| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:14 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 1573/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| POMA 1.12.0 (landing page) Pol Castellano-Escuder
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK |  | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the POMA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/POMA.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. |
| Package: POMA |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:POMA.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings POMA_1.12.0.tar.gz |
| StartedAt: 2024-04-16 02:23:46 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 02:31:01 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 435.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: POMA.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:POMA.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings POMA_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/POMA.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘POMA/DESCRIPTION’ ... OK
* this is package ‘POMA’ version ‘1.12.0’
* 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 ‘POMA’ 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
* 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 startup messages can be suppressed ... 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
PomaBoxplots: no visible global function definition for ‘is’
PomaBoxplots: no visible binding for global variable ‘ID’
PomaBoxplots: no visible binding for global variable ‘Group’
PomaBoxplots: no visible binding for global variable ‘value’
PomaBoxplots: no visible binding for global variable ‘name’
PomaClust: no visible global function definition for ‘is’
PomaClust: no visible binding for global variable ‘group’
PomaClust: no visible binding for global variable ‘clust’
PomaClust: no visible binding for global variable ‘V1’
PomaClust: no visible binding for global variable ‘V2’
PomaClust: no visible binding for global variable ‘Dim1’
PomaClust: no visible binding for global variable ‘Dim2’
PomaCorr: no visible global function definition for ‘is’
PomaCorr: no visible global function definition for ‘cor’
PomaCorr: no visible binding for global variable ‘column’
PomaCorr: no visible binding for global variable ‘cor’
PomaCorr: no visible binding for global variable ‘p’
PomaCorr: no visible global function definition for ‘p.adjust’
PomaCorr: no visible binding for global variable ‘pvalue’
PomaCorr: no visible binding for global variable ‘corr’
PomaCorr: no visible binding for global variable ‘feature1’
PomaCorr: no visible binding for global variable ‘name’
PomaCorr: no visible binding for global variable ‘value’
PomaCorr: no visible global function definition for ‘na.omit’
PomaCorr: no visible binding for global variable ‘est_corr’
PomaDESeq: no visible global function definition for ‘is’
PomaDESeq: no visible binding for global variable ‘padj’
PomaDensity: no visible global function definition for ‘is’
PomaDensity: no visible binding for global variable ‘ID’
PomaDensity: no visible binding for global variable ‘Group’
PomaDensity: no visible binding for global variable ‘value’
PomaDensity: no visible binding for global variable ‘name’
PomaEDA: no visible global function definition for ‘is’
PomaHeatmap: no visible global function definition for ‘is’
PomaImpute: no visible global function definition for ‘is’
PomaImpute: no visible global function definition for ‘aggregate’
PomaImpute: no visible binding for global variable ‘Group’
PomaImpute : <anonymous>: no visible global function definition for
‘median’
PomaImpute: no visible binding for global variable ‘group’
PomaImpute: no visible global function definition for ‘validObject’
PomaLasso: no visible global function definition for ‘is’
PomaLasso: no visible binding for global variable ‘estimate’
PomaLasso: no visible binding for global variable ‘conf.low’
PomaLasso: no visible binding for global variable ‘conf.high’
PomaLasso: no visible global function definition for ‘predict’
PomaLasso: no visible binding for global variable ‘term’
PomaLimma: no visible global function definition for ‘is’
PomaLimma: no visible binding for global variable ‘adj.P.Val’
PomaLimma: no visible global function definition for ‘as.formula’
PomaMultivariate: no visible global function definition for ‘is’
PomaMultivariate: no visible binding for global variable ‘PC1’
PomaMultivariate: no visible binding for global variable ‘PC2’
PomaMultivariate: no visible binding for global variable ‘Groups’
PomaMultivariate: no visible binding for global variable ‘ID’
PomaMultivariate: no visible global function definition for ‘reorder’
PomaMultivariate: no visible binding for global variable ‘component’
PomaMultivariate: no visible binding for global variable ‘pc_var_exp’
PomaMultivariate: no visible binding for global variable ‘feature’
PomaMultivariate: no visible binding for global variable ‘value’
PomaMultivariate: no visible binding for global variable ‘name’
PomaMultivariate: no visible binding for global variable ‘to_x’
PomaMultivariate: no visible binding for global variable ‘to_y’
PomaMultivariate: no visible binding for global variable ‘comp1’
PomaMultivariate: no visible binding for global variable ‘comp2’
PomaMultivariate: no visible binding for global variable ‘feature_sd’
PomaMultivariate: no visible binding for global variable ‘sd’
PomaMultivariate: no visible binding for global variable ‘value.var’
PomaNorm: no visible global function definition for ‘is’
PomaNorm: no visible binding for global variable ‘var’
PomaNorm : <anonymous>: no visible global function definition for ‘sd’
PomaNorm: no visible global function definition for ‘validObject’
PomaOddsRatio: no visible global function definition for ‘is’
PomaOddsRatio: no visible binding for global variable ‘group’
PomaOddsRatio: no visible global function definition for ‘matches’
PomaOddsRatio: no visible binding for global variable ‘OddsRatio’
PomaOddsRatio: no visible binding for global variable ‘feature’
PomaOddsRatio: no visible binding for global variable ‘upr’
PomaOddsRatio: no visible binding for global variable ‘lwr’
PomaOutliers: no visible global function definition for ‘is’
PomaOutliers: no visible global function definition for ‘aggregate’
PomaOutliers : <anonymous>: no visible global function definition for
‘quantile’
PomaOutliers : <anonymous>: no visible global function definition for
‘IQR’
PomaOutliers: no visible binding for global variable ‘x’
PomaOutliers: no visible binding for global variable ‘out’
PomaOutliers: no visible binding for global variable ‘Groups’
PomaOutliers : find_hull: no visible global function definition for
‘chull’
PomaOutliers: no visible binding for global variable ‘Group’
PomaOutliers: no visible binding for global variable ‘.’
