Back to Multiple platform build/check report for BioC 3.11
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for BatchQC on tokay2

This page was generated on 2020-10-17 11:56:07 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BatchQC PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 120/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BatchQC 1.16.3
Solaiappan Manimaran
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/BatchQC
Branch: RELEASE_3_11
Last Commit: e8ec016
Last Changed Date: 2020-10-11 21:45:57 -0400 (Sun, 11 Oct 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BatchQC
Version: 1.16.3
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BatchQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings BatchQC_1.16.3.tar.gz
StartedAt: 2020-10-17 01:46:14 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:51:36 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 322.2 seconds
RetCode: 0
Status:  OK  
CheckDir: BatchQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BatchQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings BatchQC_1.16.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/BatchQC.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BatchQC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BatchQC' version '1.16.3'
* 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 whether package 'BatchQC' 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
gene_plot: no visible global function definition for 'boxplot'
gene_plot: no visible binding for global variable 'batch'
gls.series.C: no visible global function definition for 'lm.fit'
sample_plot: no visible global function definition for 'boxplot'
sample_plot: no visible binding for global variable 'batch'
Undefined global functions or variables:
  batch boxplot lm.fit
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "lm.fit")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
batchQC 2.74   0.53    8.02
** running examples for arch 'x64' ... OK
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/BatchQC.Rcheck/00check.log'
for details.



Installation output

BatchQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/BatchQC_1.16.3.tar.gz && rm -rf BatchQC.buildbin-libdir && mkdir BatchQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BatchQC.buildbin-libdir BatchQC_1.16.3.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL BatchQC_1.16.3.zip && rm BatchQC_1.16.3.tar.gz BatchQC_1.16.3.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1261k  100 1261k    0     0  3504k      0 --:--:-- --:--:-- --:--:-- 3574k

install for i386

* installing *source* package 'BatchQC' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BatchQC'
    finding HTML links ... done
    BatchQCout-class                        html  
    batchQC                                 html  
    batchQC_analyze                         html  
    batchQC_condition_adjusted              html  
    batchQC_filter_genes                    html  
    batchQC_fsva_adjusted                   html  
    batchQC_num.sv                          html  
    batchQC_shapeVariation                  html  
    batchQC_sva                             html  
    batchQC_svregress_adjusted              html  
    batchqc_circosplot                      html  
    batchqc_correlation                     html  
    batchqc_corscatter                      html  
    batchqc_explained_variation             html  
    batchqc_heatmap                         html  
    batchqc_pc_explained_variation          html  
    batchqc_pca                             html  
    batchqc_pca_svd                         html  
    batchtest                               html  
    combatPlot                              html  
    example_batchqc_data                    html  
    getShinyInput                           html  
    getShinyInputCombat                     html  
    getShinyInputOrig                       html  
    getShinyInputSVA                        html  
    getShinyInputSVAf                       html  
    getShinyInputSVAr                       html  
    gnormalize                              html  
    lmFitC                                  html  
    log2CPM                                 html  
    makeSVD                                 html  
    pcRes                                   html  
    plotPC                                  html  
    plot_genewise_moments                   html  
    plot_samplewise_moments                 html  
    protein_example_data                    html  
    rnaseq_sim                              html  
    setShinyInput                           html  
    setShinyInputCombat                     html  
    setShinyInputOrig                       html  
    setShinyInputSVA                        html  
    setShinyInputSVAf                       html  
    setShinyInputSVAr                       html  
** 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 'BatchQC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BatchQC' as BatchQC_1.16.3.zip
* DONE (BatchQC)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'BatchQC' successfully unpacked and MD5 sums checked

Tests output

BatchQC.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(BatchQC)
> 
> test_check("BatchQC")

Call:
lm(formula = pc[, 1] ~ fbatch)

