Jianhong Ou
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/motifStack |
| Branch: RELEASE_3_6 |
| Last Commit: 273b1ac |
| Last Changed Date: 2018-03-13 16:50:50 -0400 (Tue, 13 Mar 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:22:06 -0400 (Thu, 12 Apr 2018).
| Package 892/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| motifStack 1.22.4 Jianhong Ou
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: motifStack |
| Version: 1.22.4 |
| Command: rm -rf motifStack.buildbin-libdir motifStack.Rcheck && mkdir motifStack.buildbin-libdir motifStack.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=motifStack.buildbin-libdir motifStack_1.22.4.tar.gz >motifStack.Rcheck\00install.out 2>&1 && cp motifStack.Rcheck\00install.out motifStack-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=motifStack.buildbin-libdir --install="check:motifStack-install.out" --force-multiarch --no-vignettes --timings motifStack_1.22.4.tar.gz |
| StartedAt: 2018-04-12 01:36:13 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:41:37 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 324.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: motifStack.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### rm -rf motifStack.buildbin-libdir motifStack.Rcheck && mkdir motifStack.buildbin-libdir motifStack.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=motifStack.buildbin-libdir motifStack_1.22.4.tar.gz >motifStack.Rcheck\00install.out 2>&1 && cp motifStack.Rcheck\00install.out motifStack-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=motifStack.buildbin-libdir --install="check:motifStack-install.out" --force-multiarch --no-vignettes --timings motifStack_1.22.4.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/motifStack.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'motifStack/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'motifStack' version '1.22.4'
* 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 'motifStack' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp40sEOb/R.INSTALL35481281e78/motifStack/man/pfm2pwm.Rd:21: missing file link 'PWM'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/motifStack.Rcheck/00install.out' for details.
* 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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
motifCircos: no visible global function definition for 'par'
motifCircos: no visible global function definition for 'plot.default'
motifCircos: no visible binding for global variable 'strwidth'
motifCircos : plotBgArc: no visible global function definition for
'polygon'
motifCircos: no visible global function definition for 'text'
motifCircos: no visible global function definition for 'segments'
motifCircos: no visible global function definition for 'points'
motifCircos: no visible global function definition for 'lines'
motifCircos: no visible global function definition for 'symbols'
motifCircos: no visible global function definition for 'strwidth'
motifCircos: no visible global function definition for 'box'
motifCloud: no visible global function definition for 'par'
motifCloud: no visible global function definition for 'plot.new'
motifCloud: no visible global function definition for 'strheight'
motifCloud: no visible global function definition for 'plot.window'
motifCloud: no visible global function definition for 'plot.default'
motifCloud : plotUnrootedTree: no visible global function definition
for 'segments'
motifCloud : plotUnrootedTree: no visible global function definition
for 'strheight'
motifCloud: no visible global function definition for 'segments'
motifCloud: no visible global function definition for 'legend'
motifPiles: no visible global function definition for 'par'
motifPiles: no visible global function definition for 'plot.default'
motifPiles: no visible binding for global variable 'strwidth'
motifPiles: no visible global function definition for 'strwidth'
motifPiles: no visible global function definition for 'points'
motifPiles: no visible global function definition for 'segments'
motifPiles: no visible global function definition for 'abline'
motifPiles: no visible global function definition for 'rect'
motifPiles: no visible global function definition for 'text'
motifStack: no visible global function definition for 'plot'
plotAffinityLogo: no visible binding for global variable 'plot.new'
plotAffinityLogo: no visible global function definition for 'plot.new'
plotAffinityLogo: no visible global function definition for 'text'
plotMotifLogo: no visible global function definition for 'plot.new'
plotMotifLogo: no visible global function definition for 'text'
plotMotifLogo: no visible global function definition for 'mtext'
plotMotifLogoStack: no visible global function definition for 'par'
plotMotifLogoStack: no visible global function definition for 'plot'
plotMotifLogoStackWithTree: no visible global function definition for
'par'
plotMotifLogoStackWithTree: no visible global function definition for
'layout'
plotMotifLogoStackWithTree: no visible global function definition for
'plot.new'
plotMotifLogoStackWithTree: no visible global function definition for
'plot'
plotMotifOverMotif: no visible global function definition for
'plot.new'
plotMotifStackWithPhylog: no visible global function definition for
'par'
plotMotifStackWithPhylog: no visible global function definition for
'plot.default'
plotMotifStackWithPhylog: no visible binding for global variable
'strwidth'
plotMotifStackWithPhylog: no visible global function definition for
'strwidth'
plotMotifStackWithPhylog: no visible global function definition for
'text'
plotMotifStackWithPhylog: no visible global function definition for
'segments'
plotMotifStackWithPhylog: no visible global function definition for
'points'
plotMotifStackWithRadialPhylog: no visible global function definition
for 'par'
plotMotifStackWithRadialPhylog: no visible global function definition
for 'plot.default'
plotMotifStackWithRadialPhylog: no visible binding for global variable
'strwidth'
plotMotifStackWithRadialPhylog : plotBgArc: no visible global function
definition for 'polygon'
plotMotifStackWithRadialPhylog: no visible global function definition
for 'text'
plotMotifStackWithRadialPhylog: no visible global function definition
for 'segments'
plotMotifStackWithRadialPhylog: no visible global function definition
for 'points'
plotMotifStackWithRadialPhylog: no visible global function definition
for 'lines'
plotMotifStackWithRadialPhylog: no visible global function definition
for 'symbols'
plotMotifStackWithRadialPhylog: no visible global function definition
for 'strwidth'
plotMotifStackWithRadialPhylog: no visible global function definition
for 'box'
plotXaxis: no visible global function definition for 'axis'
plotYaxis: no visible global function definition for 'axis'
plotYaxis: no visible global function definition for 'par'
Undefined global functions or variables:
abline axis box layout legend lines mtext par plot plot.default
plot.new plot.window points polygon rect segments strheight strwidth
symbols text
Consider adding
importFrom("graphics", "abline", "axis", "box", "layout", "legend",
"lines", "mtext", "par", "plot", "plot.default", "plot.new",
"plot.window", "points", "polygon", "rect", "segments",
"strheight", "strwidth", "symbols", "text")
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* 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: 1 WARNING, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/motifStack.Rcheck/00check.log'
for details.