PomaOutliers: no visible binding for global variable ‘PCoA1’
PomaOutliers: no visible binding for global variable ‘PCoA2’
PomaOutliers: no visible global function definition for ‘validObject’
PomaPCR: no visible global function definition for ‘is’
PomaPCR: no visible global function definition for ‘prcomp’
PomaPCR: no visible binding for global variable ‘feature’
PomaPCR: no visible binding for global variable ‘PC1’
PomaPCR: no visible global function definition for ‘lm’
PomaRandForest: no visible global function definition for ‘is’
PomaRandForest: no visible binding for global variable ‘.’
PomaRandForest: no visible binding for global variable ‘Group’
PomaRandForest: no visible binding for global variable ‘OOB’
PomaRandForest: no visible binding for global variable
‘MeanDecreaseGini’
PomaRandForest: no visible binding for global variable ‘real_names’
PomaRandForest: no visible global function definition for ‘reorder’
PomaRandForest: no visible binding for global variable ‘feature’
PomaRandForest: no visible binding for global variable ‘new_names’
PomaRankProd: no visible global function definition for ‘is’
PomaRankProd: no visible binding for global variable ‘P.value’
PomaRankProd: no visible binding for global variable ‘gene.index’
PomaSummarizedExperiment: no visible global function definition for
‘validObject’
PomaUMAP: no visible global function definition for ‘is’
PomaUMAP: no visible binding for global variable ‘group’
PomaUMAP: no visible binding for global variable ‘UMAP1’
PomaUMAP: no visible binding for global variable ‘UMAP2’
PomaUMAP: no visible binding for global variable ‘clust’
PomaUnivariate: no visible global function definition for ‘is’
PomaUnivariate: no visible binding for global variable ‘group’
PomaUnivariate : stat_ttest: no visible global function definition for
‘t.test’
PomaUnivariate: no visible global function definition for ‘p.adjust’
PomaUnivariate: no visible binding for global variable ‘pvalue’
PomaUnivariate: no visible binding for global variable ‘feature’
PomaUnivariate: no visible binding for global variable ‘FC’
PomaUnivariate: no visible binding for global variable ‘diff_means’
PomaUnivariate: no visible binding for global variable ‘pvalueAdj’
PomaUnivariate : stat_aov: no visible global function definition for
‘anova’
PomaUnivariate : stat_aov: no visible global function definition for
‘aov’
PomaUnivariate: no visible global function definition for ‘colData’
PomaUnivariate: no visible global function definition for ‘anova’
PomaUnivariate: no visible global function definition for ‘aov’
PomaUnivariate: no visible global function definition for ‘as.formula’
PomaUnivariate : <anonymous>: no visible global function definition for
‘wilcox.test’
PomaUnivariate : <anonymous>: no visible global function definition for
‘kruskal.test’
PomaUnivariate: no visible binding for global variable ‘kw_rank_sum’
PomaVolcano: no visible global function definition for ‘is’
PomaVolcano: no visible binding for global variable ‘FC’
PomaVolcano: no visible binding for global variable ‘P.Value’
PomaVolcano: no visible binding for global variable ‘adj.P.Val’
PomaVolcano: no visible binding for global variable ‘log2FoldChange’
PomaVolcano: no visible binding for global variable ‘padj’
PomaVolcano: no visible binding for global variable ‘logFC’
PomaVolcano: no visible binding for global variable ‘pvalue’
PomaVolcano: no visible binding for global variable ‘threshold’
Undefined global functions or variables:
. Dim1 Dim2 FC Group Groups ID IQR MeanDecreaseGini OOB OddsRatio
P.Value P.value PC1 PC2 PCoA1 PCoA2 UMAP1 UMAP2 V1 V2 adj.P.Val
aggregate anova aov as.formula chull clust colData column comp1 comp2
component conf.high conf.low cor corr diff_means est_corr estimate
feature feature1 feature_sd gene.index group is kruskal.test
kw_rank_sum lm log2FoldChange logFC lwr matches median na.omit name
new_names out p p.adjust padj pc_var_exp prcomp predict pvalue
pvalueAdj quantile real_names reorder sd t.test term threshold to_x
to_y upr validObject value value.var var wilcox.test x
Consider adding
importFrom("grDevices", "chull")
importFrom("methods", "is", "validObject")
importFrom("stats", "IQR", "aggregate", "anova", "aov", "as.formula",
"cor", "kruskal.test", "lm", "median", "na.omit",
"p.adjust", "prcomp", "predict", "quantile", "reorder",
"sd", "t.test", "var", "wilcox.test")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
PomaMultivariate 21.163 0.735 21.931
PomaBoxplots 15.369 0.469 15.838
PomaVolcano 5.051 0.092 5.143
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘POMA-demo.Rmd’ using ‘UTF-8’... failed
‘POMA-eda.Rmd’ using ‘UTF-8’... OK
‘POMA-normalization.Rmd’ using ‘UTF-8’... OK
ERROR
Errors in running code in vignettes:
when running code in ‘POMA-demo.Rmd’
...