Residuals:
    Min      1Q  Median      3Q     Max 
-2.7762 -1.1421 -0.0791  1.2867  2.4370 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept)  -6.1453     0.3425  -17.94   <2e-16 ***
fbatch2       5.9121     0.4843   12.21   <2e-16 ***
fbatch3      12.5239     0.4843   25.86   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 1.532 on 57 degrees of freedom
Multiple R-squared:  0.9215,	Adjusted R-squared:  0.9188 
F-statistic: 334.7 on 2 and 57 DF,  p-value: < 2.2e-16


Call:
lm(formula = pc[, 2] ~ fbatch)

Residuals:
    Min      1Q  Median      3Q     Max 
-3.7216 -0.6493  0.0871  0.8373  2.9491 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)
(Intercept)  0.17183    0.27913   0.616    0.541
fbatch2     -0.43845    0.39476  -1.111    0.271
fbatch3     -0.07704    0.39476  -0.195    0.846

Residual standard error: 1.248 on 57 degrees of freedom
Multiple R-squared:  0.02408,	Adjusted R-squared:  -0.01016 
F-statistic: 0.7033 on 2 and 57 DF,  p-value: 0.4992


Call:
lm(formula = pc[, 3] ~ fbatch)

Residuals:
    Min      1Q  Median      3Q     Max 
-5.0250 -0.5986  0.1308  0.8576  2.2028 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)
(Intercept) -0.064898   0.274133  -0.237    0.814
fbatch2     -0.001188   0.387682  -0.003    0.998
fbatch3      0.195881   0.387682   0.505    0.615

Residual standard error: 1.226 on 57 degrees of freedom
Multiple R-squared:  0.005972,	Adjusted R-squared:  -0.02891 
F-statistic: 0.1712 on 2 and 57 DF,  p-value: 0.8431


Call:
lm(formula = pc[, 4] ~ fbatch)

Residuals:
    Min      1Q  Median      3Q     Max 
-3.2343 -0.7732 -0.0477  0.5829  2.3069 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)
(Intercept) -0.11821    0.25723  -0.460    0.648
fbatch2      0.39746    0.36377   1.093    0.279
fbatch3     -0.04282    0.36377  -0.118    0.907

Residual standard error: 1.15 on 57 degrees of freedom
Multiple R-squared:  0.03031,	Adjusted R-squared:  -0.003715 
F-statistic: 0.8908 on 2 and 57 DF,  p-value: 0.416


Call:
lm(formula = pc[, 5] ~ fbatch)

Residuals:
     Min       1Q   Median       3Q      Max 
-2.56418 -0.65298  0.05001  0.75678  2.38403 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)
(Intercept)   0.1416     0.2443   0.580    0.564
fbatch2      -0.2357     0.3455  -0.682    0.498
fbatch3      -0.1891     0.3455  -0.547    0.586

Residual standard error: 1.092 on 57 degrees of freedom
Multiple R-squared:  0.00908,	Adjusted R-squared:  -0.02569 
F-statistic: 0.2612 on 2 and 57 DF,  p-value: 0.7711

   inline R code fragments

label: unnamed-chunk-1 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-2 (with options) 
List of 3
 $ eval   : symbol eval_cell_1
 $ echo   : logi FALSE
 $ message: logi FALSE

   inline R code fragments

label: unnamed-chunk-3 (with options) 
List of 3
 $ eval   : symbol eval_cell_1
 $ echo   : logi FALSE
 $ message: logi FALSE

   inline R code fragments

label: unnamed-chunk-4 (with options) 
List of 5
 $ eval      : symbol eval_cell_1
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 8
 $ fig.height: num 5

  ordinary text without R code

label: unnamed-chunk-5 (with options) 
List of 3
 $ eval   : symbol eval_cell_1
 $ echo   : logi FALSE
 $ message: logi FALSE

   inline R code fragments

label: unnamed-chunk-6 (with options) 
List of 3
 $ eval   : symbol eval_cell_1
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: unnamed-chunk-7 (with options) 
List of 5
 $ eval      : symbol eval_cell_1
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 8
 $ fig.height: num 5

  ordinary text without R code

label: unnamed-chunk-8 (with options) 
List of 5
 $ eval      : symbol eval_cell_1
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 8
 $ fig.height: num 5

