Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-06-14 14:38 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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 913/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GraphPAC 1.46.0  (landing page)
Gregory Ryslik
Snapshot Date: 2024-06-12 14:00 -0400 (Wed, 12 Jun 2024)
git_url: https://git.bioconductor.org/packages/GraphPAC
git_branch: RELEASE_3_19
git_last_commit: 114ceea
git_last_commit_date: 2024-04-30 10:29:58 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for GraphPAC on palomino3

To the developers/maintainers of the GraphPAC package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GraphPAC.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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.

raw results


Summary

Package: GraphPAC
Version: 1.46.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GraphPAC.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GraphPAC_1.46.0.tar.gz
StartedAt: 2024-06-13 04:42:02 -0400 (Thu, 13 Jun 2024)
EndedAt: 2024-06-13 04:44:57 -0400 (Thu, 13 Jun 2024)
EllapsedTime: 175.5 seconds
RetCode: 0
Status:   OK  
CheckDir: GraphPAC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GraphPAC.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GraphPAC_1.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/GraphPAC.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GraphPAC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GraphPAC' version '1.46.0'
* 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 'GraphPAC' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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
Packages in Depends field not imported from:
  'RMallow' 'TSP' 'iPAC' 'igraph'
  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 ... NOTE
Find.TSP.Path: no visible global function definition for 'dist'
Find.TSP.Path: no visible global function definition for 'ATSP'
Find.TSP.Path: no visible global function definition for 'insert_dummy'
Find.TSP.Path: no visible global function definition for 'solve_TSP'
Find.TSP.Path: no visible global function definition for 'cut_tour'
GraphClust: no visible global function definition for 'graph.empty'
GraphClust: no visible global function definition for 'V'
GraphClust: no visible global function definition for 'V<-'
GraphClust: no visible global function definition for 'add.edges'
GraphClust: no visible global function definition for 'nmc'
Plot.Protein: no visible global function definition for 'heat.colors'
Plot.Protein: no visible global function definition for 'vcount'
Plot.Protein: no visible global function definition for 'gray'
Plot.Protein: no visible global function definition for 'topo.colors'
Plot.Protein: no visible global function definition for 'cm.colors'
Plot.Protein: no visible global function definition for 'V'
Plot.Protein: no visible global function definition for 'tkplot'
Plot.Protein: no visible binding for global variable 'layout.circle'
Undefined global functions or variables:
  ATSP V V<- add.edges cm.colors cut_tour dist graph.empty gray
  heat.colors insert_dummy layout.circle nmc solve_TSP tkplot
  topo.colors vcount
Consider adding
  importFrom("grDevices", "cm.colors", "gray", "heat.colors",
             "topo.colors")
  importFrom("stats", "dist")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) Plot.Protein.Rd:33: Lost braces
    33 | This function is based on the ``tkplot" function in \emph{igraph}. Please see the documentation for that package for the necessary requirements. Special thanks to Dr. G\'{a}bor Cs\'{a}rdi (creator of the \emph{igraph} package) for his help.
       |                                                                                                                                                                           ^
checkRd: (-1) Plot.Protein.Rd:33: Lost braces
    33 | This function is based on the ``tkplot" function in \emph{igraph}. Please see the documentation for that package for the necessary requirements. Special thanks to Dr. G\'{a}bor Cs\'{a}rdi (creator of the \emph{igraph} package) for his help.
       |                                                                                                                                                                                      ^
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
              user system elapsed
Find.TSP.Path 2.95   0.42    6.74
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/GraphPAC.Rcheck/00check.log'
for details.


Installation output

GraphPAC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL GraphPAC
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'GraphPAC' ...
** using staged installation
** R
** 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
* DONE (GraphPAC)

Tests output

GraphPAC.Rcheck/tests/runTests.Rout


R version 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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("GraphPAC")

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, table, tapply,
    union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'pwalign'

The following objects are masked from 'package:Biostrings':

    PairwiseAlignments, PairwiseAlignmentsSingleSubject, aligned,
    alignedPattern, alignedSubject, compareStrings, deletion,
    errorSubstitutionMatrices, indel, insertion, mismatchSummary,
    mismatchTable, nedit, nindel, nucleotideSubstitutionMatrix,
    pairwiseAlignment, pid, qualitySubstitutionMatrices, stringDist,
    unaligned, writePairwiseAlignments

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'igraph'

The following object is masked from 'package:Biostrings':

    union

The following object is masked from 'package:XVector':

    path

The following object is masked from 'package:IRanges':

    union

The following object is masked from 'package:S4Vectors':

    union

The following objects are masked from 'package:BiocGenerics':

    normalize, path, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union


Attaching package: 'combinat'

The following object is masked from 'package:utils':

    combn

Calculating Remapped Clusters.Calculating Culled Clusters.Calculating Full Clusters.Calculating Remapped Clusters.Calculating Culled Clusters.Calculating Full Clusters.Calculating Remapped Clusters.Calculating Culled Clusters.Calculating Full Clusters.Calculating Remapped Clusters.Calculating Culled Clusters.Calculating Full Clusters.Calculating Remapped Clusters.Calculating Culled Clusters.Calculating Full Clusters.

RUNIT TEST PROTOCOL -- Thu Jun 13 04:44:44 2024 
*********************************************** 
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GraphPAC RUnit Tests - 3 test functions, 0 errors, 0 failures
Number of test functions: 3 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   4.75    4.76    9.48 

Example timings

GraphPAC.Rcheck/GraphPAC-Ex.timings

nameusersystemelapsed
Find.TSP.Path2.950.426.74
GraphClust000
Plot.Protein000
graphPAC-package000