| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:39 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1625/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rcpi 1.37.0 (landing page) Nan Xiao
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: Rcpi |
| Version: 1.37.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings Rcpi_1.37.0.tar.gz |
| StartedAt: 2023-06-06 04:58:02 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 05:00:38 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 156.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Rcpi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:Rcpi.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings Rcpi_1.37.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/Rcpi.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘Rcpi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rcpi’ version ‘1.37.0’
* 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 loading without being on the library search path ... 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 ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘Rcpi-quickref.Rmd’ using ‘UTF-8’... OK
‘Rcpi.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/Rcpi.Rcheck/00check.log’
for details.
Rcpi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL Rcpi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-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/runTests.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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.
> BiocGenerics:::testPackage('Rcpi')
RUNIT TEST PROTOCOL -- Tue Jun 6 05:00:25 2023
***********************************************
Number of test functions: 11
Number of errors: 0
Number of failures: 0
1 Test Suite :
Rcpi RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
7.041 0.463 6.422
Rcpi.Rcheck/Rcpi-Ex.timings
| name | user | system | elapsed | |
| AA2DACOR | 0.002 | 0.000 | 0.003 | |
| AA3DMoRSE | 0.001 | 0.000 | 0.001 | |
| AAACF | 0.000 | 0.001 | 0.001 | |
| AABLOSUM100 | 0.000 | 0.001 | 0.001 | |
| AABLOSUM45 | 0.000 | 0.000 | 0.001 | |
| AABLOSUM50 | 0.001 | 0.000 | 0.001 | |
| AABLOSUM62 | 0.001 | 0.000 | 0.001 | |
| AABLOSUM80 | 0.001 | 0.000 | 0.001 | |
| AABurden | 0.001 | 0.000 | 0.000 | |
| AACPSA | 0.001 | 0.000 | 0.001 | |
| AAConn | 0.000 | 0.000 | 0.001 | |
| AAConst | 0.001 | 0.000 | 0.001 | |
| AADescAll | 0.001 | 0.000 | 0.001 | |
| AAEdgeAdj | 0.001 | 0.000 | 0.001 | |
| AAEigIdx | 0.001 | 0.000 | 0.001 | |
| AAFGC | 0.001 | 0.000 | 0.001 | |
| AAGETAWAY | 0.000 | 0.001 | 0.001 | |
| AAGeom | 0.000 | 0.001 | 0.001 | |
| AAInfo | 0.000 | 0.000 | 0.001 | |
| AAMOE2D | 0.001 | 0.000 | 0.001 | |
| AAMOE3D | 0.001 | 0.000 | 0.001 | |
| AAMetaInfo | 0.000 | 0.001 | 0.000 | |
| AAMolProp | 0.000 | 0.001 | 0.001 | |
| AAPAM120 | 0.000 | 0.001 | 0.000 | |
| AAPAM250 | 0.000 | 0.001 | 0.001 | |
| AAPAM30 | 0.000 | 0.001 | 0.000 | |
| AAPAM40 | 0.000 | 0.001 | 0.001 | |
| AAPAM70 | 0.000 | 0.001 | 0.001 | |
| AARDF | 0.000 | 0.001 | 0.001 | |
| AARandic | 0.001 | 0.000 | 0.001 | |
| AATopo | 0.001 | 0.000 | 0.001 | |
| AATopoChg | 0.000 | 0.000 | 0.001 | |
| AAWHIM | 0.000 | 0.001 | 0.001 | |