  ordinary text without R code

label: unnamed-chunk-9 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-10 (with options) 
List of 5
 $ eval      : symbol eval_cell_2
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 8
 $ fig.height: num 5

   inline R code fragments

label: unnamed-chunk-11 (with options) 
List of 3
 $ eval   : symbol eval_cell_2
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: unnamed-chunk-12 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-13 (with options) 
List of 5
 $ eval      : symbol eval_cell_3
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 8
 $ fig.height: num 4

  ordinary text without R code

label: unnamed-chunk-14 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-15 (with options) 
List of 5
 $ eval      : symbol eval_cell_4
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 8
 $ fig.height: num 8

   inline R code fragments

label: unnamed-chunk-16 (with options) 
List of 5
 $ eval      : symbol eval_cell_4
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 8
 $ fig.height: num 8

  ordinary text without R code

label: unnamed-chunk-17 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-18 (with options) 
List of 5
 $ eval      : symbol eval_cell_5
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 5
 $ fig.height: num 5

  ordinary text without R code

label: unnamed-chunk-19 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-20 (with options) 
List of 5
 $ eval      : symbol eval_cell_6
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 6
 $ fig.height: num 6

   inline R code fragments

label: unnamed-chunk-21 (with options) 
List of 3
 $ eval   : symbol eval_cell_6
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: unnamed-chunk-22 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-23 (with options) 
List of 5
 $ eval      : symbol eval_cell_7
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 9
 $ fig.height: num 5

  ordinary text without R code

label: unnamed-chunk-24 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-25 (with options) 
List of 3
 $ eval   : symbol eval_cell_8
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: unnamed-chunk-26 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-27 (with options) 
List of 3
 $ eval   : symbol eval_cell_9
 $ echo   : logi FALSE
 $ message: logi FALSE

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS batchqc_report.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc187062cd6891.html --lua-filter "C:\Users\biocbuild\bbs-3.11-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.11-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --email-obfuscation none --standalone --section-divs --table-of-contents --toc-depth 2 --template batchQC.html --highlight-style pygments --css "C:/Users/biocbuild/bbs-3.11-bioc/R/library/rmarkdown/rmarkdown/templates/html_vignette/resources/vignette.css" --include-in-header "C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\Rtmp6FRBcw\rmarkdown-str18705fd47b13.html" --mathjax 
Found 3 batches
Adjusting for 1 covariate(s) or covariate level(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Number of significant surrogate variables is:  1 
Iteration (out of 5 ):1  2  3  4  5  Number of significant surrogate variables is:  1 
Iteration (out of 5 ):1  2  3  4  5  
Call:
lm(formula = pc[, 1] ~ fbatch + fcond)

Residuals:
     Min       1Q   Median       3Q      Max 
-1.95358 -0.45328  0.04717  0.60252  1.57878 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept)  -7.4258     0.2051  -36.20   <2e-16 ***
fbatch2       5.9121     0.2512   23.53   <2e-16 ***
fbatch3      12.5239     0.2512   49.85   <2e-16 ***
fcond1        2.5608     0.2051   12.48   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.7945 on 56 degrees of freedom
Multiple R-squared:  0.9793,	Adjusted R-squared:  0.9781 
F-statistic: 881.1 on 3 and 56 DF,  p-value: < 2.2e-16


Call:
lm(formula = pc[, 2] ~ fbatch + fcond)

Residuals:
    Min      1Q  Median      3Q     Max 
-3.7975 -0.6522  0.1296  0.7709  2.8918 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)
(Intercept)  0.09594    0.32455   0.296    0.769
fbatch2     -0.43845    0.39749  -1.103    0.275
fbatch3     -0.07704    0.39749  -0.194    0.847
fcond1       0.15179    0.32455   0.468    0.642

Residual standard error: 1.257 on 56 degrees of freedom
Multiple R-squared:  0.02788,	Adjusted R-squared:  -0.0242 
F-statistic: 0.5354 on 3 and 56 DF,  p-value: 0.66


Call:
lm(formula = pc[, 3] ~ fbatch + fcond)