motifStack.Rcheck/00install.out
install for i386
* installing *source* package 'motifStack' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'motifStack'
finding HTML links ... done
DNAmotifAlignment html
browseMotifs-shiny html
browseMotifs html
colorset html
getRankedUniqueMotifs html
highlightCol html
importMatrix html
mergeMotifs html
motifCircos html
motifCloud html
motifPiles html
motifSig-class html
motifSig-methods html
motifSignature html
motifStack-package html
motifStack html
ouNode-class html
pcm-class html
pcm-methods html
pfm-class html
pfm-methods html
pfm2pwm html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmp40sEOb/R.INSTALL35481281e78/motifStack/man/pfm2pwm.Rd:21: missing file link 'PWM'
plotAffinityLogo html
plotMotifLogo html
plotMotifLogoA html
plotMotifLogoStack html
plotMotifLogoStackWithTree html
plotMotifOverMotif html
plotMotifStackWithPhylog html
plotMotifStackWithRadialPhylog html
plotXaxis html
plotYaxis html
psam-class html
psam-methods html
readPCM html
reorderUPGMAtree html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'motifStack' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'motifStack' as motifStack_1.22.4.zip
* DONE (motifStack)
In R CMD INSTALL
In R CMD INSTALL
|
motifStack.Rcheck/tests_i386/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.
> require("motifStack") || stop("unable to load Package:motifStack")
Loading required package: motifStack
Loading required package: grImport
Loading required package: grid
Loading required package: XML
Loading required package: MotIV
Loading required package: BiocGenerics
Loading required package: parallel
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, cbind, colMeans, colSums, colnames, 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
Attaching package: 'MotIV'
The following object is masked from 'package:stats':
filter
Loading required package: ade4
Attaching package: 'ade4'
The following object is masked from 'package:BiocGenerics':
score
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
[1] TRUE
> #require("MotifDb") || stop("unalble to load Package::motifDb")
> BiocGenerics:::testPackage("motifStack")
Read 76 items
Read 72 items
Read 32 items
Read 28 items
Read 28 items
Read 44 items
Read 28 items
Read 36 items
Read 32 items
Read 44 items
Read 44 items
Read 32 items
Read 44 items
Read 60 items
Read 60 items
Read 55 items
Read 45 items
Read 35 items
RUNIT TEST PROTOCOL -- Thu Apr 12 01:41:18 2018
***********************************************
Number of test functions: 10
Number of errors: 0
Number of failures: 0
1 Test Suite :
motifStack RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
11.40 0.32 11.71
|
motifStack.Rcheck/tests_x64/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.
> require("motifStack") || stop("unable to load Package:motifStack")
Loading required package: motifStack
Loading required package: grImport
Loading required package: grid
Loading required package: XML
Loading required package: MotIV
Loading required package: BiocGenerics
Loading required package: parallel
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, cbind, colMeans, colSums, colnames, 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
Attaching package: 'MotIV'
The following object is masked from 'package:stats':
filter
Loading required package: ade4
Attaching package: 'ade4'
The following object is masked from 'package:BiocGenerics':
score
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
[1] TRUE
> #require("MotifDb") || stop("unalble to load Package::motifDb")
> BiocGenerics:::testPackage("motifStack")
Read 76 items
Read 72 items
Read 32 items
Read 28 items
Read 28 items
Read 44 items
Read 28 items
Read 36 items
Read 32 items
Read 44 items
Read 44 items
Read 32 items
Read 44 items
Read 60 items
Read 60 items
Read 55 items
Read 45 items
Read 35 items
RUNIT TEST PROTOCOL -- Thu Apr 12 01:41:32 2018
***********************************************
Number of test functions: 10
Number of errors: 0
Number of failures: 0
1 Test Suite :
motifStack RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
13.03 0.14 13.15
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motifStack.Rcheck/examples_i386/motifStack-Ex.timings
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motifStack.Rcheck/examples_x64/motifStack-Ex.timings
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