| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:10 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (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 1651/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rcpi 1.36.1 (landing page) Nan Xiao
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | ||||||||
|
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. |
| 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 |
##############################################################################
##############################################################################
###
### 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.
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)
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
Rcpi.Rcheck/Rcpi-Ex.timings
| name | user | system | elapsed | |
| AA2DACOR | 0.002 | 0.001 | 0.004 | |
| AA3DMoRSE | 0.001 | 0.001 | 0.002 | |
| AAACF | 0.001 | 0.001 | 0.002 | |
| AABLOSUM100 | 0.001 | 0.001 | 0.003 | |
| AABLOSUM45 | 0.001 | 0.001 | 0.002 | |
| AABLOSUM50 | 0.001 | 0.001 | 0.002 | |
| AABLOSUM62 | 0.001 | 0.001 | 0.002 | |
| AABLOSUM80 | 0.001 | 0.001 | 0.002 | |
| AABurden | 0.001 | 0.001 | 0.002 | |
| AACPSA | 0.001 | 0.001 | 0.002 | |
| AAConn | 0.001 | 0.001 | 0.002 | |
| AAConst | 0.001 | 0.001 | 0.002 | |
| AADescAll | 0.001 | 0.001 | 0.002 | |
| AAEdgeAdj | 0.001 | 0.001 | 0.002 | |
| AAEigIdx | 0.001 | 0.001 | 0.002 | |
| AAFGC | 0.001 | 0.001 | 0.001 | |
| AAGETAWAY | 0.001 | 0.000 | 0.002 | |
| AAGeom | 0.001 | 0.001 | 0.002 | |
| AAInfo | 0.002 | 0.002 | 0.004 | |
| AAMOE2D | 0.001 | 0.001 | 0.002 | |
| AAMOE3D | 0.001 | 0.001 | 0.003 | |
| AAMetaInfo | 0.001 | 0.001 | 0.002 | |
| AAMolProp | 0.001 | 0.001 | 0.002 | |
| AAPAM120 | 0.002 | 0.001 | 0.003 | |
| AAPAM250 | 0.001 | 0.001 | 0.002 | |
| AAPAM30 | 0.001 | 0.001 | 0.002 | |
| AAPAM40 | 0.001 | 0.001 | 0.004 | |
| AAPAM70 | 0.001 | 0.001 | 0.003 | |
| AARDF | 0.001 | 0.001 | 0.002 | |
| AARandic | 0.001 | 0.001 | 0.002 | |
| AATopo | 0.001 | 0.001 | 0.004 | |
| AATopoChg | 0.001 | 0.001 | 0.002 | |
| AAWHIM | 0.001 | 0.001 | 0.002 | |
| AAWalk | 0.001 | 0.001 | 0.002 | |
| AAindex | 0.001 | 0.001 | 0.003 | |
| OptAA3d | 0 | 0 | 0 | |
| acc | 0.008 | 0.005 | 0.017 | |
| calcDrugFPSim | 0 | 0 | 0 | |
| calcDrugMCSSim | 0.019 | 0.003 | 0.023 | |
| calcParProtGOSim | 0 | 0 | 0 | |
| calcParProtSeqSim | 0.006 | 0.003 | 0.009 | |
| calcTwoProtGOSim | 0.000 | 0.000 | 0.001 | |
| calcTwoProtSeqSim | 0.002 | 0.001 | 0.003 | |
| checkProt | 0.002 | 0.001 | 0.003 | |
| convMolFormat | 0.001 | 0.000 | 0.004 | |
| extractDrugAIO | 0.001 | 0.000 | 0.001 | |
| extractDrugALOGP | 0.001 | 0.000 | 0.003 | |
| extractDrugAminoAcidCount | 0.001 | 0.000 | 0.001 | |
| extractDrugApol | 0.001 | 0.000 | 0.001 | |
| extractDrugAromaticAtomsCount | 0.001 | 0.001 | 0.002 | |