Residuals:
    Min      1Q  Median      3Q     Max 
-4.6201 -0.6683  0.2035  0.6785  2.6077 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)   
(Intercept)  0.339994   0.300463   1.132  0.26264   
fbatch2     -0.001188   0.367990  -0.003  0.99744   
fbatch3      0.195881   0.367990   0.532  0.59663   
fcond1      -0.809783   0.300463  -2.695  0.00927 **
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 1.164 on 56 degrees of freedom
Multiple R-squared:  0.1201,	Adjusted R-squared:  0.07296 
F-statistic: 2.548 on 3 and 56 DF,  p-value: 0.06497


Call:
lm(formula = pc[, 4] ~ fbatch + fcond)

Residuals:
    Min      1Q  Median      3Q     Max 
-3.3476 -0.7101 -0.0702  0.6425  2.4201 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)
(Intercept) -0.23142    0.29813  -0.776    0.441
fbatch2      0.39746    0.36513   1.089    0.281
fbatch3     -0.04282    0.36513  -0.117    0.907
fcond1       0.22641    0.29813   0.759    0.451

Residual standard error: 1.155 on 56 degrees of freedom
Multiple R-squared:  0.04019,	Adjusted R-squared:  -0.01122 
F-statistic: 0.7817 on 3 and 56 DF,  p-value: 0.5091


Call:
lm(formula = pc[, 5] ~ fbatch + fcond)

Residuals:
    Min      1Q  Median      3Q     Max 
-2.6261 -0.7063  0.0244  0.7560  2.1307 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)  
(Intercept)  -0.1117     0.2764  -0.404   0.6877  
fbatch2      -0.2357     0.3385  -0.696   0.4891  
fbatch3      -0.1891     0.3385  -0.559   0.5787  
fcond1        0.5066     0.2764   1.833   0.0721 .
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 1.071 on 56 degrees of freedom
Multiple R-squared:  0.06516,	Adjusted R-squared:  0.01508 
F-statistic: 1.301 on 3 and 56 DF,  p-value: 0.2831

== testthat results  ===========================================================
[ OK: 16 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  13.28    1.31   15.54 

BatchQC.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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(BatchQC)
> 
> test_check("BatchQC")

Call:
lm(formula = pc[, 1] ~ fbatch)

Residuals:
    Min      1Q  Median      3Q     Max 
-2.7762 -1.1421 -0.0791  1.2867  2.4370 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept)  -6.1453     0.3425  -17.94   <2e-16 ***
fbatch2       5.9121     0.4843   12.21   <2e-16 ***
fbatch3      12.5239     0.4843   25.86   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 1.532 on 57 degrees of freedom
Multiple R-squared:  0.9215,	Adjusted R-squared:  0.9188 
F-statistic: 334.7 on 2 and 57 DF,  p-value: < 2.2e-16


Call:
lm(formula = pc[, 2] ~ fbatch)

Residuals:
    Min      1Q  Median      3Q     Max 
-3.7216 -0.6493  0.0871  0.8373  2.9491 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)
(Intercept)  0.17183    0.27913   0.616    0.541
fbatch2     -0.43845    0.39476  -1.111    0.271
fbatch3     -0.07704    0.39476  -0.195    0.846

Residual standard error: 1.248 on 57 degrees of freedom
Multiple R-squared:  0.02408,	Adjusted R-squared:  -0.01016 
F-statistic: 0.7033 on 2 and 57 DF,  p-value: 0.4992


Call:
lm(formula = pc[, 3] ~ fbatch)

Residuals:
    Min      1Q  Median      3Q     Max 
-5.0250 -0.5986  0.1308  0.8576  2.2028 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)
(Intercept) -0.064898   0.274133  -0.237    0.814
fbatch2     -0.001188   0.387682  -0.003    0.998
fbatch3      0.195881   0.387682   0.505    0.615

Residual standard error: 1.226 on 57 degrees of freedom
Multiple R-squared:  0.005972,	Adjusted R-squared:  -0.02891 
F-statistic: 0.1712 on 2 and 57 DF,  p-value: 0.8431