| AAWalk | 0.000 | 0.001 | 0.001 | |
| AAindex | 0.000 | 0.000 | 0.001 | |
| OptAA3d | 0 | 0 | 0 | |
| acc | 0.013 | 0.000 | 0.013 | |
| calcDrugFPSim | 2.276 | 0.247 | 0.777 | |
| calcDrugMCSSim | 0.005 | 0.000 | 0.007 | |
| calcParProtGOSim | 0 | 0 | 0 | |
| calcParProtSeqSim | 0.005 | 0.003 | 0.011 | |
| calcTwoProtGOSim | 0.001 | 0.000 | 0.001 | |
| calcTwoProtSeqSim | 0.002 | 0.000 | 0.002 | |
| checkProt | 0.001 | 0.000 | 0.001 | |
| convMolFormat | 0.001 | 0.000 | 0.001 | |
| extractDrugAIO | 0.000 | 0.000 | 0.001 | |
| extractDrugALOGP | 0.000 | 0.001 | 0.001 | |
| extractDrugAminoAcidCount | 0.000 | 0.001 | 0.001 | |
| extractDrugApol | 0.000 | 0.000 | 0.001 | |
| extractDrugAromaticAtomsCount | 0.001 | 0.000 | 0.001 | |
| extractDrugAromaticBondsCount | 0.001 | 0.000 | 0.001 | |
| extractDrugAtomCount | 0.001 | 0.000 | 0.001 | |
| extractDrugAutocorrelationCharge | 0.001 | 0.000 | 0.001 | |
| extractDrugAutocorrelationMass | 0.001 | 0.000 | 0.001 | |
| extractDrugAutocorrelationPolarizability | 0.001 | 0.000 | 0.001 | |
| extractDrugBCUT | 0.001 | 0.000 | 0.001 | |
| extractDrugBPol | 0.001 | 0.000 | 0.001 | |
| extractDrugBondCount | 0.001 | 0.000 | 0.001 | |
| extractDrugCPSA | 0.001 | 0.000 | 0.001 | |
| extractDrugCarbonTypes | 0.001 | 0.000 | 0.001 | |
| extractDrugChiChain | 0.001 | 0.000 | 0.001 | |
| extractDrugChiCluster | 0.002 | 0.000 | 0.002 | |
| extractDrugChiPath | 0.001 | 0.000 | 0.001 | |
| extractDrugChiPathCluster | 0.001 | 0.000 | 0.001 | |
| extractDrugDescOB | 0.116 | 0.068 | 0.185 | |
| extractDrugECI | 0.001 | 0.000 | 0.001 | |
| extractDrugEstate | 0.001 | 0.000 | 0.001 | |
| extractDrugEstateComplete | 0.001 | 0.000 | 0.001 | |
| extractDrugExtended | 0.001 | 0.000 | 0.000 | |
| extractDrugExtendedComplete | 0.000 | 0.000 | 0.001 | |
| extractDrugFMF | 0.001 | 0.000 | 0.001 | |
| extractDrugFragmentComplexity | 0.001 | 0.000 | 0.001 | |
| extractDrugGraph | 0.000 | 0.000 | 0.001 | |
| extractDrugGraphComplete | 0.000 | 0.001 | 0.001 | |
| extractDrugGravitationalIndex | 0.000 | 0.002 | 0.001 | |
| extractDrugHBondAcceptorCount | 0.001 | 0.000 | 0.001 | |
| extractDrugHBondDonorCount | 0.001 | 0.000 | 0.001 | |
| extractDrugHybridization | 0.001 | 0.000 | 0.001 | |
| extractDrugHybridizationComplete | 0.001 | 0.000 | 0.001 | |
| extractDrugHybridizationRatio | 0.001 | 0.000 | 0.001 | |
| extractDrugIPMolecularLearning | 0.001 | 0.000 | 0.000 | |
| extractDrugKR | 0.000 | 0.000 | 0.001 | |
| extractDrugKRComplete | 0.001 | 0.000 | 0.001 | |
| extractDrugKappaShapeIndices | 0.001 | 0.000 | 0.001 | |
| extractDrugKierHallSmarts | 0.001 | 0.000 | 0.001 | |
| extractDrugLargestChain | 0.001 | 0.000 | 0.001 | |
| extractDrugLargestPiSystem | 0.001 | 0.000 | 0.001 | |
| extractDrugLengthOverBreadth | 0.001 | 0.000 | 0.000 | |
| extractDrugLongestAliphaticChain | 0.000 | 0.000 | 0.001 | |
| extractDrugMACCS | 0.001 | 0.000 | 0.001 | |
| extractDrugMACCSComplete | 0.001 | 0.000 | 0.001 | |
| extractDrugMDE | 0.001 | 0.000 | 0.001 | |
| extractDrugMannholdLogP | 0.001 | 0.000 | 0.000 | |
| extractDrugMomentOfInertia | 0.001 | 0.000 | 0.001 | |
| extractDrugOBFP2 | 0.399 | 0.197 | 0.596 | |
