Mariano J Alvarez
| Snapshot Date: 2023-10-12 14:05:06 -0400 (Thu, 12 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/viper |
| git_branch: devel |
| git_last_commit: 8ac1760 |
| git_last_commit_date: 2023-04-25 10:31:05 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-10-13 11:40:57 -0400 (Fri, 13 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4679 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4414 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4433 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4419 |
| 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 | ||||
| Package 2208/2244 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| viper 1.35.0 (landing page) Mariano J Alvarez
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.3.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the viper package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: viper |
| Version: 1.35.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:viper.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings viper_1.35.0.tar.gz |
| StartedAt: 2023-10-13 13:58:48 -0000 (Fri, 13 Oct 2023) |
| EndedAt: 2023-10-13 14:16:07 -0000 (Fri, 13 Oct 2023) |
| EllapsedTime: 1038.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: viper.Rcheck |
| Warnings: 1 |
##############################################################################
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### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:viper.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings viper_1.35.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/viper.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘viper/DESCRIPTION’ ... OK
* this is package ‘viper’ version ‘1.35.0’
* 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 loading without being on the library search path ... 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 41.022 0.303 41.398
viperSignature-methods 28.644 0.079 28.778
shadow 19.526 0.068 19.633
msviperSynergy 14.122 0.084 14.235
msviperCombinatorial 11.251 0.107 11.382
viperRPT 10.831 0.035 10.885
plot.msviper 10.176 0.040 10.237
msviper 9.980 0.076 10.077
viper 9.638 0.052 9.708
bootstrapmsviper 8.124 0.056 8.197
ttestNull-methods 7.632 0.040 7.690
bootstrapTtest-methods 7.297 0.088 7.397
ledge 5.407 0.020 5.437
aracne2regulon 5.289 0.120 5.442
* 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’... OK
OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/viper.Rcheck/00check.log’
for details.
viper.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL viper ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-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 | 0.103 | 0.000 | 0.103 | |
| aracne2regulon | 5.289 | 0.120 | 5.442 | |
| aracne2regulon4cnv | 4.729 | 0.064 | 4.800 | |
| bootstrapTtest-methods | 7.297 | 0.088 | 7.397 | |
| bootstrapViper | 41.022 | 0.303 | 41.398 | |
| bootstrapmsviper | 8.124 | 0.056 | 8.197 | |
| distMode | 0.963 | 0.008 | 0.972 | |
| fcvarna | 0.928 | 0.016 | 0.945 | |
| filterCV-methods | 0.963 | 0.008 | 0.973 | |
| frcv | 0.941 | 0.008 | 0.950 | |
| frvarna | 0.937 | 0.004 | 0.942 | |
| integrateSignatures | 3.029 | 0.036 | 3.070 | |
| ledge | 5.407 | 0.020 | 5.437 | |
| msviper | 9.980 | 0.076 | 10.077 | |
| msviperAnnot | 3.130 | 0.020 | 3.154 | |
| msviperClass | 2.291 | 0.028 | 2.323 | |
| msviperCombinatorial | 11.251 | 0.107 | 11.382 | |
| msviperSynergy | 14.122 | 0.084 | 14.235 | |
| plot.msviper | 10.176 | 0.040 | 10.237 | |
| pruneRegulon | 1.008 | 0.012 | 1.022 | |
| rowTtest-methods | 1.910 | 0.016 | 1.930 | |
| scaleGroups | 1.047 | 0.016 | 1.064 | |
| shadow | 19.526 | 0.068 | 19.633 | |
| signatureDistance | 3.380 | 0.008 | 3.393 | |
| ttestNull-methods | 7.632 | 0.040 | 7.690 | |
| viper | 9.638 | 0.052 | 9.708 | |
| viperRPT | 10.831 | 0.035 | 10.885 | |
| viperSignature-methods | 28.644 | 0.079 | 28.778 | |
| viperSimilarity | 3.654 | 0.012 | 3.671 | |