| extractDrugAromaticBondsCount | 0.001 | 0.001 | 0.001 | |
| extractDrugAtomCount | 0.001 | 0.001 | 0.001 | |
| extractDrugAutocorrelationCharge | 0.001 | 0.001 | 0.002 | |
| extractDrugAutocorrelationMass | 0.001 | 0.001 | 0.001 | |
| extractDrugAutocorrelationPolarizability | 0.001 | 0.001 | 0.002 | |
| extractDrugBCUT | 0.000 | 0.000 | 0.001 | |
| extractDrugBPol | 0.001 | 0.000 | 0.001 | |
| extractDrugBondCount | 0.001 | 0.000 | 0.001 | |
| extractDrugCPSA | 0.001 | 0.000 | 0.002 | |
| extractDrugCarbonTypes | 0.001 | 0.001 | 0.001 | |
| extractDrugChiChain | 0.001 | 0.001 | 0.001 | |
| extractDrugChiCluster | 0.001 | 0.001 | 0.001 | |
| extractDrugChiPath | 0.001 | 0.000 | 0.001 | |
| extractDrugChiPathCluster | 0.001 | 0.000 | 0.002 | |
| extractDrugDescOB | 0.006 | 0.003 | 0.013 | |
| extractDrugECI | 0.001 | 0.000 | 0.003 | |
| extractDrugEstate | 0.001 | 0.000 | 0.001 | |
| extractDrugEstateComplete | 0.001 | 0.001 | 0.004 | |
| extractDrugExtended | 0.001 | 0.001 | 0.001 | |
| extractDrugExtendedComplete | 0.001 | 0.001 | 0.001 | |
| extractDrugFMF | 0.001 | 0.001 | 0.002 | |
| extractDrugFragmentComplexity | 0.002 | 0.001 | 0.001 | |
| extractDrugGraph | 0.001 | 0.000 | 0.001 | |
| extractDrugGraphComplete | 0.001 | 0.001 | 0.004 | |
| extractDrugGravitationalIndex | 0.001 | 0.000 | 0.002 | |
| extractDrugHBondAcceptorCount | 0.001 | 0.000 | 0.002 | |
| extractDrugHBondDonorCount | 0.001 | 0.000 | 0.001 | |
| extractDrugHybridization | 0.001 | 0.000 | 0.002 | |
| extractDrugHybridizationComplete | 0.001 | 0.000 | 0.001 | |
| extractDrugHybridizationRatio | 0.001 | 0.000 | 0.003 | |
| extractDrugIPMolecularLearning | 0.001 | 0.000 | 0.001 | |
| extractDrugKR | 0.001 | 0.000 | 0.002 | |
| extractDrugKRComplete | 0.001 | 0.000 | 0.001 | |
| extractDrugKappaShapeIndices | 0.001 | 0.000 | 0.002 | |
| extractDrugKierHallSmarts | 0.001 | 0.001 | 0.003 | |
| extractDrugLargestChain | 0.001 | 0.001 | 0.001 | |
| extractDrugLargestPiSystem | 0.000 | 0.001 | 0.001 | |
| extractDrugLengthOverBreadth | 0.001 | 0.001 | 0.001 | |
| extractDrugLongestAliphaticChain | 0.001 | 0.000 | 0.002 | |
| extractDrugMACCS | 0.001 | 0.000 | 0.004 | |
| extractDrugMACCSComplete | 0.001 | 0.001 | 0.002 | |
| extractDrugMDE | 0.002 | 0.001 | 0.001 | |
| extractDrugMannholdLogP | 0.001 | 0.001 | 0.002 | |
| extractDrugMomentOfInertia | 0.001 | 0.001 | 0.001 | |
| extractDrugOBFP2 | 0.014 | 0.004 | 0.021 | |
| extractDrugOBFP3 | 0.006 | 0.001 | 0.009 | |
| extractDrugOBFP4 | 0.005 | 0.002 | 0.009 | |
| extractDrugOBMACCS | 0.075 | 0.004 | 0.103 | |
| extractDrugPetitjeanNumber | 0.000 | 0.000 | 0.002 | |
| extractDrugPetitjeanShapeIndex | 0.001 | 0.000 | 0.002 | |
| extractDrugPubChem | 0.001 | 0.000 | 0.002 | |
| extractDrugPubChemComplete | 0.001 | 0.000 | 0.002 | |
