| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-03-18 11:46:58 -0400 (Mon, 18 Mar 2019).
| Package 1651/1676 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||
| viper 1.17.1 Mariano J Alvarez
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | ERROR | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | ERROR | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ ERROR ] |
| Package: viper |
| Version: 1.17.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:viper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings viper_1.17.1.tar.gz |
| StartedAt: 2019-03-18 05:49:19 -0400 (Mon, 18 Mar 2019) |
| EndedAt: 2019-03-18 05:52:25 -0400 (Mon, 18 Mar 2019) |
| EllapsedTime: 185.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: viper.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:viper.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings viper_1.17.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/viper.Rcheck’
* using R Under development (unstable) (2019-01-22 r76000)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘viper/DESCRIPTION’ ... OK
* this is package ‘viper’ version ‘1.17.1’
* 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 ‘viper’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
TFmode1: no visible global function definition for ‘cor’
TFmode2: no visible global function definition for ‘cor’
TFscore : <anonymous>: no visible global function definition for
‘pnorm’
aREA: no visible global function definition for ‘qnorm’
aREA: no visible global function definition for ‘txtProgressBar’
aREA : <anonymous>: no visible global function definition for
‘setTxtProgressBar’
aecdf: no visible global function definition for ‘quantile’
aecdf: no visible global function definition for ‘ecdf’
aecdf: no visible global function definition for ‘lm’
aecdf: no visible global function definition for ‘approxfun’
aecdf : dnull: no visible global function definition for ‘predict’
aecdf : dnull: no visible global function definition for ‘qnorm’
aecdf1: no visible global function definition for ‘quantile’
aecdf1: no visible global function definition for ‘ecdf’
aecdf1: no visible global function definition for ‘lm’
aecdf1: no visible global function definition for ‘predict’
aecdf1: no visible global function definition for ‘qnorm’
approxk2d: no visible binding for global variable ‘quantile’
bootstrapViper : <anonymous> : <anonymous>: no visible global function
definition for ‘qnorm’
bootstrapViper : <anonymous>: no visible global function definition for
‘txtProgressBar’
bootstrapViper : <anonymous> : <anonymous>: no visible global function
definition for ‘setTxtProgressBar’
bootstrapmsviper: no visible binding for global variable ‘median’
bootstrapmsviper: no visible global function definition for ‘pnorm’
distMode: no visible global function definition for ‘density’
groupPwea3: no visible global function definition for ‘qnorm’
groupPwea3: no visible global function definition for ‘txtProgressBar’
groupPwea3 : <anonymous>: no visible global function definition for
‘setTxtProgressBar’
groupPwea3 : <anonymous>: no visible global function definition for
‘qnorm’
groupPwea3: no visible global function definition for ‘pnorm’
msviper: no visible global function definition for ‘txtProgressBar’
msviper : <anonymous>: no visible global function definition for
‘setTxtProgressBar’
msviper: no visible global function definition for ‘pnorm’
msviperClass: no visible global function definition for ‘pnorm’
msviperCombinatorial: no visible global function definition for ‘combn’
msviperSynergy : <anonymous>: no visible global function definition for
‘qnorm’
msviperSynergy : <anonymous>: no visible global function definition for
‘quantile’
msviperSynergy : <anonymous>: no visible global function definition for
‘ecdf’
msviperSynergy : <anonymous>: no visible global function definition for
‘knots’
msviperSynergy : <anonymous>: no visible global function definition for
‘smooth.spline’
msviperSynergy : <anonymous>: no visible global function definition for
‘predict’
msviperSynergy: no visible global function definition for
‘txtProgressBar’
msviperSynergy : <anonymous>: no visible global function definition for