Call:
lm(formula = pc[, 4] ~ fbatch)

Residuals:
    Min      1Q  Median      3Q     Max 
-3.2343 -0.7732 -0.0477  0.5829  2.3069 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)
(Intercept) -0.11821    0.25723  -0.460    0.648
fbatch2      0.39746    0.36377   1.093    0.279
fbatch3     -0.04282    0.36377  -0.118    0.907

Residual standard error: 1.15 on 57 degrees of freedom
Multiple R-squared:  0.03031,	Adjusted R-squared:  -0.003715 
F-statistic: 0.8908 on 2 and 57 DF,  p-value: 0.416


Call:
lm(formula = pc[, 5] ~ fbatch)

Residuals:
     Min       1Q   Median       3Q      Max 
-2.56418 -0.65298  0.05001  0.75678  2.38403 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)
(Intercept)   0.1416     0.2443   0.580    0.564
fbatch2      -0.2357     0.3455  -0.682    0.498
fbatch3      -0.1891     0.3455  -0.547    0.586

Residual standard error: 1.092 on 57 degrees of freedom
Multiple R-squared:  0.00908,	Adjusted R-squared:  -0.02569 
F-statistic: 0.2612 on 2 and 57 DF,  p-value: 0.7711

   inline R code fragments

label: unnamed-chunk-1 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-2 (with options) 
List of 3
 $ eval   : symbol eval_cell_1
 $ echo   : logi FALSE
 $ message: logi FALSE

   inline R code fragments

label: unnamed-chunk-3 (with options) 
List of 3
 $ eval   : symbol eval_cell_1
 $ echo   : logi FALSE
 $ message: logi FALSE

   inline R code fragments

label: unnamed-chunk-4 (with options) 
List of 5
 $ eval      : symbol eval_cell_1
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 8
 $ fig.height: num 5

  ordinary text without R code

label: unnamed-chunk-5 (with options) 
List of 3
 $ eval   : symbol eval_cell_1
 $ echo   : logi FALSE
 $ message: logi FALSE

   inline R code fragments

label: unnamed-chunk-6 (with options) 
List of 3
 $ eval   : symbol eval_cell_1
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: unnamed-chunk-7 (with options) 
List of 5
 $ eval      : symbol eval_cell_1
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 8
 $ fig.height: num 5

  ordinary text without R code

label: unnamed-chunk-8 (with options) 
List of 5
 $ eval      : symbol eval_cell_1
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 8
 $ fig.height: num 5

  ordinary text without R code

label: unnamed-chunk-9 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-10 (with options) 
List of 5
 $ eval      : symbol eval_cell_2
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 8
 $ fig.height: num 5

   inline R code fragments

label: unnamed-chunk-11 (with options) 
List of 3
 $ eval   : symbol eval_cell_2
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: unnamed-chunk-12 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-13 (with options) 
List of 5
 $ eval      : symbol eval_cell_3
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 8
 $ fig.height: num 4

  ordinary text without R code

label: unnamed-chunk-14 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-15 (with options) 
List of 5
 $ eval      : symbol eval_cell_4
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 8
 $ fig.height: num 8

   inline R code fragments

label: unnamed-chunk-16 (with options) 
List of 5
 $ eval      : symbol eval_cell_4
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 8
 $ fig.height: num 8

  ordinary text without R code

label: unnamed-chunk-17 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-18 (with options) 
List of 5
 $ eval      : symbol eval_cell_5
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 5
 $ fig.height: num 5

  ordinary text without R code

label: unnamed-chunk-19 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-20 (with options) 
List of 5
 $ eval      : symbol eval_cell_6
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 6
 $ fig.height: num 6

   inline R code fragments

label: unnamed-chunk-21 (with options) 
List of 3
 $ eval   : symbol eval_cell_6
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: unnamed-chunk-22 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-23 (with options) 
List of 5
 $ eval      : symbol eval_cell_7
 $ echo      : logi FALSE
 $ message   : logi FALSE
 $ fig.width : num 9
 $ fig.height: num 5

  ordinary text without R code

label: unnamed-chunk-24 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-25 (with options) 
List of 3
 $ eval   : symbol eval_cell_8
 $ echo   : logi FALSE
 $ message: logi FALSE

  ordinary text without R code

label: unnamed-chunk-26 (with options) 
List of 1
 $ echo: logi FALSE

   inline R code fragments

label: unnamed-chunk-27 (with options) 
List of 3
 $ eval   : symbol eval_cell_9
 $ echo   : logi FALSE
 $ message: logi FALSE