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family 'Arial Narrow' not found in PostScript font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family 'Arial Narrow' not found in PostScript font database
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y, :
font family 'Arial Narrow' not found in PostScript font database
When sourcing ‘POMA-demo.R’:
Error: invalid font type
Execution halted
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/POMA.Rcheck/00check.log’
for details.
POMA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL POMA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’ * installing *source* package ‘POMA’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** 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 * DONE (POMA)
POMA.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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(POMA)
Welcome to POMA!
Version 1.12.0
POMAShiny app: https://github.com/pcastellanoescuder/POMAShiny
For more detailed package information please visit https://pcastellanoescuder.github.io/POMA/
>
> test_check("POMA")
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|
|========================================================= | 81%
|
|========================================================= | 82%
|
|========================================================== | 82%
|
|========================================================== | 83%
|
|=========================================================== | 84%
|
|=========================================================== | 85%
|
|============================================================ | 85%
|
|============================================================ | 86%
|
|============================================================= | 87%
|
|============================================================= | 88%
|
|============================================================== | 88%
|
|============================================================== | 89%
|
|=============================================================== | 90%
|
|=============================================================== | 91%
|
|================================================================ | 91%
|
|================================================================ | 92%
|
|================================================================= | 92%
|
|================================================================= | 93%
|
|================================================================== | 94%
|
|================================================================== | 95%
|
|=================================================================== | 95%
|
|=================================================================== | 96%
|
|==================================================================== | 96%
|
|==================================================================== | 97%
|
|==================================================================== | 98%
|
|===================================================================== | 98%
|
|===================================================================== | 99%
|
|======================================================================| 100%
comp 2
|
| | 0%
|
|= | 1%
|
|= | 2%
|
|== | 2%
|
|== | 3%
|
|== | 4%
|
|=== | 4%
|
|=== | 5%
|
|==== | 5%
|
|==== | 6%
|
|===== | 7%
|
|===== | 8%
|
|====== | 8%
|
|====== | 9%
|
|======= | 9%
|
|======= | 10%
|
|======== | 11%
|
|======== | 12%
|
|========= | 12%
|
|========= | 13%
|
|========== | 14%
|
|========== | 15%
|
|=========== | 15%
|
|=========== | 16%
|
|============ | 17%
|
|============ | 18%
|
|============= | 18%
|
|============= | 19%
|
|============== | 20%
|
|============== | 21%
|
|=============== | 21%
|
|=============== | 22%
|
|================ | 22%
|
|================ | 23%
|
|================= | 24%
|
|================= | 25%
|
|================== | 25%
|
|================== | 26%
|
|=================== | 27%
|
|=================== | 28%
|
|==================== | 28%
|
|==================== | 29%
|
|===================== | 29%
|
|===================== | 30%
|
|====================== | 31%
|
|====================== | 32%
|
|======================= | 33%
|
|======================== | 34%
|
|======================== | 35%
|
|========================= | 35%
|
|========================= | 36%
|
|========================== | 37%
|
|========================== | 38%
|
|=========================== | 38%
|
|=========================== | 39%
|
|============================ | 39%
|
|============================ | 40%
|
|============================ | 41%
|
|============================= | 41%
|
|============================= | 42%
|
|============================== | 42%
|
|============================== | 43%
|
|=============================== | 44%
|
|=============================== | 45%
|
|================================ | 45%
|
|================================ | 46%
|
|================================= | 47%
|
|================================= | 48%
|
|================================== | 48%
|
|================================== | 49%
|
|=================================== | 50%
|
|==================================== | 51%
|
|==================================== | 52%
|
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|
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|
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|
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|
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|
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|
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|
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|
|========================================= | 58%
|
|========================================= | 59%
|
|========================================== | 59%
|
|========================================== | 60%
|
|========================================== | 61%
|
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|
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|
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|
|============================================ | 63%
|
|============================================= | 64%
|
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|
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|
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|
|=============================================== | 67%
|
|================================================ | 68%
|
|================================================ | 69%
|
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|
|================================================= | 71%
|
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|
|================================================== | 72%
|
|=================================================== | 72%
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|========================================================== | 83%
|
