Zhen Yang
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/FEM |
| Branch: RELEASE_3_7 |
| Last Commit: a509b83 |
| Last Changed Date: 2018-04-30 10:35:34 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:53:42 -0400 (Wed, 17 Oct 2018).
| Package 485/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| FEM 3.8.0 Zhen Yang
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: FEM |
| Version: 3.8.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FEM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FEM_3.8.0.tar.gz |
| StartedAt: 2018-10-16 21:20:32 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 21:23:47 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 194.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: FEM.Rcheck |
| Warnings: 3 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FEM.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FEM_3.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/FEM.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FEM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FEM’ version ‘3.8.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘AnnotationDbi’ ‘Matrix’ ‘marray’ ‘corrplot’ ‘igraph’ ‘impute’
‘limma’ ‘org.Hs.eg.db’ ‘graph’ ‘BiocGenerics’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘FEM’ can be installed ... WARNING
Found the following significant warnings:
Note: break used in wrong context: no loop is visible
Warning: replacing previous import ‘igraph::edges’ by ‘graph::edges’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::intersection’ by ‘graph::intersection’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::degree’ by ‘graph::degree’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::union’ by ‘graph::union’ when loading ‘FEM’
Warning: replacing previous import ‘limma::plotMA’ by ‘BiocGenerics::plotMA’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::path’ by ‘BiocGenerics::path’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::colSums’ by ‘BiocGenerics::colSums’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::colMeans’ by ‘BiocGenerics::colMeans’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::rowMeans’ by ‘BiocGenerics::rowMeans’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::rowSums’ by ‘BiocGenerics::rowSums’ when loading ‘FEM’
Warning: replacing previous import ‘Matrix::which’ by ‘BiocGenerics::which’ when loading ‘FEM’
Warning: replacing previous import ‘igraph::normalize’ by ‘BiocGenerics::normalize’ when loading ‘FEM’
See ‘/Users/biocbuild/bbs-3.7-bioc/meat/FEM.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... NOTE
installed size is 13.6Mb
sub-directories of 1Mb or more:
data 13.4Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘graph’
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 ... WARNING
Invalid citation information in ‘inst/CITATION’:
Error in tools:::.parse_CITATION_file(file, meta$Encoding): non-ASCII input in a CITATION file without a declared encoding
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DoEpiMod: no visible global function definition for ‘mappedkeys’
DoEpiMod: no visible global function definition for ‘write.table’
DoExpMod: no visible global function definition for ‘mappedkeys’
DoExpMod: no visible global function definition for ‘write.table’
DoFEMbi: no visible global function definition for ‘mappedkeys’
DoFEMbi: no visible global function definition for ‘write.table’
FemModShow : mycircle : <anonymous>: no visible global function
definition for ‘symbols’
FemModShow: no visible global function definition for ‘pdf’
FemModShow: no visible global function definition for ‘dev.off’
GenStatM: no visible global function definition for ‘data’
GenStatM: no visible binding for global variable ‘probe450kfemanno’
GenStatM: no visible binding for global variable ‘probeEPICfemanno’
GenStatM: no visible global function definition for ‘model.matrix’
GenStatMsp: no visible global function definition for ‘data’
GenStatMsp: no visible binding for global variable ‘probe450kfemanno’
GenStatMsp: no visible binding for global variable ‘probeEPICfemanno’
GenStatMsp: no visible global function definition for ‘model.matrix’
GenStatR: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
data dev.off mappedkeys model.matrix pdf probe450kfemanno
