| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-27 05:50:30 -0000 (Mon, 27 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6083 |
| 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 BioNAR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioNAR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 208/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BioNAR 1.1.0 (landing page) Anatoly Sorokin
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: BioNAR |
| Version: 1.1.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BioNAR_1.1.0.tar.gz |
| StartedAt: 2023-03-24 22:01:50 -0000 (Fri, 24 Mar 2023) |
| EndedAt: 2023-03-24 22:13:28 -0000 (Fri, 24 Mar 2023) |
| EllapsedTime: 698.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: BioNAR.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BioNAR_1.1.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BioNAR.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘BioNAR/DESCRIPTION’ ... OK
* this is package ‘BioNAR’ version ‘1.1.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BioNAR’ 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 ... NOTE
Package in Depends field not imported from: ‘Rdpack’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
clusteringSummary 13.808 0.024 13.832
plotEntropy 12.301 0.336 12.650
calcEntropy 11.681 0.256 11.950
getEntropy 10.888 0.240 11.135
getCentralityMatrix 9.652 0.148 9.801
getGraphCentralityECDF 9.376 0.128 9.512
runPermDisease 7.600 0.032 7.637
annotateTopOntoOVG 6.605 0.044 6.652
annotateGoBP 6.146 0.212 6.360
annotateGOont 5.481 0.340 5.959
annotateGoMF 5.427 0.104 5.532
calcAllClustering 5.125 0.015 5.153
FitDegree 1.948 0.300 8.479
getRandomGraphCentrality 1.122 0.130 15.027
* 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 ...
‘BioNAR_overview.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘BioNAR_overview.Rmd’ using rmarkdown
Killed
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/BioNAR.Rcheck/00check.log’
for details.
BioNAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BioNAR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘BioNAR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use snapshotDate(): 2023-03-16 loading from cache ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use snapshotDate(): 2023-03-16 loading from cache ** testing if installed package can be loaded from final location Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use snapshotDate(): 2023-03-16 loading from cache ** testing if installed package keeps a record of temporary installation path * DONE (BioNAR)
BioNAR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
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.
> library(testthat)
> library(BioNAR)
Loading required package: igraph
Attaching package: 'igraph'
The following object is masked from 'package:testthat':
compare
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: poweRlaw
Loading required package: latex2exp
Loading required package: RSpectra
Loading required package: Rdpack
Using 'localHub=TRUE'
If offline, please also see BiocManager vignette section on offline use
snapshotDate(): 2023-03-21
loading from cache
Attaching package: 'BioNAR'
The following object is masked from 'package:igraph':
permute
>
> test_check("BioNAR")
Loading required package: synaptome.data
Loading required package: AnnotationHub
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:igraph':
normalize, path, union
