Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:06:33 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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

CHECK results for graph on palomino4


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.

raw results

Package 830/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
graph 1.75.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/graph
git_branch: master
git_last_commit: b88531e
git_last_commit_date: 2022-04-26 10:54:46 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: graph
Version: 1.75.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:graph.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings graph_1.75.0.tar.gz
StartedAt: 2022-06-24 02:15:43 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 02:16:52 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 69.2 seconds
RetCode: 0
Status:   OK  
CheckDir: graph.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:graph.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings graph_1.75.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/graph.Rcheck'
* using R version 4.2.0 Patched (2022-06-02 r82447 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'graph/DESCRIPTION' ... OK
* this is package 'graph' version '1.75.0'
* 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 whether package 'graph' 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/graph/libs/x64/BioC_graph.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.16-bioc/meat/graph.Rcheck/00check.log'
for details.



Installation output

graph.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/graph_1.75.0.tar.gz && rm -rf graph.buildbin-libdir && mkdir graph.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=graph.buildbin-libdir graph_1.75.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL graph_1.75.0.zip && rm graph_1.75.0.tar.gz graph_1.75.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  327k  100  327k    0     0  4195k      0 --:--:-- --:--:-- --:--:-- 4247k
only one architecture so ignoring '--merge-multiarch'
* installing *source* package 'graph' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c graph.c -o graph.o
gcc -shared -s -static-libgcc -o graph.dll tmp.def graph.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
mv graph.dll BioC_graph.dll
installing to F:/biocbuild/bbs-3.16-bioc/meat/graph.buildbin-libdir/00LOCK-graph/00new/graph/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'graph' as graph_1.75.0.zip
* DONE (graph)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'graph' successfully unpacked and MD5 sums checked

Tests output

graph.Rcheck/tests/graph_unit_tests.Rout


R version 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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 -- Fri Jun 24 02:16:39 2022 
*********************************************** 
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 
   3.60    0.12    4.25 

Example timings

graph.Rcheck/graph-Ex.timings

nameusersystemelapsed
DFS0.030.000.03
IMCA0.140.000.14
MAPKsig0.080.030.11
MultiGraph-class0.110.000.11
acc-methods000
addEdge0.030.000.03
addNode0.000.010.01
adj-methods000
adjacencyMatrix000
apoptosisGraph0.030.000.04
attrData-class000
aveNumEdges000
biocRepos000
boundary0.010.000.01
calcProb000
calcSumProb000
clearNode0.020.000.02
clusterGraph-class0.010.000.01
clusteringCoefficient-methods0.020.000.02
combineNodes0.070.000.08
distGraph-class000
duplicatedEdges000
edgeMatrix0.020.000.02
edgeSets0.020.020.03
edgeWeights000
fromGXL-methods0.170.000.18
graph-class000
graph2SparseM0.090.000.09
graphAM-class000
graphBAM-class0.030.000.03
graphExamples0.020.000.02
graphNEL-class000
inEdges000
leaves0.000.010.01
listEdges0.010.000.02
matrix2Graph0.020.000.01
mostEdges0.010.000.02
numNoEdges000
pancrCaIni0.130.000.12
randomEGraph000
randomGraph0.020.000.02
randomNodeGraph000
removeEdge000
removeNode0.010.000.02
renderInfo-class000
reverseEdgeDirections0.020.000.01
simpleEdge-class000
standardLabeling0.040.000.05
subGraph000
toDotR-methods0.020.000.03
ugraph0.010.000.01
validGraph000