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|
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|
|============================================================ | 85%
|
|============================================================ | 86%
|
|============================================================= | 87%
|
|============================================================= | 88%
|
|============================================================== | 88%
|
|============================================================== | 89%
|
|=============================================================== | 90%
|
|=============================================================== | 91%
|
|================================================================ | 91%
|
|================================================================ | 92%
|
|================================================================= | 92%
|
|================================================================= | 93%
|
|================================================================== | 94%
|
|================================================================== | 95%
|
|=================================================================== | 95%
|
|=================================================================== | 96%
|
|==================================================================== | 96%
|
|==================================================================== | 97%
|
|==================================================================== | 98%
|
|===================================================================== | 98%
|
|===================================================================== | 99%
|
|======================================================================| 100%
comp 3
|
| | 0%
|
|= | 1%
|
|= | 2%
|
|== | 2%
|
|== | 3%
|
|== | 4%
|
|=== | 4%
|
|=== | 5%
|
|==== | 5%
|
|==== | 6%
|
|===== | 7%
|
|===== | 8%
|
|====== | 8%
|
|====== | 9%
|
|======= | 9%
|
|======= | 10%
|
|======== | 11%
|
|======== | 12%
|
|========= | 12%
|
|========= | 13%
|
|========== | 14%
|
|========== | 15%
|
|=========== | 15%
|
|=========== | 16%
|
|============ | 17%
|
|============ | 18%
|
|============= | 18%
|
|============= | 19%
|
|============== | 20%
|
|============== | 21%
|
|=============== | 21%
|
|=============== | 22%
|
|================ | 22%
|
|================ | 23%
|
|================= | 24%
|
|================= | 25%
|
|================== | 25%
|
|================== | 26%
|
|=================== | 27%
|
|=================== | 28%
|
|==================== | 28%
|
|==================== | 29%
|
|===================== | 29%
|
|===================== | 30%
|
|====================== | 31%
|
|====================== | 32%
|
|======================= | 33%
|
|======================== | 34%
|
|======================== | 35%
|
|========================= | 35%
|
|========================= | 36%
|
|========================== | 37%
|
|========================== | 38%
|
|=========================== | 38%
|
|=========================== | 39%
|
|============================ | 39%
|
|============================ | 40%
|
|============================ | 41%
|
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|
|============================= | 42%
|
|============================== | 42%
|
|============================== | 43%
|
|=============================== | 44%
|
|=============================== | 45%
|
|================================ | 45%
|
|================================ | 46%
|
|================================= | 47%
|
|================================= | 48%
|
|================================== | 48%
|
|================================== | 49%
|
|=================================== | 50%
|
|==================================== | 51%
|
|==================================== | 52%
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|========================================= | 59%
|
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|
|========================================== | 60%
|
|========================================== | 61%
|
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|
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|
|============================================ | 62%
|
|============================================ | 63%
|
|============================================= | 64%
|
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|
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|
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|
|=============================================== | 67%
|
|================================================ | 68%
|
|================================================ | 69%
|
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|
|================================================= | 71%
|
|================================================== | 71%
|
|================================================== | 72%
|
|=================================================== | 72%
|
|=================================================== | 73%
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|========================================================== | 83%
|
|=========================================================== | 84%
|
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|
|============================================================ | 85%
|
|============================================================ | 86%
|
|============================================================= | 87%
|
|============================================================= | 88%
|
|============================================================== | 88%
|
|============================================================== | 89%
|
|=============================================================== | 90%
|
|=============================================================== | 91%
|
|================================================================ | 91%
|
|================================================================ | 92%
|
|================================================================= | 92%
|
|================================================================= | 93%
|
|================================================================== | 94%
|
|================================================================== | 95%
|
|=================================================================== | 95%
|
|=================================================================== | 96%
|
|==================================================================== | 96%
|
|==================================================================== | 97%
|
|==================================================================== | 98%
|
|===================================================================== | 98%
|
|===================================================================== | 99%
|
|======================================================================| 100%
comp 4
|
| | 0%
|
|= | 1%
|
|= | 2%
|
|== | 2%
|
