Anatoly Sorokin
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/BioNAR |
| git_branch: RELEASE_3_17 |
| git_last_commit: ca4c31e |
| git_last_commit_date: 2023-08-09 19:49:47 -0400 (Wed, 09 Aug 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:59 -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 210/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BioNAR 1.2.5 (landing page) Anatoly Sorokin
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the BioNAR 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: BioNAR |
| Version: 1.2.5 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNAR_1.2.5.tar.gz |
| StartedAt: 2023-10-17 05:50:07 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 06:00:26 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 618.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BioNAR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BioNAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BioNAR_1.2.5.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BioNAR.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 ‘BioNAR/DESCRIPTION’ ... OK
* this is package ‘BioNAR’ version ‘1.2.5’
* 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 ... NOTE
installed size is 6.7Mb
sub-directories of 1Mb or more:
extdata 6.1Mb
* 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 ... 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.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘addNoise’ ‘gofs’ ‘highlightRate’ ‘plotSigmoid’ ‘storeFitInfo’
‘storeParInfo’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
clusterORA : forafun: no visible binding for global variable ‘pathway’
clusterORA : forafun: no visible binding for global variable ‘size’
clusterORA : forafun: no visible binding for global variable ‘overlap’
clusterORA : forafun: no visible binding for global variable ‘pval’
clusterORA : forafun: no visible binding for global variable ‘padj’
clusterORA : forafun: no visible binding for global variable
‘overlapGenes’
clusterORA : forafun: no visible binding for global variable ‘FL’
clusterORA : forafun: no visible binding for global variable ‘N’
clusterORA : forafun: no visible binding for global variable ‘Fn’
clusterORA : forafun: no visible binding for global variable ‘Cn’
clusterORA : forafun: no visible binding for global variable ‘Mu’
clusterORA : forafun: no visible binding for global variable ‘OR’
clusterORA : forafun: no visible binding for global variable ‘CIw’
clusterORA : forafun: no visible binding for global variable ‘Fe’
clusterORA : forafun: no visible binding for global variable ‘Fc’
clusterORA : forafun: no visible binding for global variable ‘palt’
plotSigmoid: no visible binding for global variable ‘yiR1’
plotSigmoid: no visible binding for global variable ‘yiR2’
plotSigmoid: no visible binding for global variable ‘yiR3’
plotSigmoid: no visible binding for global variable ‘yiR4’
plotSigmoid: no visible binding for global variable ‘yiR5’
Undefined global functions or variables:
CIw Cn FL Fc Fe Fn Mu N OR overlap overlapGenes padj palt pathway
pval size yiR1 yiR2 yiR3 yiR4 yiR5
* 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 15.727 0.119 20.840
calcEntropy 10.697 0.190 14.116
plotEntropy 10.273 0.182 13.466
getEntropy 9.301 0.131 12.970
getGraphCentralityECDF 7.740 0.113 10.200
getCentralityMatrix 7.389 0.126 9.674
annotateTopOntoOVG 6.924 0.133 9.123
calcAllClustering 6.894 0.053 8.998
runPermDisease 6.428 0.077 8.398
annotateGOont 4.979 0.454 7.001
annotateGoBP 4.652 0.097 6.193
FitDegree 1.733 0.067 9.451
getRandomGraphCentrality 0.329 0.025 16.792
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BioNAR.Rcheck/00check.log’
for details.
BioNAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BioNAR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 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 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 loading from cache ** testing if installed package keeps a record of temporary installation path * DONE (BioNAR)
BioNAR.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(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
loading from cache
Attaching package: 'BioNAR'
The following object is masked from 'package:igraph':
permute
>
> test_check("BioNAR")
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
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
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
This graph was created by an old(er) igraph version.
Call upgrade_graph() on it to use with the current igraph version
For now we convert it on the fly...
