Mariano J Alvarez
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/viper |
| git_branch: master |
| git_last_commit: 138410a |
| git_last_commit_date: 2021-10-26 12:12:35 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:58 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the viper package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/viper.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2058/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| viper 1.29.0 (landing page) Mariano J Alvarez
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: viper |
| Version: 1.29.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:viper.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings viper_1.29.0.tar.gz |
| StartedAt: 2022-03-17 20:35:31 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:38:42 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 190.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: viper.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:viper.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings viper_1.29.0.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/viper.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'viper/DESCRIPTION' ... OK
* this is package 'viper' version '1.29.0'
* package encoding: UTF-8
* 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 '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 binding for global variable 'tl2'
aecdf1: no visible binding for global variable 'iq2'
aecdf1: no visible global function definition for 'epd'
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 '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 epd
fisher.test grid hsv image iq2 knots layout lines lm mad median
p.adjust par pnorm predict pt punif qnorm quantile residuals rgb2hsv
runif setTxtProgressBar smooth.spline text tl2 txtProgressBar
Consider adding
importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
importFrom("graphics", "abline", "axis", "box", "grid", "image",
"layout", "lines", "par", "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 ... OK
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
bootstrapViper 13.55 5.45 19.00
viperSignature-methods 12.68 0.78 13.45
shadow 12.00 1.07 13.08
msviperSynergy 7.18 1.25 8.43
msviperCombinatorial 6.58 0.19 6.77
msviper 6.00 0.28 6.28
viperRPT 5.13 0.24 5.36
plot.msviper 5.05 0.30 5.35
viper 4.94 0.29 5.24
* 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, 2 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/viper.Rcheck/00check.log'
for details.
viper.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL viper
###
##############################################################################
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'viper' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'viper'
finding HTML links ... done
aREA html
aecdf html
approxk2d html
aracne2regulon html
aracne2regulon4cnv html
as.dist.signatureDistance html
bootstrapTtest-methods html
bootstrapViper html
bootstrapmsviper html
comNames html
distMode html
fcvarna html
filterCV-methods html
filterColMatrix html
filterRowMatrix html
frcv html
frvarna html
groupPwea3 html
integrateSignatures html
ledge html
loadExpset html
msviper-class html
msviper html
msviperAnnot html
msviperClass html
msviperCombinatorial html
msviperSynergy html
plot.msviper html
pruneRegulon html
pwea3NULLf html
pwea3NULLgroups html
regulon-class html
rowTtest-methods html
scale.signatureDistance html
scaleGroups html
shadow html
shadowRegulon html
sigT html
signatureDistance-class html
signatureDistance html
summary.msviper html
ttestNull-methods html
viper html
viperRPT html
viperSignature-class html
viperSignature-methods html
viperSimilarity html
** 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 (viper)
Making 'packages.html' ... done
viper.Rcheck/viper-Ex.timings
| name | user | system | elapsed | |
| approxk2d | 0.06 | 0.03 | 0.09 | |
| aracne2regulon | 2.94 | 0.67 | 3.61 | |
| aracne2regulon4cnv | 2.47 | 0.51 | 2.98 | |
| bootstrapTtest-methods | 3.62 | 0.57 | 4.19 | |
| bootstrapViper | 13.55 | 5.45 | 19.00 | |
| bootstrapmsviper | 3.31 | 0.41 | 3.72 | |
| distMode | 0.81 | 0.06 | 0.87 | |
| fcvarna | 0.85 | 0.00 | 0.85 | |
| filterCV-methods | 0.84 | 0.03 | 0.87 | |
| frcv | 0.81 | 0.02 | 0.83 | |
| frvarna | 0.80 | 0.04 | 0.85 | |
| integrateSignatures | 1.94 | 0.13 | 2.06 | |
| ledge | 3.33 | 0.39 | 3.72 | |
| msviper | 6.00 | 0.28 | 6.28 | |
| msviperAnnot | 2.75 | 0.06 | 2.81 | |
| msviperClass | 1.84 | 0.00 | 1.89 | |
| msviperCombinatorial | 6.58 | 0.19 | 6.77 | |
| msviperSynergy | 7.18 | 1.25 | 8.43 | |
| plot.msviper | 5.05 | 0.30 | 5.35 | |
| pruneRegulon | 1.16 | 0.01 | 1.17 | |
| rowTtest-methods | 1.73 | 0.03 | 1.77 | |
| scaleGroups | 0.89 | 0.10 | 0.98 | |
| shadow | 12.00 | 1.07 | 13.08 | |
| signatureDistance | 1.61 | 0.08 | 1.69 | |
| ttestNull-methods | 3.28 | 0.38 | 3.65 | |
| viper | 4.94 | 0.29 | 5.24 | |
| viperRPT | 5.13 | 0.24 | 5.36 | |
| viperSignature-methods | 12.68 | 0.78 | 13.45 | |
| viperSimilarity | 1.52 | 0.11 | 1.63 | |