|== | 3%
|
|== | 4%
|
|=== | 4%
|
|=== | 5%
|
|==== | 5%
|
|==== | 6%
|
|===== | 7%
|
|===== | 8%
|
|====== | 8%
|
|====== | 9%
|
|======= | 9%
|
|======= | 10%
|
|======== | 11%
|
|======== | 12%
|
|========= | 12%
|
|========= | 13%
|
|========== | 14%
|
|========== | 15%
|
|=========== | 15%
|
|=========== | 16%
|
|============ | 17%
|
|============ | 18%
|
|============= | 18%
|
|============= | 19%
|
|============== | 20%
|
|============== | 21%
|
|=============== | 21%
|
|=============== | 22%
|
|================ | 22%
|
|================ | 23%
|
|================= | 24%
|
|================= | 25%
|
|================== | 25%
|
|================== | 26%
|
|=================== | 27%
|
|=================== | 28%
|
|==================== | 28%
|
|==================== | 29%
|
|===================== | 29%
|
|===================== | 30%
|
|====================== | 31%
|
|====================== | 32%
|
|======================= | 33%
|
|======================== | 34%
|
|======================== | 35%
|
|========================= | 35%
|
|========================= | 36%
|
|========================== | 37%
|
|========================== | 38%
|
|=========================== | 38%
|
|=========================== | 39%
|
|============================ | 39%
|
|============================ | 40%
|
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|
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|
|============================= | 42%
|
|============================== | 42%
|
|============================== | 43%
|
|=============================== | 44%
|
|=============================== | 45%
|
|================================ | 45%
|
|================================ | 46%
|
|================================= | 47%
|
|================================= | 48%
|
|================================== | 48%
|
|================================== | 49%
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|================================================ | 68%
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|======================================================== | 79%
|
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|
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|
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|
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|
|========================================================== | 83%
|
|=========================================================== | 84%
|
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|
|============================================================ | 85%
|
|============================================================ | 86%
|
|============================================================= | 87%
|
|============================================================= | 88%
|
|============================================================== | 88%
|
|============================================================== | 89%
|
|=============================================================== | 90%
|
|=============================================================== | 91%
|
|================================================================ | 91%
|
|================================================================ | 92%
|
|================================================================= | 92%
|
|================================================================= | 93%
|
|================================================================== | 94%
|
|================================================================== | 95%
|
|=================================================================== | 95%
|
|=================================================================== | 96%
|
|==================================================================== | 96%
|
|==================================================================== | 97%
|
|==================================================================== | 98%
|
|===================================================================== | 98%
|
|===================================================================== | 99%
|
|======================================================================| 100%
comp 1
|
| | 0%
|
|= | 2%
|
|=== | 4%
|
|==== | 6%
|
|====== | 8%
|
|======= | 10%
|
|======== | 12%
|
|========== | 14%
|
|=========== | 16%
|
|============= | 18%
|
|============== | 20%
|
|=============== | 22%
|
|================= | 24%
|
|================== | 26%
|
|==================== | 28%
|
|===================== | 30%
|
|====================== | 32%
|
|======================== | 34%
|
|========================= | 36%
|
|=========================== | 38%
|
|============================ | 40%
|
|============================= | 42%
|
|=============================== | 44%
|
|================================ | 46%
|
|================================== | 48%
|
|=================================== | 50%
|
|==================================== | 52%
|
|====================================== | 54%
|
|======================================= | 56%
|
|========================================= | 58%
|
|========================================== | 60%
|
|=========================================== | 62%
|
|============================================= | 64%
|
|============================================== | 66%
|
|================================================ | 68%
|
|================================================= | 70%
|
|================================================== | 72%
|
|==================================================== | 74%
|
|===================================================== | 76%
|
|======================================================= | 78%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================== | 88%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|===================================================================== | 98%
|
|======================================================================| 100%
comp 2
|
| | 0%
|
|= | 2%
|
|=== | 4%
|
|==== | 6%
|
|====== | 8%
|
|======= | 10%
|
|======== | 12%
|
|========== | 14%
|
|=========== | 16%
|
|============= | 18%
|
|============== | 20%
|
|=============== | 22%
|
|================= | 24%
|
|================== | 26%
|
|==================== | 28%
|
|===================== | 30%
|
|====================== | 32%
|
|======================== | 34%
|
|========================= | 36%
|
|=========================== | 38%
|
|============================ | 40%
|
|============================= | 42%
|
|=============================== | 44%
|
|================================ | 46%
|
|================================== | 48%
|
|=================================== | 50%
|
|==================================== | 52%
|
|====================================== | 54%
|
|======================================= | 56%
|
|========================================= | 58%
|
|========================================== | 60%
|
|=========================================== | 62%
|
