Bing Zhang
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/NetSAM |
| Branch: RELEASE_3_11 |
| Last Commit: 3e361ff |
| Last Changed Date: 2020-04-27 14:34:59 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:16 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE NetSAM PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1192/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| NetSAM 1.28.0 Bing Zhang
| 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: NetSAM |
| Version: 1.28.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NetSAM.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings NetSAM_1.28.0.tar.gz |
| StartedAt: 2020-10-17 06:29:12 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:30:44 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 91.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: NetSAM.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:NetSAM.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings NetSAM_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/NetSAM.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'NetSAM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'NetSAM' version '1.28.0'
* 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 'NetSAM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'methods'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 'methods' which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
'graph' 'igraph' 'seriation'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' call which should be '::': 'igraph:::degree'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'NetSAM/R/zzz.R':
.onLoad calls:
cat("******************************************\n")
cat("* *\n")
cat("* Welcome to use NetSAM ! *\n")
cat("* *\n")
cat("******************************************\n")
require(methods)
Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
generate messages.
See section 'Good practice' in '?.onAttach'.
******************************************
* *
* Welcome to use NetSAM ! *
* *
******************************************
NetSAM : calculateRandomWalkerAdjectMatrix: no visible global function
definition for 'V'
NetSAM : calculateRandomWalkerAdjectMatrix: no visible global function
definition for 'add.edges'
NetSAM : calculateRandomWalkerAdjectMatrix: no visible global function
definition for 'get.adjacency'
NetSAM : transformFromWalktrapToHclust: no visible global function
definition for 'as.dendrogram'
NetSAM : transformFromWalktrapToHclust: no visible global function
definition for 'order.dendrogram'
NetSAM : evaluateWalktrapStep: no visible global function definition
for 'walktrap.community'
NetSAM : evaluateWalktrapStep: no visible global function definition
for 'as.dist'
NetSAM : evaluateWalktrapStep: no visible global function definition
for 'seriate'
NetSAM : evaluateWalktrapStep: no visible global function definition
for 'get_order'
NetSAM : identifySig: no visible global function definition for
'degree.sequence.game'
NetSAM : identifySig: no visible global function definition for
'walktrap.community'
NetSAM : identifySig: no visible global function definition for 'sd'
NetSAM : identifySig: no visible global function definition for 'pnorm'
NetSAM : identifyHierOr: no visible global function definition for
'induced.subgraph'
NetSAM : createHMIFile: no visible global function definition for 'V'
NetSAM: no visible global function definition for 'read.graph'
NetSAM: no visible global function definition for 'graph.edgelist'
NetSAM: no visible global function definition for
'igraph.from.graphNEL'
NetSAM: no visible global function definition for 'V'
NetSAM: no visible global function definition for 'vcount'
NetSAM: no visible global function definition for 'ecount'
NetSAM: no visible global function definition for 'simplify'
NetSAM: no visible global function definition for 'clusters'
NetSAM: no visible global function definition for 'induced.subgraph'
NetSAM: no visible global function definition for 'get.edgelist'
NetSAM: no visible global function definition for 'write.table'
Undefined global functions or variables:
V add.edges as.dendrogram as.dist clusters degree.sequence.game
ecount get.adjacency get.edgelist get_order graph.edgelist
igraph.from.graphNEL induced.subgraph order.dendrogram pnorm
read.graph sd seriate simplify vcount walktrap.community write.table
Consider adding
importFrom("stats", "as.dendrogram", "as.dist", "order.dendrogram",
"pnorm", "sd")
importFrom("utils", "write.table")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
NetSAM 6.41 0.04 6.5
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
NetSAM 9.32 0.11 10.02
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.11-bioc/meat/NetSAM.Rcheck/00check.log'
for details.
NetSAM.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/NetSAM_1.28.0.tar.gz && rm -rf NetSAM.buildbin-libdir && mkdir NetSAM.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=NetSAM.buildbin-libdir NetSAM_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL NetSAM_1.28.0.zip && rm NetSAM_1.28.0.tar.gz NetSAM_1.28.0.zip
###
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% 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 29789 100 29789 0 0 131k 0 --:--:-- --:--:-- --:--:-- 136k
install for i386
* installing *source* package 'NetSAM' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'NetSAM'
finding HTML links ... done
NetSAM-package html
NetSAM html
inputNetwork html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
******************************************
* *
* Welcome to use NetSAM ! *
* *
******************************************
** testing if installed package can be loaded from final location
******************************************
* *
* Welcome to use NetSAM ! *
* *
******************************************
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'NetSAM' ...
** testing if installed package can be loaded
******************************************
* *
* Welcome to use NetSAM ! *
* *
******************************************
* MD5 sums
packaged installation of 'NetSAM' as NetSAM_1.28.0.zip
* DONE (NetSAM)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'NetSAM' successfully unpacked and MD5 sums checked
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NetSAM.Rcheck/tests_i386/runTests.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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("NetSAM")
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Attaching package: 'seriation'
The following object is masked from 'package:igraph':
permute
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 objects are masked from 'package:igraph':
normalize, path, union
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: 'graph'
The following objects are masked from 'package:igraph':
degree, edges, intersection
******************************************
* *
* Welcome to use NetSAM ! *
* *
******************************************
Network has 320 nodes and 769 edges
Identifying the hierarchical modules of the network...
Start to analysis subnetwork 1 !
Evaluate Leve 1 network...
Evaluate Level 2 networks...
Evaluate Level 3 networks...
Evaluate Level 4 networks...
Reorder the genes in the one dimentional layout...
Processing completed!
RUNIT TEST PROTOCOL -- Sat Oct 17 06:30:23 2020
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
NetSAM RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
9.42 0.32 9.73
|
NetSAM.Rcheck/tests_x64/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-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("NetSAM")
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Attaching package: 'seriation'
The following object is masked from 'package:igraph':
permute
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 objects are masked from 'package:igraph':
normalize, path, union
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: 'graph'
The following objects are masked from 'package:igraph':
degree, edges, intersection
******************************************
* *
* Welcome to use NetSAM ! *
* *
******************************************
Network has 320 nodes and 769 edges
Identifying the hierarchical modules of the network...
Start to analysis subnetwork 1 !
Evaluate Leve 1 network...
Evaluate Level 2 networks...
Evaluate Level 3 networks...
Evaluate Level 4 networks...
Reorder the genes in the one dimentional layout...
Processing completed!
RUNIT TEST PROTOCOL -- Sat Oct 17 06:30:35 2020
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
NetSAM RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
11.35 0.21 11.57
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NetSAM.Rcheck/examples_i386/NetSAM-Ex.timings
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NetSAM.Rcheck/examples_x64/NetSAM-Ex.timings
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