| Back to Build/check report for BioC 3.17: simplified long |
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This page was generated on 2023-03-01 07:38:42 -0000 (Wed, 01 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4266 |
| 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 graph package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/graph.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 844/2171 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| graph 1.77.2 (landing page) Bioconductor Package Maintainer
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: graph |
| Version: 1.77.2 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:graph.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings graph_1.77.2.tar.gz |
| StartedAt: 2023-02-28 05:08:14 -0000 (Tue, 28 Feb 2023) |
| EndedAt: 2023-02-28 05:09:48 -0000 (Tue, 28 Feb 2023) |
| EllapsedTime: 94.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graph.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:graph.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings graph_1.77.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/graph.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* 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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘graph/DESCRIPTION’ ... OK
* this is package ‘graph’ version ‘1.77.2’
* 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 ‘graph’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* 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 ... NOTE
'library' or 'require' call to ‘package’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘graph_unit_tests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘GraphClass.Rmd’ using ‘UTF-8’... OK
‘MultiGraphClass.Rmd’ using ‘UTF-8’... OK
‘clusterGraph.Rmd’ using ‘UTF-8’... OK
‘graph.Rnw’... OK
‘graphAttributes.Rnw’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/graph.Rcheck/00check.log’
for details.
graph.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL graph ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘graph’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c graph.c -o graph.o gcc -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o graph.so graph.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR mv graph.so BioC_graph.so installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-graph/00new/graph/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (graph)
graph.Rcheck/tests/graph_unit_tests.Rout
R Under development (unstable) (2023-01-14 r83615) -- "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.
> BiocGenerics:::testPackage("graph", pattern="_test.R")
Attaching package: 'BiocGenerics'
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
RUNIT TEST PROTOCOL -- Tue Feb 28 05:09:09 2023
***********************************************
Number of test functions: 208
Number of errors: 0
Number of failures: 0
1 Test Suite :
graph RUnit Tests - 208 test functions, 0 errors, 0 failures
Number of test functions: 208
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
5.153 0.213 5.360
graph.Rcheck/graph-Ex.timings
| name | user | system | elapsed | |
| DFS | 0.044 | 0.000 | 0.043 | |
| IMCA | 0.161 | 0.028 | 0.189 | |
| MAPKsig | 0.133 | 0.000 | 0.132 | |
| MultiGraph-class | 0.147 | 0.003 | 0.150 | |
| acc-methods | 0.009 | 0.000 | 0.009 | |
| addEdge | 0.048 | 0.000 | 0.048 | |
| addNode | 0.010 | 0.000 | 0.009 | |
| adj-methods | 0.000 | 0.003 | 0.003 | |
| adjacencyMatrix | 0.002 | 0.001 | 0.002 | |
| apoptosisGraph | 0.014 | 0.000 | 0.014 | |
| attrData-class | 0.001 | 0.000 | 0.001 | |
| aveNumEdges | 0.005 | 0.000 | 0.004 | |
| biocRepos | 0.001 | 0.000 | 0.001 | |
| boundary | 0.000 | 0.003 | 0.004 | |
| calcProb | 0.000 | 0.000 | 0.001 | |
| calcSumProb | 0.002 | 0.002 | 0.005 | |
| clearNode | 0.012 | 0.000 | 0.012 | |
| clusterGraph-class | 0.026 | 0.000 | 0.026 | |
| clusteringCoefficient-methods | 0.036 | 0.000 | 0.036 | |
| combineNodes | 0.095 | 0.000 | 0.095 | |
| distGraph-class | 0.001 | 0.000 | 0.001 | |
| duplicatedEdges | 0 | 0 | 0 | |
| edgeMatrix | 0.010 | 0.000 | 0.009 | |
| edgeSets | 0.034 | 0.000 | 0.034 | |
| edgeWeights | 0.01 | 0.00 | 0.01 | |
| fromGXL-methods | 0.243 | 0.004 | 0.252 | |
| graph-class | 0.004 | 0.000 | 0.005 | |
| graph2SparseM | 0.121 | 0.000 | 0.121 | |
| graphAM-class | 0.010 | 0.000 | 0.011 | |
| graphBAM-class | 0.041 | 0.000 | 0.041 | |
| graphExamples | 0.005 | 0.000 | 0.004 | |
| graphNEL-class | 0.008 | 0.000 | 0.007 | |
| inEdges | 0.007 | 0.000 | 0.007 | |
| leaves | 0.005 | 0.004 | 0.009 | |
| listEdges | 0.008 | 0.004 | 0.012 | |
| matrix2Graph | 0.016 | 0.004 | 0.020 | |
| mostEdges | 0.06 | 0.00 | 0.06 | |
| numNoEdges | 0.003 | 0.000 | 0.003 | |
| pancrCaIni | 0.167 | 0.000 | 0.166 | |
| randomEGraph | 0.005 | 0.000 | 0.005 | |
| randomGraph | 0.004 | 0.000 | 0.004 | |
| randomNodeGraph | 0.003 | 0.000 | 0.003 | |
| removeEdge | 0.01 | 0.00 | 0.01 | |
| removeNode | 0.007 | 0.000 | 0.007 | |
| renderInfo-class | 0.006 | 0.000 | 0.007 | |
| reverseEdgeDirections | 0.004 | 0.000 | 0.004 | |
| simpleEdge-class | 0.001 | 0.000 | 0.001 | |
| standardLabeling | 0.063 | 0.000 | 0.063 | |
| subGraph | 0.001 | 0.000 | 0.002 | |
| toDotR-methods | 0.019 | 0.004 | 0.023 | |
| ugraph | 0.01 | 0.00 | 0.01 | |
| validGraph | 0.001 | 0.000 | 0.001 | |