| extractDrugOBFP3 | 0.006 | 0.000 | 0.007 | |
| extractDrugOBFP4 | 0.005 | 0.000 | 0.006 | |
| extractDrugOBMACCS | 0.006 | 0.007 | 0.013 | |
| extractDrugPetitjeanNumber | 0.001 | 0.000 | 0.001 | |
| extractDrugPetitjeanShapeIndex | 0.001 | 0.000 | 0.001 | |
| extractDrugPubChem | 0.001 | 0.000 | 0.000 | |
| extractDrugPubChemComplete | 0.001 | 0.000 | 0.001 | |
| extractDrugRotatableBondsCount | 0.001 | 0.000 | 0.001 | |
| extractDrugRuleOfFive | 0.000 | 0.000 | 0.001 | |
| extractDrugShortestPath | 0.001 | 0.000 | 0.001 | |
| extractDrugShortestPathComplete | 0.001 | 0.000 | 0.001 | |
| extractDrugStandard | 0.001 | 0.000 | 0.001 | |
| extractDrugStandardComplete | 0 | 0 | 0 | |
| extractDrugTPSA | 0.000 | 0.000 | 0.001 | |
| extractDrugVABC | 0.000 | 0.001 | 0.001 | |
| extractDrugVAdjMa | 0.000 | 0.001 | 0.001 | |
| extractDrugWHIM | 0.000 | 0.001 | 0.000 | |
| extractDrugWeight | 0.001 | 0.000 | 0.001 | |
| extractDrugWeightedPath | 0.001 | 0.000 | 0.001 | |
| extractDrugWienerNumbers | 0.001 | 0.000 | 0.001 | |
| extractDrugXLogP | 0.000 | 0.001 | 0.000 | |
| extractDrugZagrebIndex | 0.000 | 0.001 | 0.001 | |
| extractPCMBLOSUM | 0.009 | 0.005 | 0.015 | |
| extractPCMDescScales | 0.015 | 0.000 | 0.015 | |
| extractPCMFAScales | 0.015 | 0.007 | 0.022 | |
| extractPCMMDSScales | 0.014 | 0.001 | 0.014 | |
| extractPCMPropScales | 0.017 | 0.000 | 0.017 | |
| extractPCMScales | 0.035 | 0.000 | 0.035 | |
| extractProtAAC | 0.003 | 0.000 | 0.003 | |
| extractProtAPAAC | 1.089 | 0.167 | 1.259 | |
| extractProtCTDC | 0.004 | 0.000 | 0.004 | |
| extractProtCTDD | 0.005 | 0.000 | 0.005 | |
| extractProtCTDT | 0.002 | 0.004 | 0.006 | |
| extractProtCTriad | 0.123 | 0.007 | 0.130 | |
| extractProtDC | 0.005 | 0.000 | 0.005 | |
| extractProtGeary | 0.169 | 0.008 | 0.178 | |
| extractProtMoran | 0.173 | 0.036 | 0.210 | |
| extractProtMoreauBroto | 0.159 | 0.004 | 0.163 | |
| extractProtPAAC | 0.590 | 0.036 | 0.628 | |
| extractProtPSSM | 0.001 | 0.000 | 0.001 | |
| extractProtPSSMAcc | 0.001 | 0.000 | 0.001 | |
| extractProtPSSMFeature | 0.001 | 0.000 | 0.001 | |
| extractProtQSO | 0.989 | 0.008 | 0.999 | |
| extractProtSOCN | 0.993 | 0.000 | 0.994 | |
| extractProtTC | 0.016 | 0.035 | 0.053 | |
| getCPI | 0.004 | 0.000 | 0.005 | |
| getDrug | 0.000 | 0.000 | 0.001 | |
| getFASTAFromKEGG | 0 | 0 | 0 | |
| getFASTAFromUniProt | 0 | 0 | 0 | |
| getMolFromCAS | 0 | 0 | 0 | |
| getMolFromChEMBL | 0 | 0 | 0 | |
| getMolFromDrugBank | 0 | 0 | 0 | |
| getMolFromKEGG | 0 | 0 | 0 | |
| getMolFromPubChem | 0 | 0 | 0 | |
| getPDBFromRCSBPDB | 0 | 0 | 0 | |
| getPPI | 0.001 | 0.001 | 0.003 | |
| getProt | 0 | 0 | 0 | |
| getSeqFromKEGG | 0 | 0 | 0 | |
| getSeqFromRCSBPDB | 0 | 0 | 0 | |
| getSeqFromUniProt | 0 | 0 | 0 | |
| getSmiFromChEMBL | 0 | 0 | 0 | |
| getSmiFromDrugBank | 0 | 0 | 0 | |
| getSmiFromKEGG | 0 | 0 | 0 | |
| getSmiFromPubChem | 0.001 | 0.000 | 0.000 | |
| readFASTA | 0.001 | 0.000 | 0.002 | |
| readMolFromSDF | 0.002 | 0.000 | 0.002 | |
| readMolFromSmi | 0.001 | 0.000 | 0.001 | |
| readPDB | 0.927 | 0.000 | 0.931 | |
| searchDrug | 0.002 | 0.000 | 0.002 | |
| segProt | 0.002 | 0.000 | 0.003 | |