.003
AAACF0.0000.0020.002
AABLOSUM1000.0010.0010.002
AABLOSUM450.0010.0010.002
AABLOSUM500.0010.0020.002
AABLOSUM620.0010.0010.002
AABLOSUM800.0010.0020.001
AABurden0.0010.0010.002
AACPSA0.0010.0020.003
AAConn0.0010.0010.002
AAConst0.0010.0010.002
AADescAll0.0010.0020.002
AAEdgeAdj0.0010.0010.002
AAEigIdx0.0010.0020.003
AAFGC0.0010.0020.002
AAGETAWAY0.0010.0020.002
AAGeom0.0010.0010.002
AAInfo0.0010.0010.002
AAMOE2D0.0010.0020.002
AAMOE3D0.0000.0010.002
AAMetaInfo0.0000.0020.001
AAMolProp0.0000.0010.002
AAPAM1200.0010.0020.002
AAPAM2500.0010.0020.002
AAPAM300.0010.0010.003
AAPAM400.0010.0010.003
AAPAM700.0000.0010.002
AARDF0.0000.0010.002
AARandic0.0000.0010.002
AATopo0.0000.0010.002
AATopoChg0.0000.0010.001
AAWHIM0.0000.0010.002
AAWalk0.0000.0010.002
AAindex0.0000.0010.002
OptAA3d000
acc0.0090.0060.015
calcDrugFPSim000
calcDrugMCSSim0.0190.0030.023
calcParProtGOSim000
calcParProtSeqSim0.0060.0020.009
calcTwoProtGOSim0.0000.0000.001
calcTwoProtSeqSim0.0020.0000.003
checkProt0.0010.0000.002
convMolFormat0.0000.0000.001
extractDrugAIO0.0010.0000.001
extractDrugALOGP0.0010.0010.002
extractDrugAminoAcidCount0.0010.0000.001
extractDrugApol0.0010.0010.001
extractDrugAromaticAtomsCount0.0010.0000.001
extractDrugAromaticBondsCount0.0010.0000.001
extractDrugAtomCount0.0010.0000.001
extractDrugAutocorrelationCharge0.0000.0000.002
extractDrugAutocorrelationMass0.0000.0000.001
extractDrugAutocorrelationPolarizability0.0010.0000.001
extractDrugBCUT0.0000.0000.001
extractDrugBPol0.0010.0010.003
extractDrugBondCount0.0000.0010.001
extractDrugCPSA0.0010.0000.001
extractDrugCarbonTypes0.0010.0000.001
extractDrugChiChain0.0010.0010.001
extractDrugChiCluster0.0010.0000.001
extractDrugChiPath0.0010.0000.001
extractDrugChiPathCluster0.0010.0000.001
extractDrugDescOB0.0050.0020.008
extractDrugECI0.0010.0010.002
extractDrugEstate0.0000.0010.002
extractDrugEstateComplete0.0000.0000.001
extractDrugExtended0.0000.0010.001
extractDrugExtendedComplete0.0010.0000.003
extractDrugFMF0.0010.0000.002
extractDrugFragmentComplexity0.0010.0000.002
extractDrugGraph0.0010.0000.001
extractDrugGraphComplete0.0010.0000.001
extractDrugGravitationalIndex0.0010.0000.001
extractDrugHBondAcceptorCount0.0010.0010.001
extractDrugHBondDonorCount0.0010.0000.001
extractDrugHybridization0.0010.0010.001
extractDrugHybridizationComplete0.0010.0000.001
extractDrugHybridizationRatio0.0010.0000.001
extractDrugIPMolecularLearning0.0010.0000.001
extractDrugKR0.0010.0000.001
extractDrugKRComplete0.0000.0010.001
extractDrugKappaShapeIndices0.0010.0000.002
extractDrugKierHallSmarts0.0010.0000.002
extractDrugLargestChain0.0010.0000.002
extractDrugLargestPiSystem0.0010.0010.001
extractDrugLengthOverBreadth0.0010.0000.001
extractDrugLongestAliphaticChain0.0010.0010.001
extractDrugMACCS0.0010.0000.001
extractDrugMACCSComplete0.0000.0000.002
extractDrugMDE0.0010.0000.001
extractDrugMannholdLogP0.0010.0010.001
extractDrugMomentOfInertia0.0010.0000.001
extractDrugOBFP20.0120.0040.016
extractDrugOBFP30.0050.0020.008
extractDrugOBFP40.0970.0040.102
extractDrugOBMACCS0.0060.0040.009
extractDrugPetitjeanNumber0.0010.0000.001
extractDrugPetitjeanShapeIndex0.0010.0000.001
extractDrugPubChem0.0010.0000.001
extractDrugPubChemComplete0.0000.0000.001
extractDrugRotatableBondsCount0.0000.0010.001
extractDrugRuleOfFive000
extractDrugShortestPath0.0000.0010.001
extractDrugShortestPathComplete0.0010.0000.002
extractDrugStandard0.0010.0000.001
extractDrugStandardComplete0.0000.0000.001
extractDrugTPSA0.0010.0010.002
extractDrugVABC0.0010.0000.001
extractDrugVAdjMa0.0010.0010.001
extractDrugWHIM0.0010.0000.001
extractDrugWeight0.0010.0000.001
extractDrugWeightedPath0.0010.0010.001
extractDrugWienerNumbers0.0010.0000.001
extractDrugXLogP0.0010.0010.001
extractDrugZagrebIndex0.0000.0000.001
extractPCMBLOSUM0.0110.0010.013
extractPCMDescScales0.0130.0010.013
extractPCMFAScales0.0330.0060.040
extractPCMMDSScales0.0110.0020.013
extractPCMPropScales0.0140.0000.015
extractPCMScales0.0170.0030.021
extractProtAAC0.0020.0010.003
extractProtAPAAC0.7470.0200.770
extractProtCTDC0.0040.0010.004
extractProtCTDD0.0050.0020.007
extractProtCTDT0.0060.0000.007
extractProtCTriad0.0880.0110.099
extractProtDC0.0030.0050.007
extractProtGeary0.1050.0080.113
extractProtMoran0.1120.0090.122
extractProtMoreauBroto0.1090.0080.117
extractProtPAAC0.3470.0110.358
extractProtPSSM0.0010.0000.002
extractProtPSSMAcc0.0010.0000.001
extractProtPSSMFeature0.0010.0000.002
extractProtQSO0.6000.0160.617
extractProtSOCN0.5980.0100.612
extractProtTC0.0310.0940.128
getCPI0.0030.0010.004
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt0.0000.0010.000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG000
getMolFromPubChem0.0000.0010.001
getPDBFromRCSBPDB000
getPPI0.0020.0020.006
getProt000
getSeqFromKEGG000
getSeqFromRCSBPDB000
getSeqFromUniProt000
getSmiFromChEMBL0.0000.0000.001
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA0.0010.0000.001
readMolFromSDF0.0020.0010.003
readMolFromSmi0.0010.0010.001
readPDB0.7670.0050.777
searchDrug0.0020.0000.002
segProt0.0020.0010.003