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) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
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 120/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BatchQC 1.16.3 Solaiappan Manimaran
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: 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 |
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###
### 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
###
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* 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.
BatchQC.Rcheck/00install.out
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###
### 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
###
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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
|
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
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"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
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"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
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BatchQC.Rcheck/examples_i386/BatchQC-Ex.timings
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BatchQC.Rcheck/examples_x64/BatchQC-Ex.timings
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