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This page was generated on 2023-10-20 09:38:10 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 14:00:07 -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)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for Rcpi on kjohnson2


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: 1.36.1
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: 2023-10-18 17:41:05 -0400 (Wed, 18 Oct 2023)
EndedAt: 2023-10-18 17:44:45 -0400 (Wed, 18 Oct 2023)
EllapsedTime: 220.0 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-mac-arm64/meat/Rcpi.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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 Monterey 12.6.7
* 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-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 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 
  7.577   0.537  11.936 

Example timings

Rcpi.Rcheck/Rcpi-Ex.timings

nameusersystemelapsed
AA2DACOR0.0020.0010.004
AA3DMoRSE0.0010.0010.002
AAACF0.0010.0010.002
AABLOSUM1000.0010.0010.003
AABLOSUM450.0010.0010.002
AABLOSUM500.0010.0010.002
AABLOSUM620.0010.0010.002
AABLOSUM800.0010.0010.002
AABurden0.0010.0010.002
AACPSA0.0010.0010.002
AAConn0.0010.0010.002
AAConst0.0010.0010.002
AADescAll0.0010.0010.002
AAEdgeAdj0.0010.0010.002
AAEigIdx0.0010.0010.002
AAFGC0.0010.0010.001
AAGETAWAY0.0010.0000.002
AAGeom0.0010.0010.002
AAInfo0.0020.0020.004
AAMOE2D0.0010.0010.002
AAMOE3D0.0010.0010.003
AAMetaInfo0.0010.0010.002
AAMolProp0.0010.0010.002
AAPAM1200.0020.0010.003
AAPAM2500.0010.0010.002
AAPAM300.0010.0010.002
AAPAM400.0010.0010.004
AAPAM700.0010.0010.003
AARDF0.0010.0010.002
AARandic0.0010.0010.002
AATopo0.0010.0010.004
AATopoChg0.0010.0010.002
AAWHIM0.0010.0010.002
AAWalk0.0010.0010.002
AAindex0.0010.0010.003
OptAA3d000
acc0.0080.0050.017
calcDrugFPSim000
calcDrugMCSSim0.0190.0030.023
calcParProtGOSim000
calcParProtSeqSim0.0060.0030.009
calcTwoProtGOSim0.0000.0000.001
calcTwoProtSeqSim0.0020.0010.003
checkProt0.0020.0010.003
convMolFormat0.0010.0000.004
extractDrugAIO0.0010.0000.001
extractDrugALOGP0.0010.0000.003
extractDrugAminoAcidCount0.0010.0000.001
extractDrugApol0.0010.0000.001
extractDrugAromaticAtomsCount0.0010.0010.002
extractDrugAromaticBondsCount0.0010.0010.001
extractDrugAtomCount0.0010.0010.001
extractDrugAutocorrelationCharge0.0010.0010.002
extractDrugAutocorrelationMass0.0010.0010.001
extractDrugAutocorrelationPolarizability0.0010.0010.002
extractDrugBCUT0.0000.0000.001
extractDrugBPol0.0010.0000.001
extractDrugBondCount0.0010.0000.001
extractDrugCPSA0.0010.0000.002
extractDrugCarbonTypes0.0010.0010.001
extractDrugChiChain0.0010.0010.001
extractDrugChiCluster0.0010.0010.001
extractDrugChiPath0.0010.0000.001
extractDrugChiPathCluster0.0010.0000.002
extractDrugDescOB0.0060.0030.013
extractDrugECI0.0010.0000.003
extractDrugEstate0.0010.0000.001
extractDrugEstateComplete0.0010.0010.004
extractDrugExtended0.0010.0010.001
extractDrugExtendedComplete0.0010.0010.001
extractDrugFMF0.0010.0010.002
extractDrugFragmentComplexity0.0020.0010.001