|============================================= | 64%
|
|============================================== | 66%
|
|================================================ | 68%
|
|================================================= | 70%
|
|================================================== | 72%
|
|==================================================== | 74%
|
|===================================================== | 76%
|
|======================================================= | 78%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================== | 88%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|===================================================================== | 98%
|
|======================================================================| 100%
comp 3
|
| | 0%
|
|= | 2%
|
|=== | 4%
|
|==== | 6%
|
|====== | 8%
|
|======= | 10%
|
|======== | 12%
|
|========== | 14%
|
|=========== | 16%
|
|============= | 18%
|
|============== | 20%
|
|=============== | 22%
|
|================= | 24%
|
|================== | 26%
|
|==================== | 28%
|
|===================== | 30%
|
|====================== | 32%
|
|======================== | 34%
|
|========================= | 36%
|
|=========================== | 38%
|
|============================ | 40%
|
|============================= | 42%
|
|=============================== | 44%
|
|================================ | 46%
|
|================================== | 48%
|
|=================================== | 50%
|
|==================================== | 52%
|
|====================================== | 54%
|
|======================================= | 56%
|
|========================================= | 58%
|
|========================================== | 60%
|
|=========================================== | 62%
|
|============================================= | 64%
|
|============================================== | 66%
|
|================================================ | 68%
|
|================================================= | 70%
|
|================================================== | 72%
|
|==================================================== | 74%
|
|===================================================== | 76%
|
|======================================================= | 78%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================== | 88%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|===================================================================== | 98%
|
|======================================================================| 100%
comp 1
|
| | 0%
|
|= | 2%
|
|=== | 4%
|
|==== | 6%
|
|====== | 8%
|
|======= | 10%
|
|======== | 12%
|
|========== | 14%
|
|=========== | 16%
|
|============= | 18%
|
|============== | 20%
|
|=============== | 22%
|
|================= | 24%
|
|================== | 26%
|
|==================== | 28%
|
|===================== | 30%
|
|====================== | 32%
|
|======================== | 34%
|
|========================= | 36%
|
|=========================== | 38%
|
|============================ | 40%
|
|============================= | 42%
|
|=============================== | 44%
|
|================================ | 46%
|
|================================== | 48%
|
|=================================== | 50%
|
|==================================== | 52%
|
|====================================== | 54%
|
|======================================= | 56%
|
|========================================= | 58%
|
|========================================== | 60%
|
|=========================================== | 62%
|
|============================================= | 64%
|
|============================================== | 66%
|
|================================================ | 68%
|
|================================================= | 70%
|
|================================================== | 72%
|
|==================================================== | 74%
|
|===================================================== | 76%
|
|======================================================= | 78%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================== | 88%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|===================================================================== | 98%
|
|======================================================================| 100%
comp 2
|
| | 0%
|
|= | 2%
|
|=== | 4%
|
|==== | 6%
|
|====== | 8%
|
|======= | 10%
|
|======== | 12%
|
|========== | 14%
|
|=========== | 16%
|
|============= | 18%
|
|============== | 20%
|
|=============== | 22%
|
|================= | 24%
|
|================== | 26%
|
|==================== | 28%
|
|===================== | 30%
|
|====================== | 32%
|
|======================== | 34%
|
|========================= | 36%
|
|=========================== | 38%
|
|============================ | 40%
|
|============================= | 42%
|
|=============================== | 44%
|
|================================ | 46%
|
|================================== | 48%
|
|=================================== | 50%
|
|==================================== | 52%
|
|====================================== | 54%
|
|======================================= | 56%
|
|========================================= | 58%
|
|========================================== | 60%
|
|=========================================== | 62%
|
|============================================= | 64%
|
|============================================== | 66%
|
|================================================ | 68%
|
|================================================= | 70%
|
|================================================== | 72%
|
|==================================================== | 74%
|
|===================================================== | 76%
|
|======================================================= | 78%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================== | 88%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|===================================================================== | 98%
|
|======================================================================| 100%
comp 3
|
| | 0%
|
|= | 2%
|
|=== | 4%
|
|==== | 6%
|
|====== | 8%
|
|======= | 10%
|
|======== | 12%
|
|========== | 14%
|
|=========== | 16%
|
|============= | 18%
|
|============== | 20%
|
|=============== | 22%
|
|================= | 24%
|
|================== | 26%
|
|==================== | 28%
|
|===================== | 30%
|
|====================== | 32%
|
|======================== | 34%
|
|========================= | 36%
|
|=========================== | 38%
|
|============================ | 40%
|
|============================= | 42%
|
|=============================== | 44%
|
|================================ | 46%
|
|================================== | 48%
|
|=================================== | 50%
|
|==================================== | 52%
|
|====================================== | 54%
|
|======================================= | 56%
|