"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS batchqc_report.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandocb6811094070.html --lua-filter "C:\Users\biocbuild\bbs-3.11-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.11-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --email-obfuscation none --standalone --section-divs --table-of-contents --toc-depth 2 --template batchQC.html --highlight-style pygments --css "C:/Users/biocbuild/bbs-3.11-bioc/R/library/rmarkdown/rmarkdown/templates/html_vignette/resources/vignette.css" --include-in-header "C:\Users\biocbuild\bbs-3.11-bioc\tmpdir\RtmpGiO5mu\rmarkdown-strb682a0016a4.html" --mathjax 
Found 3 batches
Adjusting for 1 covariate(s) or covariate level(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Number of significant surrogate variables is:  1 
Iteration (out of 5 ):1  2  3  4  5  Number of significant surrogate variables is:  1 
Iteration (out of 5 ):1  2  3  4  5  
Call:
lm(formula = pc[, 1] ~ fbatch + fcond)

Residuals:
     Min       1Q   Median       3Q      Max 
-1.95358 -0.45328  0.04717  0.60252  1.57878 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept)  -7.4258     0.2051  -36.20   <2e-16 ***
fbatch2       5.9121     0.2512   23.53   <2e-16 ***
fbatch3      12.5239     0.2512   49.85   <2e-16 ***
fcond1        2.5608     0.2051   12.48   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.7945 on 56 degrees of freedom
Multiple R-squared:  0.9793,	Adjusted R-squared:  0.9781 
F-statistic: 881.1 on 3 and 56 DF,  p-value: < 2.2e-16


Call:
lm(formula = pc[, 2] ~ fbatch + fcond)

Residuals:
    Min      1Q  Median      3Q     Max 
-3.7975 -0.6522  0.1296  0.7709  2.8918 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)
(Intercept)  0.09594    0.32455   0.296    0.769
fbatch2     -0.43845    0.39749  -1.103    0.275
fbatch3     -0.07704    0.39749  -0.194    0.847
fcond1       0.15179    0.32455   0.468    0.642

Residual standard error: 1.257 on 56 degrees of freedom
Multiple R-squared:  0.02788,	Adjusted R-squared:  -0.0242 
F-statistic: 0.5354 on 3 and 56 DF,  p-value: 0.66


Call:
lm(formula = pc[, 3] ~ fbatch + fcond)

Residuals:
    Min      1Q  Median      3Q     Max 
-4.6201 -0.6683  0.2035  0.6785  2.6077 

Coefficients:
             Estimate Std. Error t value Pr(>|t|)   
(Intercept)  0.339994   0.300463   1.132  0.26264   
fbatch2     -0.001188   0.367990  -0.003  0.99744   
fbatch3      0.195881   0.367990   0.532  0.59663   
fcond1      -0.809783   0.300463  -2.695  0.00927 **
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 1.164 on 56 degrees of freedom
Multiple R-squared:  0.1201,	Adjusted R-squared:  0.07296 
F-statistic: 2.548 on 3 and 56 DF,  p-value: 0.06497


Call:
lm(formula = pc[, 4] ~ fbatch + fcond)

Residuals:
    Min      1Q  Median      3Q     Max 
-3.3476 -0.7101 -0.0702  0.6425  2.4201 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)
(Intercept) -0.23142    0.29813  -0.776    0.441
fbatch2      0.39746    0.36513   1.089    0.281
fbatch3     -0.04282    0.36513  -0.117    0.907
fcond1       0.22641    0.29813   0.759    0.451

