Antoine Bodein
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/timeOmics |
| git_branch: RELEASE_3_13 |
| git_last_commit: 65fbb16 |
| git_last_commit_date: 2021-05-19 12:51:17 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:25 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the timeOmics package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/timeOmics.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 1919/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| timeOmics 1.4.0 (landing page) Antoine Bodein
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: timeOmics |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:timeOmics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings timeOmics_1.4.0.tar.gz |
| StartedAt: 2021-10-15 06:38:59 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 06:43:33 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 273.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: timeOmics.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:timeOmics.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings timeOmics_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/timeOmics.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'timeOmics/DESCRIPTION' ... OK
* this is package 'timeOmics' version '1.4.0'
* 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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'timeOmics' can be installed ... OK
* checking installed package size ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
.mutate_cluster: no visible binding for global variable 'cluster'
.mutate_cluster: no visible binding for global variable 'contrib.max'
check_legend.block.name: no visible global function definition for 'is'
dmatrix.spearman.dissimilarity: no visible global function definition
for 'cor'
filter.getCluster: no visible binding for global variable 'block'
filter.getCluster: no visible binding for global variable 'cluster'
getCluster.block.pls: no visible binding for global variable 'block'
getCluster.block.pls: no visible binding for global variable 'molecule'
getCluster.block.pls: no visible binding for global variable 'comp'
getCluster.block.spls: no visible binding for global variable 'block'
getCluster.block.spls: no visible binding for global variable
'molecule'
getCluster.block.spls: no visible binding for global variable 'comp'
getCluster.mixo_pls: no visible binding for global variable 'comp'
getCluster.mixo_spls: no visible binding for global variable 'comp'
getCluster.pca: no visible binding for global variable 'comp'
getCluster.spca: no visible binding for global variable 'comp'
getNcomp: no visible global function definition for 'is'
getUpDownCluster: no visible global function definition for 'is'
get_MSE: no visible binding for global variable 'feature'
get_MSE: no visible global function definition for 'na.omit'
get_MSE: no visible binding for global variable 'Y_i'
get_MSE: no visible binding for global variable 'Y_hat'
get_MSE: no visible binding for global variable 'error'
lmms.filter.lines: no visible global function definition for 'is'
lmms.filter.lines: no visible global function definition for 'slot'
lmms.filter.lines: no visible binding for global variable 'feature'
lmms.filter.lines: no visible binding for global variable 'BP.test'
lmms.filter.lines: no visible binding for global variable 'MSE'
lmms.filter.lines: no visible binding for global variable 'val'
plot.ncomp.tune.silhouette: no visible global function definition for
'is'
plot.ncomp.tune.silhouette: no visible binding for global variable
'ncomp'
plot.proportionality: no visible binding for global variable 'cluster1'
plot.proportionality: no visible binding for global variable 'value'
plot.proportionality: no visible binding for global variable
'insideout'
plot.spca.tune.silhouette: no visible binding for global variable
'comp'
plot.spca.tune.silhouette: no visible binding for global variable 'X'
plot.spca.tune.silhouette: no visible binding for global variable
'na.omit'
plot.spca.tune.silhouette: no visible binding for global variable
'contrib'
plot.spca.tune.silhouette: no visible binding for global variable
'value'
plotLong: no visible binding for global variable 'block'
plotLong: no visible binding for global variable 'new.block'
plotLong: no visible global function definition for 'is'
plotLong: no visible binding for global variable '.'
plotLong: no visible binding for global variable 'value'
plotLong: no visible binding for global variable 'molecule'
proportionality: no visible global function definition for 'is'
proportionality: no visible binding for global variable 'molecule'
proportionality: no visible binding for global variable 'cluster'
proportionality: no visible binding for global variable '.'
proportionality : <anonymous>: no visible binding for global variable
'.'
proportionality: no visible binding for global variable 'feature1'
proportionality: no visible binding for global variable 'feature2'
proportionality: no visible binding for global variable 'cluster1'
proportionality: no visible binding for global variable 'cluster2'
proportionality: no visible global function definition for 'na.omit'
sd_new: no visible global function definition for 'sd'
silhouette: no visible binding for global variable 'silhouette.coef'
stat_median: no visible binding for global variable 'cluster1'
stat_median: no visible binding for global variable 'cluster2'
stat_median: no visible binding for global variable 'value'
stat_median: no visible global function definition for 'median'
stat_median: no visible binding for global variable 'Pvalue'
stat_median: no visible binding for global variable 'na.omit'
tune.silhouette.get_choice_keepX: no visible global function definition
for 'na.omit'
tune.silhouette.get_choice_keepX: no visible binding for global
variable 'comp'
tune.silhouette.get_choice_keepX: no visible binding for global
variable 'direction'
tune.silhouette.get_choice_keepX: no visible binding for global
variable 'Pval.pos'
tune.silhouette.get_choice_keepX: no visible binding for global
variable 'Pval.neg'
tune.silhouette.get_choice_keepX: no visible binding for global
variable 'distance_from_origin'
tune.silhouette.get_choice_keepX: no visible binding for global
variable 'Pval.dir'
tune.silhouette.get_choice_keepX: no visible binding for global
variable 'Pval.value'
tune.silhouette.get_choice_keepX : <anonymous>: no visible binding for
global variable 'Pval.value'
tune.silhouette.get_choice_keepX : <anonymous>: no visible binding for
global variable 'distance_from_origin'
tune.silhouette.get_choice_keepX : <anonymous>: no visible binding for
global variable '.'