probeEPICfemanno symbols write.table
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "symbols")
importFrom("stats", "model.matrix")
importFrom("utils", "data", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: DoEpiMod.Rd:44-46: Dropping empty section \details
prepare_Rd: DoEpiMod.Rd:71-73: Dropping empty section \note
prepare_Rd: DoEpiMod.Rd:77-79: Dropping empty section \seealso
prepare_Rd: DoExpMod.Rd:93: Dropping empty section \keyword
prepare_Rd: DoExpMod.Rd:94: Dropping empty section \keyword
prepare_Rd: DoExpMod.Rd:46-48: Dropping empty section \details
prepare_Rd: DoExpMod.Rd:72-74: Dropping empty section \note
prepare_Rd: DoExpMod.Rd:78-80: Dropping empty section \seealso
prepare_Rd: DoFEMbi.Rd:45-47: Dropping empty section \details
prepare_Rd: DoFEMbi.Rd:71-73: Dropping empty section \note
prepare_Rd: DoFEMbi.Rd:77-79: Dropping empty section \seealso
prepare_Rd: DoIntEpi450k.Rd:34-36: Dropping empty section \details
prepare_Rd: DoIntEpi450k.Rd:52-54: Dropping empty section \note
prepare_Rd: DoIntEpi450k.Rd:58-60: Dropping empty section \seealso
prepare_Rd: DoIntEpi450k.Rd:61-63: Dropping empty section \examples
prepare_Rd: DoIntExp.Rd:29-31: Dropping empty section \details
prepare_Rd: DoIntExp.Rd:47-49: Dropping empty section \note
prepare_Rd: DoIntExp.Rd:53-55: Dropping empty section \seealso
prepare_Rd: DoIntExp.Rd:56-57: Dropping empty section \examples
prepare_Rd: DoIntFEM450k.Rd:45-47: Dropping empty section \details
prepare_Rd: DoIntFEM450k.Rd:64-66: Dropping empty section \note
prepare_Rd: DoIntFEM450k.Rd:70-72: Dropping empty section \seealso
prepare_Rd: DoIntFEM450k.Rd:73-75: Dropping empty section \examples
prepare_Rd: FEM-package.Rd:47-48: Dropping empty section \seealso
prepare_Rd: FEM-package.Rd:49-51: Dropping empty section \examples
prepare_Rd: FemModShow.Rd:33-35: Dropping empty section \details
prepare_Rd: FemModShow.Rd:47-49: Dropping empty section \note
prepare_Rd: FemModShow.Rd:53-55: Dropping empty section \seealso
prepare_Rd: GenStatM.Rd:29-31: Dropping empty section \details
prepare_Rd: GenStatM.Rd:47-49: Dropping empty section \note
prepare_Rd: GenStatM.Rd:53-55: Dropping empty section \seealso
prepare_Rd: GenStatM.Rd:56-58: Dropping empty section \examples
prepare_Rd: GenStatMsp.Rd:32-34: Dropping empty section \details
prepare_Rd: GenStatMsp.Rd:51-53: Dropping empty section \note
prepare_Rd: GenStatMsp.Rd:57-59: Dropping empty section \seealso
prepare_Rd: GenStatMsp.Rd:60-62: Dropping empty section \examples
prepare_Rd: GenStatR.Rd:26-28: Dropping empty section \details
prepare_Rd: GenStatR.Rd:43-45: Dropping empty section \note
prepare_Rd: GenStatR.Rd:49-51: Dropping empty section \seealso
prepare_Rd: GenStatR.Rd:52-54: Dropping empty section \examples
prepare_Rd: Realdata.Rd:28-29: Dropping empty section \format
prepare_Rd: Realdata.Rd:30-32: Dropping empty section \details
prepare_Rd: Realdata.Rd:33-35: Dropping empty section \source
prepare_Rd: Toydata.Rd:27-29: Dropping empty section \details
prepare_Rd: Toydata.Rd:30-32: Dropping empty section \source
prepare_Rd: probe450kfemanno.Rd:27-28: Dropping empty section \format
prepare_Rd: probe450kfemanno.Rd:29-30: Dropping empty section \details
prepare_Rd: probe450kfemanno.Rd:31-33: Dropping empty section \source
prepare_Rd: probe450kfemanno.Rd:40-41: Dropping empty section \examples
prepare_Rd: probeEPICfemanno.Rd:27-28: Dropping empty section \format
prepare_Rd: probeEPICfemanno.Rd:29-30: Dropping empty section \details
prepare_Rd: probeEPICfemanno.Rd:31-33: Dropping empty section \source
prepare_Rd: probeEPICfemanno.Rd:40-41: Dropping empty section \examples
* 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 ... WARNING
Warning: package needs dependence on R (>= 2.10)
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... NOTE
The following files contain a license that requires
distribution of original sources:
‘xcolor.sty’
Please ensure that you have complied with it.
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
FemModShow 12.912 1.228 14.191
Toydata 7.868 0.359 8.267
DoFEMbi 7.997 0.142 8.202
DoEpiMod 7.598 0.211 7.855
DoExpMod 7.284 0.072 7.396
* 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 WARNINGs, 6 NOTEs
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/FEM.Rcheck/00check.log’
for details.