| extractDrugRotatableBondsCount | 0.001 | 0.000 | 0.002 | |
| extractDrugRuleOfFive | 0.001 | 0.000 | 0.002 | |
| extractDrugShortestPath | 0.001 | 0.001 | 0.001 | |
| extractDrugShortestPathComplete | 0.000 | 0.001 | 0.001 | |
| extractDrugStandard | 0.001 | 0.001 | 0.002 | |
| extractDrugStandardComplete | 0.001 | 0.000 | 0.002 | |
| extractDrugTPSA | 0.001 | 0.000 | 0.001 | |
| extractDrugVABC | 0.001 | 0.000 | 0.001 | |
| extractDrugVAdjMa | 0.001 | 0.000 | 0.001 | |
| extractDrugWHIM | 0.001 | 0.000 | 0.001 | |
| extractDrugWeight | 0.001 | 0.000 | 0.001 | |
| extractDrugWeightedPath | 0.001 | 0.000 | 0.002 | |
| extractDrugWienerNumbers | 0.001 | 0.000 | 0.001 | |
| extractDrugXLogP | 0.001 | 0.000 | 0.001 | |
| extractDrugZagrebIndex | 0.001 | 0.001 | 0.001 | |
| extractPCMBLOSUM | 0.011 | 0.002 | 0.018 | |
| extractPCMDescScales | 0.012 | 0.001 | 0.018 | |
| extractPCMFAScales | 0.017 | 0.003 | 0.024 | |
| extractPCMMDSScales | 0.019 | 0.002 | 0.026 | |
| extractPCMPropScales | 0.013 | 0.001 | 0.015 | |
| extractPCMScales | 0.016 | 0.003 | 0.023 | |
| extractProtAAC | 0.003 | 0.001 | 0.004 | |
| extractProtAPAAC | 0.712 | 0.024 | 0.947 | |
| extractProtCTDC | 0.003 | 0.001 | 0.006 | |
| extractProtCTDD | 0.004 | 0.002 | 0.007 | |
| extractProtCTDT | 0.005 | 0.002 | 0.009 | |
| extractProtCTriad | 0.091 | 0.009 | 0.133 | |
| extractProtDC | 0.003 | 0.005 | 0.013 | |
| extractProtGeary | 0.133 | 0.009 | 0.212 | |
| extractProtMoran | 0.127 | 0.008 | 0.206 | |
| extractProtMoreauBroto | 0.117 | 0.008 | 0.192 | |
| extractProtPAAC | 0.392 | 0.006 | 0.609 | |
| extractProtPSSM | 0.001 | 0.000 | 0.001 | |
| extractProtPSSMAcc | 0.002 | 0.000 | 0.002 | |
| extractProtPSSMFeature | 0.001 | 0.000 | 0.002 | |
| extractProtQSO | 0.733 | 0.016 | 1.107 | |
| extractProtSOCN | 0.712 | 0.013 | 1.071 | |
| extractProtTC | 0.029 | 0.073 | 0.148 | |
| getCPI | 0.003 | 0.002 | 0.004 | |
| getDrug | 0 | 0 | 0 | |
| getFASTAFromKEGG | 0 | 0 | 0 | |
| getFASTAFromUniProt | 0 | 0 | 0 | |
| getMolFromCAS | 0 | 0 | 0 | |
| getMolFromChEMBL | 0 | 0 | 0 | |
| getMolFromDrugBank | 0 | 0 | 0 | |
| getMolFromKEGG | 0.000 | 0.001 | 0.000 | |
| getMolFromPubChem | 0.001 | 0.000 | 0.001 | |
| getPDBFromRCSBPDB | 0 | 0 | 0 | |
| getPPI | 0.002 | 0.002 | 0.008 | |
| getProt | 0.000 | 0.001 | 0.000 | |
| getSeqFromKEGG | 0 | 0 | 0 | |
| getSeqFromRCSBPDB | 0.000 | 0.001 | 0.000 | |
| getSeqFromUniProt | 0 | 0 | 0 | |
| getSmiFromChEMBL | 0 | 0 | 0 | |
| getSmiFromDrugBank | 0 | 0 | 0 | |
| getSmiFromKEGG | 0 | 0 | 0 | |
| getSmiFromPubChem | 0 | 0 | 0 | |
| readFASTA | 0.001 | 0.001 | 0.004 | |
| readMolFromSDF | 0.003 | 0.002 | 0.007 | |
| readMolFromSmi | 0.001 | 0.001 | 0.003 | |
| readPDB | 0.733 | 0.011 | 1.109 | |
| searchDrug | 0.002 | 0.000 | 0.004 | |
| segProt | 0.003 | 0.001 | 0.005 | |