tune.silhouette.get_slopes: no visible global function definition for
'is'
tune.silhouette.get_slopes: no visible binding for global variable
'origin'
tune.silhouette.get_slopes: no visible binding for global variable
'destination'
tune.silhouette.get_slopes: no visible binding for global variable '.'
tune.silhouette.get_slopes: no visible binding for global variable
'comp'
tune.silhouette.get_slopes: no visible binding for global variable
'direction'
tune.silhouette.get_slopes: no visible binding for global variable
'slope.pos'
tune.silhouette.get_slopes: no visible binding for global variable
'slope.neg'
tune.silhouette.get_slopes: no visible binding for global variable
'Z_score.pos'
tune.silhouette.get_slopes: no visible global function definition for
'pnorm'
tune.silhouette.get_slopes: no visible binding for global variable
'Z_score.neg'
tuneCluster.block.spls: no visible binding for global variable
'silhouette.coef'
tuneCluster.spca: no visible binding for global variable
'silhouette.coef'
tuneCluster.spls: no visible binding for global variable
'silhouette.coef'
unscale: no visible global function definition for 'is'
Undefined global functions or variables:
. BP.test MSE Pval.dir Pval.neg Pval.pos Pval.value Pvalue X Y_hat
Y_i Z_score.neg Z_score.pos block cluster cluster1 cluster2 comp
contrib contrib.max cor destination direction distance_from_origin
error feature feature1 feature2 insideout is median molecule na.omit
ncomp new.block origin pnorm sd silhouette.coef slope.neg slope.pos
slot val value
Consider adding
importFrom("methods", "is", "slot")
importFrom("stats", "cor", "median", "na.omit", "pnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
tuneCluster.block.spls 12.78 0 12.78
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
tuneCluster.block.spls 17.64 0 17.64
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* 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
'C:/Users/biocbuild/bbs-3.13-bioc/meat/timeOmics.Rcheck/00check.log'
for details.
timeOmics.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/timeOmics_1.4.0.tar.gz && rm -rf timeOmics.buildbin-libdir && mkdir timeOmics.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=timeOmics.buildbin-libdir timeOmics_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL timeOmics_1.4.0.zip && rm timeOmics_1.4.0.tar.gz timeOmics_1.4.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2085k 100 2085k 0 0 3063k 0 --:--:-- --:--:-- --:--:-- 3062k
install for i386
* installing *source* package 'timeOmics' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: wrong number of arguments to '*'
** help
*** installing help indices
converting help for package 'timeOmics'
finding HTML links ... done
dmatrix.spearman.dissimilarity html
getCluster html
getNcomp html
getSilhouette html
getUpDownCluster html
get_demo_cluster html
get_demo_silhouette html
lmms.filter.lines html
plotLong html
proportionality html
timeOmics.simdata html
tuneCluster.block.spls html
tuneCluster.spca html
tuneCluster.spls html
unscale html
*** copying figures
** 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
install for x64
* installing *source* package 'timeOmics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'timeOmics' as timeOmics_1.4.0.zip
* DONE (timeOmics)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'timeOmics' successfully unpacked and MD5 sums checked
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timeOmics.Rcheck/tests_i386/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(timeOmics)
Loading required package: mixOmics
Loading required package: MASS
Loading required package: lattice
Loading required package: ggplot2
Loaded mixOmics 6.16.3
Thank you for using mixOmics!
Tutorials: http://mixomics.org
Bookdown vignette: https://mixomicsteam.github.io/Bookdown
Questions, issues: Follow the prompts at http://mixomics.org/contact-us
Cite us: citation('mixOmics')
>
> test_check("timeOmics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 263 ]
>
> proc.time()
user system elapsed
51.98 0.46 52.46
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timeOmics.Rcheck/tests_x64/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(timeOmics)
Loading required package: mixOmics
Loading required package: MASS
Loading required package: lattice
Loading required package: ggplot2
Loaded mixOmics 6.16.3
Thank you for using mixOmics!
Tutorials: http://mixomics.org
Bookdown vignette: https://mixomicsteam.github.io/Bookdown
Questions, issues: Follow the prompts at http://mixomics.org/contact-us
Cite us: citation('mixOmics')
>
> test_check("timeOmics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 263 ]
>
> proc.time()
user system elapsed
55.45 0.28 55.71
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timeOmics.Rcheck/examples_i386/timeOmics-Ex.timings
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timeOmics.Rcheck/examples_x64/timeOmics-Ex.timings
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