FEM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL FEM ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘FEM’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘igraph::edges’ by ‘graph::edges’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::intersection’ by ‘graph::intersection’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::degree’ by ‘graph::degree’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::union’ by ‘graph::union’ when loading ‘FEM’ Warning: replacing previous import ‘limma::plotMA’ by ‘BiocGenerics::plotMA’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::path’ by ‘BiocGenerics::path’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::colSums’ by ‘BiocGenerics::colSums’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::colMeans’ by ‘BiocGenerics::colMeans’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::rowMeans’ by ‘BiocGenerics::rowMeans’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::rowSums’ by ‘BiocGenerics::rowSums’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::which’ by ‘BiocGenerics::which’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::normalize’ by ‘BiocGenerics::normalize’ when loading ‘FEM’ Note: break used in wrong context: no loop is visible Note: break used in wrong context: no loop is visible Note: break used in wrong context: no loop is visible Note: break used in wrong context: no loop is visible Note: break used in wrong context: no loop is visible Note: break used in wrong context: no loop is visible Note: break used in wrong context: no loop is visible Note: break used in wrong context: no loop is visible ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Warning: replacing previous import ‘igraph::edges’ by ‘graph::edges’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::intersection’ by ‘graph::intersection’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::degree’ by ‘graph::degree’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::union’ by ‘graph::union’ when loading ‘FEM’ Warning: replacing previous import ‘limma::plotMA’ by ‘BiocGenerics::plotMA’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::path’ by ‘BiocGenerics::path’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::colSums’ by ‘BiocGenerics::colSums’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::colMeans’ by ‘BiocGenerics::colMeans’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::rowMeans’ by ‘BiocGenerics::rowMeans’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::rowSums’ by ‘BiocGenerics::rowSums’ when loading ‘FEM’ Warning: replacing previous import ‘Matrix::which’ by ‘BiocGenerics::which’ when loading ‘FEM’ Warning: replacing previous import ‘igraph::normalize’ by ‘BiocGenerics::normalize’ when loading ‘FEM’ * DONE (FEM)
FEM.Rcheck/tests/runTests.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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("FEM")
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: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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Attaching package: 'Matrix'
The following object is masked from 'package:S4Vectors':
expand
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
corrplot 0.84 loaded
Attaching package: 'igraph'
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: 'graph'
The following objects are masked from 'package:igraph':
degree, edges, intersection
[1] ".setUp"
[1] "Constructing weighted network"
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
[1] 7
[1] 8
[1] 9
[1] 10
[1] 11
[1] 12
[1] 13
[1] 14
[1] 15
[1] 16
[1] 17
[1] 18
[1] 19
[1] 20
[1] 21
[1] 22
[1] 23
[1] 24
[1] 25
[1] 26
[1] 27
[1] 28
[1] 29
[1] 30
[1] 31
[1] 32
[1] 33
[1] 34
[1] 35
[1] 36
[1] 37
[1] 38
[1] 39
[1] 40
[1] 41
[1] 42
[1] 43
[1] 44
[1] 45
[1] 46
[1] 47
[1] 48
[1] 49
[1] 50
[1] 51
[1] 52
[1] 53
[1] 54
[1] 55
[1] 56
[1] 57
[1] 58
[1] 59
[1] 60
[1] 61
[1] 62
[1] 63
[1] 64
[1] 65
[1] 66
[1] 67
[1] 68
[1] 69
[1] 70
[1] 71
[1] 72
[1] 73
[1] 74
[1] 75
[1] 76
[1] 77
[1] 78
[1] 79
[1] 80
[1] 81
[1] 82
[1] 83
[1] 84
[1] 85
[1] 86
[1] 87
[1] 88
[1] 89
[1] 90
[1] 91
[1] 92
[1] 93
[1] 94
[1] 95
[1] 96
[1] 97
[1] 98
[1] 99
[1] 100
[1] 101
[1] 102
[1] 103
[1] 104
[1] 105
[1] 106
[1] 107
[1] 108
[1] 109
[1] 110
[1] 111
[1] 112
[1] 113
[1] 114
[1] 115
[1] 116
[1] 117
[1] 118
[1] 119
[1] 120
[1] 121
[1] 122
[1] 123
[1] 124
[1] 125
[1] 126
[1] 127
[1] 128
[1] 129
[1] 130
[1] 131
[1] 132
[1] 133
[1] 134
[1] 135
[1] 136
[1] 137
[1] 138
[1] 139
[1] 140
[1] 141
[1] 142
[1] 143
[1] 144
[1] 145
[1] "Running Spin-Glass algorithm"
[1] "Done for seed 1"
[1] "Module Sizes="
166929
36
[1] "Modularity values="
166929
4.170086
[1] "Starting Monte Carlo Runs"
[1] "Done for seed/module 1"
166929
0
[1] "Summarising and generating output"
[1] 1
[1] "166929"
RUNIT TEST PROTOCOL -- Tue Oct 16 21:23:41 2018
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
FEM RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
There were 13 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
12.451 0.491 12.965
FEM.Rcheck/FEM-Ex.timings
| name | user | system | elapsed | |
| DoEpiMod | 7.598 | 0.211 | 7.855 | |
| DoExpMod | 7.284 | 0.072 | 7.396 | |
| DoFEMbi | 7.997 | 0.142 | 8.202 | |
| FemModShow | 12.912 | 1.228 | 14.191 | |
| Realdata | 0.001 | 0.000 | 0.001 | |
| Toydata | 7.868 | 0.359 | 8.267 | |