‘setTxtProgressBar’
plot.msviper: no visible global function definition for ‘par’
plot.msviper: no visible global function definition for ‘layout’
plot.msviper: no visible global function definition for ‘rgb2hsv’
plot.msviper: no visible global function definition for ‘col2rgb’
plot.msviper: no visible global function definition for ‘plot’
plot.msviper: no visible global function definition for ‘hsv’
plot.msviper: no visible global function definition for ‘lines’
plot.msviper: no visible global function definition for ‘smooth.spline’
plot.msviper: no visible global function definition for ‘text’
plot.msviper: no visible global function definition for ‘axis’
plot.msviper: no visible global function definition for ‘abline’
plot.msviper: no visible global function definition for ‘image’
plot.msviper: no visible global function definition for ‘box’
plot.msviper: no visible global function definition for ‘grid’
ppwea3NULLf : <anonymous> : <anonymous>: no visible global function
definition for ‘pnorm’
pwea3NULLf : <anonymous>: no visible global function definition for
‘quantile’
pwea3NULLf : <anonymous>: no visible global function definition for
‘ecdf’
pwea3NULLf : <anonymous>: no visible global function definition for
‘knots’
pwea3NULLf : <anonymous>: no visible global function definition for
‘smooth.spline’
pwea3NULLf : <anonymous> : <anonymous>: no visible global function
definition for ‘predict’
pwea3NULLf : <anonymous> : <anonymous>: no visible global function
definition for ‘qnorm’
pwea3NULLf: no visible global function definition for ‘txtProgressBar’
pwea3NULLf : <anonymous>: no visible global function definition for
‘setTxtProgressBar’
pwea3NULLgroups: no visible global function definition for ‘qnorm’
pwea3NULLgroups: no visible global function definition for
‘txtProgressBar’
pwea3NULLgroups : <anonymous>: no visible global function definition
for ‘setTxtProgressBar’
regulonDist : <anonymous>: no visible global function definition for
‘fisher.test’
scaleGroups : <anonymous>: no visible global function definition for
‘qnorm’
scaleGroups: no visible global function definition for ‘runif’
selectTFs : <anonymous>: no visible global function definition for
‘combn’
shadow: no visible global function definition for ‘combn’
shadow : <anonymous>: no visible global function definition for
‘quantile’
shadow : <anonymous>: no visible global function definition for ‘ecdf’
shadow : <anonymous>: no visible global function definition for ‘knots’
shadow : <anonymous>: no visible global function definition for
‘smooth.spline’
shadow : <anonymous>: no visible global function definition for
‘predict’
shadow: no visible global function definition for ‘txtProgressBar’
shadow : <anonymous>: no visible global function definition for
‘setTxtProgressBar’
shadowRegulon: no visible global function definition for ‘pnorm’
shadowRegulon : <anonymous>: no visible global function definition for
‘qnorm’
shadowRegulon : <anonymous>: no visible global function definition for
‘pnorm’
shadowRegulon: no visible global function definition for ‘combn’
signatureDistance: no visible global function definition for ‘qnorm’
summary.msviper: no visible global function definition for ‘p.adjust’
viper: no visible global function definition for ‘punif’
viper : <anonymous>: no visible global function definition for ‘median’
viper : <anonymous>: no visible global function definition for ‘mad’
viper : <anonymous>: no visible global function definition for
‘txtProgressBar’
viper : <anonymous> : <anonymous>: no visible global function
definition for ‘setTxtProgressBar’
viperRPT : <anonymous>: no visible global function definition for
‘residuals’
viperRPT : <anonymous>: no visible global function definition for ‘lm’
viperRPT : <anonymous>: no visible global function definition for
‘smooth.spline’
viperSimilarity: no visible global function definition for ‘qnorm’
bootstrapTtest,matrix : <anonymous>: no visible global function
definition for ‘qnorm’
bootstrapTtest,matrix : <anonymous>: no visible global function
definition for ‘pt’
bootstrapTtest,matrix: no visible global function definition for
‘txtProgressBar’
bootstrapTtest,matrix : <anonymous>: no visible global function