|========================================= | 58%
|
|========================================== | 60%
|
|=========================================== | 62%
|
|============================================= | 64%
|
|============================================== | 66%
|
|================================================ | 68%
|
|================================================= | 70%
|
|================================================== | 72%
|
|==================================================== | 74%
|
|===================================================== | 76%
|
|======================================================= | 78%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================== | 88%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|===================================================================== | 98%
|
|======================================================================| 100%
comp 4
|
| | 0%
|
|= | 2%
|
|=== | 4%
|
|==== | 6%
|
|====== | 8%
|
|======= | 10%
|
|======== | 12%
|
|========== | 14%
|
|=========== | 16%
|
|============= | 18%
|
|============== | 20%
|
|=============== | 22%
|
|================= | 24%
|
|================== | 26%
|
|==================== | 28%
|
|===================== | 30%
|
|====================== | 32%
|
|======================== | 34%
|
|========================= | 36%
|
|=========================== | 38%
|
|============================ | 40%
|
|============================= | 42%
|
|=============================== | 44%
|
|================================ | 46%
|
|================================== | 48%
|
|=================================== | 50%
|
|==================================== | 52%
|
|====================================== | 54%
|
|======================================= | 56%
|
|========================================= | 58%
|
|========================================== | 60%
|
|=========================================== | 62%
|
|============================================= | 64%
|
|============================================== | 66%
|
|================================================ | 68%
|
|================================================= | 70%
|
|================================================== | 72%
|
|==================================================== | 74%
|
|===================================================== | 76%
|
|======================================================= | 78%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================== | 88%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|===================================================================== | 98%
|
|======================================================================| 100%
comp 1
|
| | 0%
|
|= | 2%
|
|=== | 4%
|
|==== | 6%
|
|====== | 8%
|
|======= | 10%
|
|======== | 12%
|
|========== | 14%
|
|=========== | 16%
|
|============= | 18%
|
|============== | 20%
|
|=============== | 22%
|
|================= | 24%
|
|================== | 26%
|
|==================== | 28%
|
|===================== | 30%
|
|====================== | 32%
|
|======================== | 34%
|
|========================= | 36%
|
|=========================== | 38%
|
|============================ | 40%
|
|============================= | 42%
|
|=============================== | 44%
|
|================================ | 46%
|
|================================== | 48%
|
|=================================== | 50%
|
|==================================== | 52%
|
|====================================== | 54%
|
|======================================= | 56%
|
|========================================= | 58%
|
|========================================== | 60%
|
|=========================================== | 62%
|
|============================================= | 64%
|
|============================================== | 66%
|
|================================================ | 68%
|
|================================================= | 70%
|
|================================================== | 72%
|
|==================================================== | 74%
|
|===================================================== | 76%
|
|======================================================= | 78%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================== | 88%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|===================================================================== | 98%
|
|======================================================================| 100%
comp 2
|
| | 0%
|
|= | 2%
|
|=== | 4%
|
|==== | 6%
|
|====== | 8%
|
|======= | 10%
|
|======== | 12%
|
|========== | 14%
|
|=========== | 16%
|
|============= | 18%
|
|============== | 20%
|
|=============== | 22%
|
|================= | 24%
|
|================== | 26%
|
|==================== | 28%
|
|===================== | 30%
|
|====================== | 32%
|
|======================== | 34%
|
|========================= | 36%
|
|=========================== | 38%
|
|============================ | 40%
|
|============================= | 42%
|
|=============================== | 44%
|
|================================ | 46%
|
|================================== | 48%
|
|=================================== | 50%
|
|==================================== | 52%
|
|====================================== | 54%
|
|======================================= | 56%
|
|========================================= | 58%
|
|========================================== | 60%
|
|=========================================== | 62%
|
|============================================= | 64%
|
|============================================== | 66%
|
|================================================ | 68%
|
|================================================= | 70%
|
|================================================== | 72%
|
|==================================================== | 74%
|
|===================================================== | 76%
|
|======================================================= | 78%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================== | 88%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|===================================================================== | 98%
|
|======================================================================| 100%
comp 3
|
| | 0%
|
|= | 2%
|
|=== | 4%
|
|==== | 6%
|
|====== | 8%
|
|======= | 10%
|
|======== | 12%
|
|========== | 14%
|
|=========== | 16%
|
|============= | 18%
|
|============== | 20%
|
|=============== | 22%
|
|================= | 24%
|
|================== | 26%
|
|==================== | 28%
|
|===================== | 30%
|
|====================== | 32%
|
|======================== | 34%
|
|========================= | 36%
|
|=========================== | 38%
|
|============================ | 40%
|
|============================= | 42%
|
|=============================== | 44%
|
|================================ | 46%
|
|================================== | 48%
|
|=================================== | 50%
|
