| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:34 -0000 (Wed, 08 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
| 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2129/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| viper 1.33.0 (landing page) Mariano J Alvarez
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: viper |
| Version: 1.33.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:viper.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings viper_1.33.0.tar.gz |
| StartedAt: 2023-02-07 18:49:45 -0000 (Tue, 07 Feb 2023) |
| EndedAt: 2023-02-07 18:57:26 -0000 (Tue, 07 Feb 2023) |
| EllapsedTime: 461.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: viper.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:viper.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings viper_1.33.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/viper.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘viper/DESCRIPTION’ ... OK
* this is package ‘viper’ version ‘1.33.0’
* 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 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 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 40.803 0.832 41.774
viperSignature-methods 29.771 0.911 34.077
shadow 19.829 0.031 19.872
msviperSynergy 14.469 0.099 14.607
msviperCombinatorial 11.672 0.339 12.892
plot.msviper 10.392 0.156 10.729
viperRPT 10.399 0.040 10.454
msviper 10.190 0.056 10.253
viper 9.573 0.032 9.607
bootstrapmsviper 8.028 0.043 8.077
bootstrapTtest-methods 7.500 0.051 7.559
ttestNull-methods 7.253 0.036 7.296
aracne2regulon 5.195 0.584 9.046
ledge 5.609 0.024 5.634
aracne2regulon4cnv 5.073 0.027 5.245
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘viper.Rnw’ using ‘UTF-8’... failed to complete the test
ERROR
Errors in running code in vignettes:
when running code in ‘viper.Rnw’
...
> nullmodel <- ttestNull(dset, "description", c("CB",
+ "CC"), "N", per = 1000, repos = TRUE, verbose = FALSE)
> regulon
Object of class regulon with 621 regulators, 6249 targets and 172240 interactions
> mrs <- msviper(signature, regulon, nullmodel, verbose = FALSE)
Killed
... incomplete output. Crash?
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘viper.Rnw’ using Sweave
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
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, aperm, 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.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Killed
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/viper.Rcheck/00check.log’
for details.
viper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL viper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘viper’ ... ** using staged installation ** 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 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)
viper.Rcheck/viper-Ex.timings
| name | user | system | elapsed | |
| approxk2d | 0.099 | 0.008 | 0.118 | |
| aracne2regulon | 5.195 | 0.584 | 9.046 | |
| aracne2regulon4cnv | 5.073 | 0.027 | 5.245 | |
| bootstrapTtest-methods | 7.500 | 0.051 | 7.559 | |
| bootstrapViper | 40.803 | 0.832 | 41.774 | |
| bootstrapmsviper | 8.028 | 0.043 | 8.077 | |
| distMode | 0.962 | 0.028 | 0.990 | |
| fcvarna | 0.957 | 0.012 | 0.969 | |
| filterCV-methods | 0.983 | 0.028 | 1.012 | |
| frcv | 0.962 | 0.004 | 0.966 | |
| frvarna | 0.949 | 0.015 | 0.966 | |
| integrateSignatures | 2.983 | 0.028 | 3.012 | |
| ledge | 5.609 | 0.024 | 5.634 | |
| msviper | 10.190 | 0.056 | 10.253 | |
| msviperAnnot | 3.216 | 0.008 | 3.226 | |
| msviperClass | 2.423 | 0.012 | 2.436 | |
| msviperCombinatorial | 11.672 | 0.339 | 12.892 | |
| msviperSynergy | 14.469 | 0.099 | 14.607 | |
| plot.msviper | 10.392 | 0.156 | 10.729 | |
| pruneRegulon | 1.029 | 0.028 | 1.071 | |
| rowTtest-methods | 1.934 | 0.028 | 1.971 | |
| scaleGroups | 1.034 | 0.041 | 1.075 | |
| shadow | 19.829 | 0.031 | 19.872 | |
| signatureDistance | 3.438 | 0.020 | 3.460 | |
| ttestNull-methods | 7.253 | 0.036 | 7.296 | |
| viper | 9.573 | 0.032 | 9.607 | |
| viperRPT | 10.399 | 0.040 | 10.454 | |
| viperSignature-methods | 29.771 | 0.911 | 34.077 | |
| viperSimilarity | 3.286 | 0.020 | 3.307 | |