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: BiocFileCache
Loading required package: dbplyr
An object of class "law"
Slot "fit":
Reference class object of class "displ"
Field "xmin":
[1] 11
Field "pars":
[1] 2.634402
Field "no_pars":
[1] 1
Slot "p":
[1] 0.8
Slot "alpha":
[1] 2.634402
Slot "SDxmin":
[1] 2.167948
Slot "SDalpha":
[1] 0.0247062
[ FAIL 0 | WARN 15 | SKIP 4 | PASS 104 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (4)
[ FAIL 0 | WARN 15 | SKIP 4 | PASS 104 ]
>
> proc.time()
user system elapsed
49.396 2.072 76.780
BioNAR.Rcheck/BioNAR-Ex.timings
| name | user | system | elapsed | |
| FitDegree | 1.948 | 0.300 | 8.479 | |
| addEdgeAtts | 0.084 | 0.000 | 0.085 | |
| annotateGOont | 5.481 | 0.340 | 5.959 | |
| annotateGeneNames | 0.267 | 0.012 | 0.279 | |
| annotateGoBP | 6.146 | 0.212 | 6.360 | |
| annotateGoCC | 4.701 | 0.072 | 4.774 | |
| annotateGoMF | 5.427 | 0.104 | 5.532 | |
| annotatePresynaptic | 1.973 | 0.004 | 1.977 | |
| annotateSCHanno | 2.281 | 0.020 | 2.354 | |
| annotateTopOntoOVG | 6.605 | 0.044 | 6.652 | |
| annotateVertex | 0.004 | 0.000 | 0.005 | |
| applpMatrixToGraph | 0.002 | 0.000 | 0.003 | |
| buildFromSynaptomeByEntrez | 0.689 | 0.028 | 0.717 | |
| buildFromSynaptomeGeneTable | 0.450 | 0.032 | 0.481 | |
| buildNetwork | 0.003 | 0.000 | 0.004 | |
| calcAllClustering | 5.125 | 0.015 | 5.153 | |
| calcBridgeness | 0.080 | 0.013 | 0.098 | |
| calcCentrality | 0.070 | 0.002 | 0.072 | |
| calcCentralityExternalDistances | 0.569 | 0.035 | 0.605 | |
| calcCentralityInternalDistances | 0.518 | 0.020 | 0.538 | |
| calcClustering | 0.004 | 0.000 | 0.005 | |
| calcDiseasePairs | 0.614 | 0.016 | 0.633 | |
| calcEntropy | 11.681 | 0.256 | 11.950 | |
| calcMembership | 0.007 | 0.011 | 0.018 | |
| calcReclusterMatrix | 0.009 | 0.005 | 0.013 | |
| calcSparsness | 0.705 | 0.012 | 0.717 | |
| clusterORA | 0.175 | 0.008 | 0.188 | |
| clusteringSummary | 13.808 | 0.024 | 13.832 | |
| degreeBinnedGDAs | 0.273 | 0.028 | 0.301 | |
| escapeAnnotation | 0 | 0 | 0 | |
| evalCentralitySignificance | 0.543 | 0.044 | 0.587 | |
| findLCC | 0.005 | 0.000 | 0.005 | |
| getAnnotationList | 0.075 | 0.000 | 0.075 | |
| getAnnotationVertexList | 0.086 | 0.004 | 0.090 | |
| getBridgeness | 0.073 | 0.008 | 0.081 | |
| getCentralityMatrix | 9.652 | 0.148 | 9.801 | |
| getClusterSubgraphByID | 0.000 | 0.004 | 0.003 | |
| getClustering | 0.007 | 0.008 | 0.017 | |
| getCommunityGraph | 0.007 | 0.000 | 0.007 | |
| getDType | 0.001 | 0.000 | 0.000 | |
| getDiseases | 0.000 | 0.000 | 0.001 | |
| getEntropy | 10.888 | 0.240 | 11.135 | |
| getEntropyRate | 0.007 | 0.000 | 0.007 | |
| getGraphCentralityECDF | 9.376 | 0.128 | 9.512 | |
| getRandomGraphCentrality | 1.122 | 0.130 | 15.027 | |
| getRobustness | 0.494 | 0.028 | 0.526 | |
| layoutByCluster | 0.230 | 0.004 | 0.238 | |
| layoutByRecluster | 0.476 | 0.008 | 0.485 | |
| makeConsensusMatrix | 0.517 | 0.068 | 0.585 | |
| normModularity | 0.969 | 0.052 | 1.085 | |
| permute | 0.000 | 0.000 | 0.001 | |
| plotBridgeness | 0.516 | 0.036 | 0.576 | |
| plotEntropy | 12.301 | 0.336 | 12.650 | |
| prepareGDA | 0.293 | 0.004 | 0.300 | |
| recluster | 0.006 | 0.004 | 0.010 | |
| removeVertexTerm | 0.002 | 0.000 | 0.002 | |
| runPermDisease | 7.600 | 0.032 | 7.637 | |
| sampleDegBinnedGDA | 0.356 | 0.008 | 0.364 | |
| sampleGraphClust | 0.002 | 0.004 | 0.008 | |
| unescapeAnnotation | 0.001 | 0.000 | 0.001 | |
| zeroNA | 0 | 0 | 0 | |