|==================================== | 52%
|
|====================================== | 54%
|
|======================================= | 56%
|
|========================================= | 58%
|
|========================================== | 60%
|
|=========================================== | 62%
|
|============================================= | 64%
|
|============================================== | 66%
|
|================================================ | 68%
|
|================================================= | 70%
|
|================================================== | 72%
|
|==================================================== | 74%
|
|===================================================== | 76%
|
|======================================================= | 78%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================== | 88%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|===================================================================== | 98%
|
|======================================================================| 100%
comp 4
|
| | 0%
|
|= | 2%
|
|=== | 4%
|
|==== | 6%
|
|====== | 8%
|
|======= | 10%
|
|======== | 12%
|
|========== | 14%
|
|=========== | 16%
|
|============= | 18%
|
|============== | 20%
|
|=============== | 22%
|
|================= | 24%
|
|================== | 26%
|
|==================== | 28%
|
|===================== | 30%
|
|====================== | 32%
|
|======================== | 34%
|
|========================= | 36%
|
|=========================== | 38%
|
|============================ | 40%
|
|============================= | 42%
|
|=============================== | 44%
|
|================================ | 46%
|
|================================== | 48%
|
|=================================== | 50%
|
|==================================== | 52%
|
|====================================== | 54%
|
|======================================= | 56%
|
|========================================= | 58%
|
|========================================== | 60%
|
|=========================================== | 62%
|
|============================================= | 64%
|
|============================================== | 66%
|
|================================================ | 68%
|
|================================================= | 70%
|
|================================================== | 72%
|
|==================================================== | 74%
|
|===================================================== | 76%
|
|======================================================= | 78%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================== | 88%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|===================================================================== | 98%
|
|======================================================================| 100%
comp 5
|
| | 0%
|
|= | 2%
|
|=== | 4%
|
|==== | 6%
|
|====== | 8%
|
|======= | 10%
|
|======== | 12%
|
|========== | 14%
|
|=========== | 16%
|
|============= | 18%
|
|============== | 20%
|
|=============== | 22%
|
|================= | 24%
|
|================== | 26%
|
|==================== | 28%
|
|===================== | 30%
|
|====================== | 32%
|
|======================== | 34%
|
|========================= | 36%
|
|=========================== | 38%
|
|============================ | 40%
|
|============================= | 42%
|
|=============================== | 44%
|
|================================ | 46%
|
|================================== | 48%
|
|=================================== | 50%
|
|==================================== | 52%
|
|====================================== | 54%
|
|======================================= | 56%
|
|========================================= | 58%
|
|========================================== | 60%
|
|=========================================== | 62%
|
|============================================= | 64%
|
|============================================== | 66%
|
|================================================ | 68%
|
|================================================= | 70%
|
|================================================== | 72%
|
|==================================================== | 74%
|
|===================================================== | 76%
|
|======================================================= | 78%
|
|======================================================== | 80%
|
|========================================================= | 82%
|
|=========================================================== | 84%
|
|============================================================ | 86%
|
|============================================================== | 88%
|
|=============================================================== | 90%
|
|================================================================ | 92%
|
|================================================================== | 94%
|
|=================================================================== | 96%
|
|===================================================================== | 98%
|
|======================================================================| 100%
Rank Product analysis for unpaired case
done Table1: Genes called significant under class1 < class2
Table2: Genes called significant under class1 > class2
Rank Product analysis for unpaired case
done Table1: Genes called significant under class1 < class2
Table2: Genes called significant under class1 > class2
Rank Product analysis for unpaired case
done Table1: Genes called significant under class1 < class2
Table2: Genes called significant under class1 > class2
Rank Product analysis for unpaired case
done Table1: Genes called significant under class1 < class2
Table2: Genes called significant under class1 > class2
Rank Product analysis for unpaired case
done Table1: Genes called significant under class1 < class2
Table2: Genes called significant under class1 > class2
[ FAIL 0 | WARN 692 | SKIP 0 | PASS 312 ]
[ FAIL 0 | WARN 692 | SKIP 0 | PASS 312 ]
>
> proc.time()
user system elapsed
201.722 6.070 207.891
POMA.Rcheck/POMA-Ex.timings
| name | user | system | elapsed | |
| PomaBoxplots | 15.369 | 0.469 | 15.838 | |
| PomaClust | 0.460 | 0.040 | 0.499 | |
| PomaCorr | 1.163 | 0.008 | 1.171 | |
| PomaDESeq | 4.674 | 0.099 | 4.774 | |
| PomaDensity | 2.820 | 0.176 | 2.995 | |
| PomaHeatmap | 1.610 | 0.073 | 1.682 | |
| PomaImpute | 0.051 | 0.004 | 0.055 | |
| PomaLasso | 1.944 | 0.048 | 1.992 | |
| PomaLimma | 0.297 | 0.000 | 0.297 | |
| PomaMultivariate | 21.163 | 0.735 | 21.931 | |
| PomaNorm | 0.073 | 0.004 | 0.077 | |
| PomaOddsRatio | 0.231 | 0.016 | 0.247 | |
| PomaOutliers | 0.626 | 0.004 | 0.630 | |
| PomaPCR | 0.279 | 0.004 | 0.283 | |
| PomaRandForest | 0.378 | 0.020 | 0.398 | |
| PomaRankProd | 1.889 | 0.108 | 1.998 | |
| PomaSummarizedExperiment | 0.021 | 0.000 | 0.021 | |
| PomaUMAP | 3.489 | 0.044 | 3.532 | |
| PomaUnivariate | 1.007 | 0.036 | 1.043 | |
| PomaVolcano | 5.051 | 0.092 | 5.143 | |