| Back to First build/check report with an "external build node" |
This page was generated on 2023-06-01 18:17:19 -0400 (Thu, 01 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| xps15 | Linux (Ubuntu 23.04) | x86_64 | 4.3.0 Patched (2023-05-23 r84466) -- "Already Tomorrow" | 544 |
| 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: 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 45/91 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||||
| graph 1.79.0 (landing page) Bioconductor Package Maintainer
| xps15 | Linux (Ubuntu 23.04) / x86_64 | OK | OK | OK | ||||||||
| Package: graph |
| Version: 1.79.0 |
| Command: /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:graph.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings graph_1.79.0.tar.gz |
| StartedAt: 2023-06-01 13:11:32 -0700 (Thu, 01 Jun 2023) |
| EndedAt: 2023-06-01 13:13:02 -0700 (Thu, 01 Jun 2023) |
| EllapsedTime: 90.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: graph.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/hpages/bbs-3.18-bioc/R/bin/R CMD check --install=check:graph.install-out.txt --library=/home/hpages/bbs-3.18-bioc-testing/Rlibs --timings graph_1.79.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/hpages/bbs-3.18-bioc-testing/meat/graph.Rcheck’
* using R version 4.3.0 Patched (2023-05-23 r84466)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0
GNU Fortran (Ubuntu 12.2.0-17ubuntu1) 12.2.0
* running under: Ubuntu 23.04
* using session charset: UTF-8
* checking for file ‘graph/DESCRIPTION’ ... OK
* this is package ‘graph’ version ‘1.79.0’
* 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 12.2.0-17ubuntu1) 12.2.0’
* 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 loading without being on the library search path ... 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.Rmd’ using ‘UTF-8’... OK
‘graphAttributes.Rnw’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/hpages/bbs-3.18-bioc-testing/meat/graph.Rcheck/00check.log’
for details.
graph.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/hpages/bbs-3.18-bioc/R/bin/R CMD INSTALL graph ### ############################################################################## ############################################################################## * installing to library ‘/home/hpages/bbs-3.18-bioc-testing/Rlibs’ * installing *source* package ‘graph’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 12.2.0-17ubuntu1) 12.2.0’ gcc -I"/home/hpages/bbs-3.18-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c graph.c -o graph.o gcc -shared -L/usr/local/lib -o graph.so graph.o mv graph.so BioC_graph.so installing to /home/hpages/bbs-3.18-bioc-testing/Rlibs/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 version 4.3.0 Patched (2023-05-23 r84466) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 -- Thu Jun 1 13:12:20 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
3.805 0.121 3.907
graph.Rcheck/graph-Ex.timings
| name | user | system | elapsed | |
| DFS | 0.030 | 0.004 | 0.034 | |
| IMCA | 0.007 | 0.011 | 0.019 | |
| MAPKsig | 0.002 | 0.000 | 0.002 | |
| MultiGraph-class | 0.125 | 0.012 | 0.137 | |
| acc-methods | 0.004 | 0.000 | 0.005 | |
| addEdge | 0.034 | 0.000 | 0.034 | |
| addNode | 0.007 | 0.001 | 0.008 | |
| adj-methods | 0.002 | 0.000 | 0.002 | |
| adjacencyMatrix | 0.002 | 0.000 | 0.002 | |
| apoptosisGraph | 0.002 | 0.000 | 0.002 | |
| attrData-class | 0.001 | 0.000 | 0.001 | |
| aveNumEdges | 0.004 | 0.000 | 0.003 | |
| biocRepos | 0.002 | 0.000 | 0.001 | |
| boundary | 0.003 | 0.000 | 0.002 | |
| calcProb | 0 | 0 | 0 | |
| calcSumProb | 0.004 | 0.000 | 0.005 | |
| clearNode | 0.007 | 0.000 | 0.007 | |
| clusterGraph-class | 0.021 | 0.000 | 0.021 | |
| clusteringCoefficient-methods | 0.025 | 0.000 | 0.025 | |
| combineNodes | 0.061 | 0.000 | 0.061 | |
| distGraph-class | 0.000 | 0.001 | 0.001 | |
| duplicatedEdges | 0 | 0 | 0 | |
| edgeMatrix | 0.005 | 0.001 | 0.007 | |
| edgeSets | 0.044 | 0.000 | 0.044 | |
| edgeWeights | 0.013 | 0.001 | 0.013 | |
| fromGXL-methods | 0.246 | 0.003 | 0.250 | |
| graph-class | 0.019 | 0.000 | 0.019 | |
| graph2SparseM | 0.127 | 0.000 | 0.139 | |
| graphAM-class | 0.011 | 0.000 | 0.011 | |
| graphBAM-class | 0.030 | 0.001 | 0.030 | |
| graphExamples | 0.005 | 0.000 | 0.004 | |
| graphNEL-class | 0.007 | 0.000 | 0.007 | |
| inEdges | 0.007 | 0.000 | 0.006 | |
| leaves | 0.006 | 0.004 | 0.009 | |
| listEdges | 0.011 | 0.000 | 0.012 | |
| matrix2Graph | 0.011 | 0.000 | 0.010 | |
| mostEdges | 0.012 | 0.000 | 0.012 | |
| numNoEdges | 0.002 | 0.000 | 0.003 | |
| pancrCaIni | 0.002 | 0.000 | 0.002 | |
| randomEGraph | 0.004 | 0.000 | 0.005 | |
| randomGraph | 0.003 | 0.000 | 0.003 | |
| randomNodeGraph | 0.003 | 0.000 | 0.003 | |
| removeEdge | 0.009 | 0.000 | 0.010 | |
| removeNode | 0.006 | 0.000 | 0.006 | |
| renderInfo-class | 0.006 | 0.000 | 0.006 | |
| reverseEdgeDirections | 0.004 | 0.000 | 0.003 | |
| simpleEdge-class | 0.001 | 0.000 | 0.001 | |
| standardLabeling | 0.060 | 0.004 | 0.064 | |
| subGraph | 0.001 | 0.000 | 0.001 | |
| toDotR-methods | 0.027 | 0.000 | 0.027 | |
| ugraph | 0.009 | 0.000 | 0.010 | |
| validGraph | 0.001 | 0.000 | 0.001 | |