Gregory Ryslik
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/GraphPAC |
| Branch: RELEASE_3_11 |
| Last Commit: b3beffe |
| Last Changed Date: 2020-04-27 14:32:27 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:54:54 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE GraphPAC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 775/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GraphPAC 1.30.0 Gregory Ryslik
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: GraphPAC |
| Version: 1.30.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GraphPAC.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GraphPAC_1.30.0.tar.gz |
| StartedAt: 2020-10-17 02:00:13 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 02:02:05 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 112.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GraphPAC.Rcheck |
| Warnings: 0 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GraphPAC.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GraphPAC_1.30.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/GraphPAC.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GraphPAC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GraphPAC’ version ‘1.30.0’
* 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 ‘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 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
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 ... 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
Find.TSP.Path 4.175 0.123 5.09
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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
‘/home/biocbuild/bbs-3.11-bioc/meat/GraphPAC.Rcheck/00check.log’
for details.
GraphPAC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL GraphPAC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-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)
GraphPAC.Rcheck/tests/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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("GraphPAC")
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
Attaching package: 'gdata'
The following object is masked from 'package:stats':
nobs
The following object is masked from 'package:utils':
object.size
The following object is masked from 'package:base':
startsWith
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from 'package:gdata':
combine
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, which.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:gdata':
first, first<-
The following object is masked from 'package:base':
expand.grid
Attaching package: 'IRanges'
The following object is masked from 'package:gdata':
trim
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
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: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 -- Sat Oct 17 02:02:02 2020
***********************************************
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
6.276 0.311 6.590
GraphPAC.Rcheck/GraphPAC-Ex.timings
| name | user | system | elapsed | |
| Find.TSP.Path | 4.175 | 0.123 | 5.090 | |
| GraphClust | 0 | 0 | 0 | |
| Plot.Protein | 0.000 | 0.000 | 0.001 | |
| graphPAC-package | 0 | 0 | 0 | |