| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:59:23 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE rexposome PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1469/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| rexposome 1.10.0 Carles Hernandez-Ferrer
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ OK ] | OK |
| Package: rexposome |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rexposome.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rexposome_1.10.0.tar.gz |
| StartedAt: 2020-10-17 04:32:41 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 04:36:41 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 240.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: rexposome.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:rexposome.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings rexposome_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/rexposome.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rexposome/DESCRIPTION’ ... OK
* this is package ‘rexposome’ version ‘1.10.0’
* 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 ‘rexposome’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.0Mb
sub-directories of 1Mb or more:
data 2.8Mb
extdata 2.2Mb
* 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
* 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
imputeLOD: multiple local function definitions for ‘faux’ with
different formal arguments
plotHistogram,ExposomeSet: no visible binding for global variable
‘..density..’
Undefined global functions or variables:
..density..
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
clustering-methods 29.572 0.167 30.743
plotCorrelation-methods 16.799 0.119 17.208
correlation-methods 6.819 0.110 6.934
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/rexposome.Rcheck/00check.log’
for details.
rexposome.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rexposome ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘rexposome’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (rexposome)
rexposome.Rcheck/rexposome-Ex.timings
| name | user | system | elapsed | |
| classification-methods | 0.025 | 0.007 | 0.032 | |
| clustering-methods | 29.572 | 0.167 | 30.743 | |
| correlation-methods | 6.819 | 0.110 | 6.934 | |
| ex_imp | 0.029 | 0.002 | 0.030 | |
| expo | 0.035 | 0.019 | 0.054 | |
| expo_c | 0.015 | 0.002 | 0.018 | |
| expos-methods | 0.344 | 0.014 | 0.357 | |
| exposureNames-methods | 0.030 | 0.006 | 0.035 | |
| exwas-methods | 0.467 | 0.022 | 0.488 | |
| familyNames-methods | 0.023 | 0.003 | 0.025 | |
| highAndLow-methods | 1.070 | 0.012 | 1.083 | |
| ilod-methods | 0 | 0 | 0 | |
| imputation-methods | 0.001 | 0.000 | 0.001 | |
| imputeLOD | 0 | 0 | 0 | |
| loadExposome | 0.059 | 0.002 | 0.062 | |
| loadImputed | 0.021 | 0.002 | 0.023 | |
| me | 0.005 | 0.003 | 0.007 | |
| mexwas-methods | 1.860 | 0.010 | 1.874 | |
| ndim-methods | 0.115 | 0.005 | 0.121 | |
| normalityTest-methods | 0.359 | 0.007 | 0.367 | |
| pca-methods | 0.117 | 0.005 | 0.122 | |
| phenotypeNames-methods | 0.027 | 0.003 | 0.030 | |
| plotClassification-methods | 0.000 | 0.000 | 0.001 | |
| plotCorrelation-methods | 16.799 | 0.119 | 17.208 | |
| plotEXP-methods | 0.331 | 0.006 | 0.339 | |
| plotEffect-methods | 1.063 | 0.017 | 1.081 | |
| plotExwas-methods | 0.671 | 0.010 | 0.682 | |
| plotFamily-methods | 3.053 | 0.062 | 3.125 | |
| plotHistogram-methods | 0.384 | 0.004 | 0.388 | |
| plotLOD-methods | 0.659 | 0.006 | 0.667 | |
| plotMissings-methods | 0.768 | 0.007 | 0.914 | |
| plotPCA-methods | 1.886 | 0.015 | 1.905 | |
| plotPHE-methods | 0.352 | 0.011 | 0.364 | |
| readExposome | 0.072 | 0.002 | 0.083 | |
| standardize-methods | 1.055 | 0.016 | 1.316 | |
| tableLOD-methods | 0.269 | 0.010 | 0.345 | |
| tableMissings-methods | 0.042 | 0.010 | 0.111 | |
| tef-methods | 0.483 | 0.024 | 0.528 | |
| toES | 0.206 | 0.005 | 0.212 | |
| trans-methods | 0.353 | 0.007 | 0.362 | |
| volcano_plot | 1.041 | 0.035 | 1.083 | |