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 109 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test_bridgeness.R:34:5', 'test_bridgeness.R:64:5'
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 109 ]
Deleting unused snapshots:
• bridgeness/entropyplot.svg
• fitdegree/powerfitplot.svg
>
> proc.time()
user system elapsed
46.034 2.273 85.284
BioNAR.Rcheck/BioNAR-Ex.timings
| name | user | system | elapsed | |
| FitDegree | 1.733 | 0.067 | 9.451 | |
| addEdgeAtts | 0.066 | 0.003 | 0.100 | |
| annotateGOont | 4.979 | 0.454 | 7.001 | |
| annotateGeneNames | 0.275 | 0.011 | 0.370 | |
| annotateGoBP | 4.652 | 0.097 | 6.193 | |
| annotateGoCC | 2.933 | 0.064 | 3.878 | |
| annotateGoMF | 3.190 | 0.061 | 4.183 | |
| annotatePresynaptic | 1.282 | 0.034 | 1.690 | |
| annotateSCHanno | 1.797 | 0.077 | 2.420 | |
| annotateTopOntoOVG | 6.924 | 0.133 | 9.123 | |
| annotateVertex | 0.004 | 0.001 | 0.005 | |
| applpMatrixToGraph | 0.002 | 0.001 | 0.003 | |
| buildFromSynaptomeByEntrez | 0.748 | 0.030 | 1.009 | |
| buildFromSynaptomeGeneTable | 0.556 | 0.026 | 0.749 | |
| buildNetwork | 0.004 | 0.001 | 0.007 | |
| calcAllClustering | 6.894 | 0.053 | 8.998 | |
| calcBridgeness | 0.100 | 0.010 | 0.142 | |
| calcCentrality | 0.061 | 0.004 | 0.086 | |
| calcCentralityExternalDistances | 0.488 | 0.013 | 0.654 | |
| calcCentralityInternalDistances | 0.484 | 0.010 | 0.633 | |
| calcClustering | 0.005 | 0.001 | 0.011 | |
| calcDiseasePairs | 0.517 | 0.011 | 0.687 | |
| calcEntropy | 10.697 | 0.190 | 14.116 | |
| calcMembership | 0.013 | 0.011 | 0.032 | |
| calcReclusterMatrix | 0.017 | 0.006 | 0.031 | |
| calcSparsness | 0.780 | 0.030 | 1.042 | |
| clusterORA | 0.347 | 0.021 | 0.509 | |
| clusteringSummary | 15.727 | 0.119 | 20.840 | |
| degreeBinnedGDAs | 0.262 | 0.010 | 0.359 | |
| escapeAnnotation | 0.000 | 0.000 | 0.001 | |
| evalCentralitySignificance | 0.461 | 0.015 | 0.622 | |
| findLCC | 0.005 | 0.002 | 0.007 | |
| getAnnotationList | 0.062 | 0.004 | 0.082 | |
| getAnnotationVertexList | 0.074 | 0.011 | 0.108 | |
| getBridgeness | 0.085 | 0.010 | 0.125 | |
| getCentralityMatrix | 7.389 | 0.126 | 9.674 | |
| getClusterSubgraphByID | 0.005 | 0.004 | 0.010 | |
| getClustering | 0.011 | 0.010 | 0.028 | |
| getCommunityGraph | 0.008 | 0.004 | 0.015 | |
| getDType | 0.001 | 0.000 | 0.000 | |
| getDiseases | 0 | 0 | 0 | |
| getEntropy | 9.301 | 0.131 | 12.970 | |
| getEntropyRate | 0.007 | 0.004 | 0.013 | |
| getGNP | 0.003 | 0.006 | 0.014 | |
| getGraphCentralityECDF | 7.740 | 0.113 | 10.200 | |
| getPA | 0.003 | 0.004 | 0.009 | |
| getRandomGraphCentrality | 0.329 | 0.025 | 16.792 | |
| getRobustness | 0.688 | 0.056 | 0.960 | |
| layoutByCluster | 0.072 | 0.005 | 0.096 | |
| layoutByRecluster | 0.152 | 0.008 | 0.211 | |
| makeConsensusMatrix | 0.701 | 0.055 | 0.952 | |
| normModularity | 1.093 | 0.037 | 1.461 | |
| permute | 0.000 | 0.000 | 0.001 | |
| plotBridgeness | 0.564 | 0.026 | 0.758 | |
| plotEntropy | 10.273 | 0.182 | 13.466 | |
| prepareGDA | 0.237 | 0.008 | 0.317 | |
| recluster | 0.013 | 0.005 | 0.021 | |
| removeVertexTerm | 0.003 | 0.004 | 0.008 | |
| runPermDisease | 6.428 | 0.077 | 8.398 | |
| sampleDegBinnedGDA | 0.351 | 0.011 | 0.379 | |
| sampleGraphClust | 0.014 | 0.005 | 0.020 | |
| unescapeAnnotation | 0.001 | 0.001 | 0.002 | |
| zeroNA | 0.000 | 0.000 | 0.001 | |