extractDrugGraph0.0010.0000.001
extractDrugGraphComplete0.0010.0010.004
extractDrugGravitationalIndex0.0010.0000.002
extractDrugHBondAcceptorCount0.0010.0000.002
extractDrugHBondDonorCount0.0010.0000.001
extractDrugHybridization0.0010.0000.002
extractDrugHybridizationComplete0.0010.0000.001
extractDrugHybridizationRatio0.0010.0000.003
extractDrugIPMolecularLearning0.0010.0000.001
extractDrugKR0.0010.0000.002
extractDrugKRComplete0.0010.0000.001
extractDrugKappaShapeIndices0.0010.0000.002
extractDrugKierHallSmarts0.0010.0010.003
extractDrugLargestChain0.0010.0010.001
extractDrugLargestPiSystem0.0000.0010.001
extractDrugLengthOverBreadth0.0010.0010.001
extractDrugLongestAliphaticChain0.0010.0000.002
extractDrugMACCS0.0010.0000.004
extractDrugMACCSComplete0.0010.0010.002
extractDrugMDE0.0020.0010.001
extractDrugMannholdLogP0.0010.0010.002
extractDrugMomentOfInertia0.0010.0010.001
extractDrugOBFP20.0140.0040.021
extractDrugOBFP30.0060.0010.009
extractDrugOBFP40.0050.0020.009
extractDrugOBMACCS0.0750.0040.103
extractDrugPetitjeanNumber0.0000.0000.002
extractDrugPetitjeanShapeIndex0.0010.0000.002
extractDrugPubChem0.0010.0000.002
extractDrugPubChemComplete0.0010.0000.002
extractDrugRotatableBondsCount0.0010.0000.002
extractDrugRuleOfFive0.0010.0000.002
extractDrugShortestPath0.0010.0010.001
extractDrugShortestPathComplete0.0000.0010.001
extractDrugStandard0.0010.0010.002
extractDrugStandardComplete0.0010.0000.002
extractDrugTPSA0.0010.0000.001
extractDrugVABC0.0010.0000.001
extractDrugVAdjMa0.0010.0000.001
extractDrugWHIM0.0010.0000.001
extractDrugWeight0.0010.0000.001
extractDrugWeightedPath0.0010.0000.002
extractDrugWienerNumbers0.0010.0000.001
extractDrugXLogP0.0010.0000.001
extractDrugZagrebIndex0.0010.0010.001
extractPCMBLOSUM0.0110.0020.018
extractPCMDescScales0.0120.0010.018
extractPCMFAScales0.0170.0030.024
extractPCMMDSScales0.0190.0020.026
extractPCMPropScales0.0130.0010.015
extractPCMScales0.0160.0030.023
extractProtAAC0.0030.0010.004
extractProtAPAAC0.7120.0240.947
extractProtCTDC0.0030.0010.006
extractProtCTDD0.0040.0020.007
extractProtCTDT0.0050.0020.009
extractProtCTriad0.0910.0090.133
extractProtDC0.0030.0050.013
extractProtGeary0.1330.0090.212
extractProtMoran0.1270.0080.206
extractProtMoreauBroto0.1170.0080.192
extractProtPAAC0.3920.0060.609
extractProtPSSM0.0010.0000.001
extractProtPSSMAcc0.0020.0000.002
extractProtPSSMFeature0.0010.0000.002
extractProtQSO0.7330.0161.107
extractProtSOCN0.7120.0131.071
extractProtTC0.0290.0730.148
getCPI0.0030.0020.004
getDrug000
getFASTAFromKEGG000
getFASTAFromUniProt000
getMolFromCAS000
getMolFromChEMBL000
getMolFromDrugBank000
getMolFromKEGG0.0000.0010.000
getMolFromPubChem0.0010.0000.001
getPDBFromRCSBPDB000
getPPI0.0020.0020.008
getProt0.0000.0010.000
getSeqFromKEGG000
getSeqFromRCSBPDB0.0000.0010.000
getSeqFromUniProt000
getSmiFromChEMBL000
getSmiFromDrugBank000
getSmiFromKEGG000
getSmiFromPubChem000
readFASTA0.0010.0010.004
readMolFromSDF0.0030.0020.007
readMolFromSmi0.0010.0010.003
readPDB0.7330.0111.109
searchDrug0.0020.0000.004
segProt0.0030.0010.005