Residual standard error: 1.155 on 56 degrees of freedom
Multiple R-squared:  0.04019,	Adjusted R-squared:  -0.01122 
F-statistic: 0.7817 on 3 and 56 DF,  p-value: 0.5091


Call:
lm(formula = pc[, 5] ~ fbatch + fcond)

Residuals:
    Min      1Q  Median      3Q     Max 
-2.6261 -0.7063  0.0244  0.7560  2.1307 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)  
(Intercept)  -0.1117     0.2764  -0.404   0.6877  
fbatch2      -0.2357     0.3385  -0.696   0.4891  
fbatch3      -0.1891     0.3385  -0.559   0.5787  
fcond1        0.5066     0.2764   1.833   0.0721 .
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 1.071 on 56 degrees of freedom
Multiple R-squared:  0.06516,	Adjusted R-squared:  0.01508 
F-statistic: 1.301 on 3 and 56 DF,  p-value: 0.2831

== testthat results  ===========================================================
[ OK: 16 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  11.39    1.01   13.01 

Example timings

BatchQC.Rcheck/examples_i386/BatchQC-Ex.timings

nameusersystemelapsed
batchQC2.740.538.02
batchQC_analyze0.280.050.33
batchQC_condition_adjusted0.030.010.05
batchQC_filter_genes0.040.000.05
batchQC_fsva_adjusted0.240.020.25
batchQC_num.sv0.120.000.12
batchQC_shapeVariation0.110.000.11
batchQC_sva0.220.000.22
batchQC_svregress_adjusted0.200.010.22
batchqc_circosplot0.130.000.12
batchqc_correlation0.250.000.25
batchqc_corscatter0.060.000.07
batchqc_explained_variation0.030.000.03
batchqc_heatmap0.240.000.23
batchqc_pc_explained_variation0.040.000.05
batchqc_pca0.070.000.06
batchqc_pca_svd0.200.020.22
batchtest0.060.000.06
combatPlot0.070.000.07
getShinyInput0.090.030.12
getShinyInputCombat000
getShinyInputOrig0.080.030.11
getShinyInputSVA000
getShinyInputSVAf000
getShinyInputSVAr000
gnormalize000
log2CPM0.060.000.06
plot_genewise_moments0.190.000.19
plot_samplewise_moments0.110.000.11
rnaseq_sim0.260.030.30
setShinyInput000
setShinyInputCombat000
setShinyInputOrig000
setShinyInputSVA000
setShinyInputSVAf000
setShinyInputSVAr000

BatchQC.Rcheck/examples_x64/BatchQC-Ex.timings

nameusersystemelapsed
batchQC2.720.393.75
batchQC_analyze0.330.020.34
batchQC_condition_adjusted0.050.000.05
batchQC_filter_genes0.060.000.06
batchQC_fsva_adjusted0.270.000.27
batchQC_num.sv0.750.000.75
batchQC_shapeVariation0.090.000.09
batchQC_sva0.230.000.23
batchQC_svregress_adjusted0.240.000.24
batchqc_circosplot0.140.000.14
batchqc_correlation0.190.000.19
batchqc_corscatter0.040.000.04
batchqc_explained_variation0.020.000.02
batchqc_heatmap0.110.010.12
batchqc_pc_explained_variation0.030.000.03
batchqc_pca0.030.020.05
batchqc_pca_svd0.130.000.13
batchtest0.040.000.04
combatPlot0.070.000.07
getShinyInput0.060.050.11
getShinyInputCombat000
getShinyInputOrig0.040.010.06
getShinyInputSVA000
getShinyInputSVAf000
getShinyInputSVAr000
gnormalize000
log2CPM0.040.000.03
plot_genewise_moments0.10.00.1
plot_samplewise_moments0.040.000.05
rnaseq_sim0.110.050.16
setShinyInput000
setShinyInputCombat000
setShinyInputOrig000
setShinyInputSVA000
setShinyInputSVAf000
setShinyInputSVAr000