definition for ‘setTxtProgressBar’
rowTtest,matrix: no visible global function definition for ‘pt’
ttestNull,matrix : <anonymous>: no visible global function definition
for ‘qnorm’
ttestNull,matrix : <anonymous>: no visible global function definition
for ‘pt’
ttestNull,matrix: no visible global function definition for
‘txtProgressBar’
ttestNull,matrix : <anonymous>: no visible global function definition
for ‘setTxtProgressBar’
viperSignature,matrix : <anonymous>: no visible global function
definition for ‘qnorm’
viperSignature,matrix: no visible global function definition for
‘txtProgressBar’
viperSignature,matrix : <anonymous> : <anonymous>: no visible global
function definition for ‘qnorm’
viperSignature,matrix : <anonymous>: no visible global function
definition for ‘setTxtProgressBar’
viperSignature,matrix: no visible global function definition for
‘combn’
Undefined global functions or variables:
abline approxfun axis box col2rgb combn cor density ecdf fisher.test
grid hsv image knots layout lines lm mad median p.adjust par plot
pnorm predict pt punif qnorm quantile residuals rgb2hsv runif
setTxtProgressBar smooth.spline text txtProgressBar
Consider adding
importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
importFrom("graphics", "abline", "axis", "box", "grid", "image",
"layout", "lines", "par", "plot", "text")
importFrom("stats", "approxfun", "cor", "density", "ecdf",
"fisher.test", "knots", "lm", "mad", "median", "p.adjust",
"pnorm", "predict", "pt", "punif", "qnorm", "quantile",
"residuals", "runif", "smooth.spline")
importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
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 ... WARNING
Codoc mismatches from documentation object 'pruneRegulon':
pruneRegulon
Code: function(regulon, cutoff = 50, adaptive = TRUE, eliminate =
FALSE, wm = NULL)
Docs: function(regulon, cutoff = 50, adaptive = TRUE, eliminate =
FALSE)
Argument names in code not in docs:
wm
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'viper'
‘mvws’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... ERROR
Running examples in ‘viper-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: msviper
> ### Title: msVIPER
> ### Aliases: msviper
>
> ### ** Examples
>
> data(bcellViper, package="bcellViper")
> sig <- rowTtest(dset, "description", c("CB", "CC"), "N")$statistic
> dnull <- ttestNull(dset, "description", c("CB", "CC"), "N", per=100) # Only 100 permutations to reduce computation time, but it is recommended to perform at least 1000 permutations
Mon Mar 18 05:52:07 2019
Computing the null model distribution by 100 permutations.
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Mon Mar 18 05:52:10 2019
> mra <- msviper(sig, regulon, dnull)
Computing regulon enrichment with aREA algorithm
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Estimating the normalized enrichment scores
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|======================================================================| 100%Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) :
NA/NaN/Inf in 'y'
Calls: msviper ... t -> sapply -> lapply -> FUN -> aecdf -> lm -> lm.fit
Execution halted
* 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 ERROR, 2 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/viper.Rcheck/00check.log’
for details.
viper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL viper ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘viper’ ... ** 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 * DONE (viper)
viper.Rcheck/viper-Ex.timings
| name | user | system | elapsed | |
| approxk2d | 0.126 | 0.009 | 0.135 | |
| aracne2regulon | 3.404 | 0.852 | 4.274 | |
| aracne2regulon4cnv | 2.853 | 0.708 | 3.561 | |
| bootstrapTtest-methods | 6.226 | 1.628 | 7.856 | |
| bootstrapViper | 32.596 | 4.574 | 37.187 | |
| bootstrapmsviper | 8.994 | 3.135 | 12.312 | |
| distMode | 1.243 | 0.087 | 1.331 | |
| fcvarna | 1.124 | 0.059 | 1.182 | |
| filterCV-methods | 1.462 | 0.062 | 1.523 | |
| frcv | 1.224 | 0.060 | 1.284 | |
| frvarna | 1.408 | 0.066 | 1.474 | |
| integrateSignatures | 2.813 | 0.789 | 3.603 | |
| ledge | 5.995 | 0.919 | 6.914 | |