Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:58 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the BatchQC package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BatchQC.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 126/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BatchQC 1.20.0 (landing page) Solaiappan Manimaran
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: BatchQC |
Version: 1.20.0 |
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BatchQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BatchQC_1.20.0.tar.gz |
StartedAt: 2021-10-14 19:54:08 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 19:58:43 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 274.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: BatchQC.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BatchQC.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BatchQC_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BatchQC.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'BatchQC/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'BatchQC' version '1.20.0' * 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 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 ** 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-3.13-bioc/meat/BatchQC.Rcheck/00check.log' for details.
BatchQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BatchQC_1.20.0.tar.gz && rm -rf BatchQC.buildbin-libdir && mkdir BatchQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BatchQC.buildbin-libdir BatchQC_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BatchQC_1.20.0.zip && rm BatchQC_1.20.0.tar.gz BatchQC_1.20.0.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 1264k 100 1264k 0 0 2402k 0 --:--:-- --:--:-- --:--:-- 2408k 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_1.20.0.zip * DONE (BatchQC) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'BatchQC' successfully unpacked and MD5 sums checked
BatchQC.Rcheck/tests_i386/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(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 : logi TRUE $ echo : logi FALSE $ message: logi FALSE inline R code fragments label: unnamed-chunk-3 (with options) List of 3 $ eval : logi TRUE $ echo : logi FALSE $ message: logi FALSE inline R code fragments label: unnamed-chunk-4 (with options) List of 5 $ eval : logi TRUE $ 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 : logi TRUE $ echo : logi FALSE $ message: logi FALSE inline R code fragments label: unnamed-chunk-6 (with options) List of 3 $ eval : logi TRUE $ echo : logi FALSE $ message: logi FALSE ordinary text without R code label: unnamed-chunk-7 (with options) List of 5 $ eval : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ echo : logi FALSE $ message: logi FALSE "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS batchqc_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc1e8847197996.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --standalone --section-divs --table-of-contents --toc-depth 2 --template batchQC.html --highlight-style pygments --css "C:/Users/biocbuild/bbs-3.13-bioc/R/library/rmarkdown/rmarkdown/templates/html_vignette/resources/vignette.css" --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpYP4lCZ\rmarkdown-str1e8868116256.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 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ] > > proc.time() user system elapsed 11.21 1.10 13.26 |
BatchQC.Rcheck/tests_x64/testthat.Rout R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(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 : logi TRUE $ echo : logi FALSE $ message: logi FALSE inline R code fragments label: unnamed-chunk-3 (with options) List of 3 $ eval : logi TRUE $ echo : logi FALSE $ message: logi FALSE inline R code fragments label: unnamed-chunk-4 (with options) List of 5 $ eval : logi TRUE $ 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 : logi TRUE $ echo : logi FALSE $ message: logi FALSE inline R code fragments label: unnamed-chunk-6 (with options) List of 3 $ eval : logi TRUE $ echo : logi FALSE $ message: logi FALSE ordinary text without R code label: unnamed-chunk-7 (with options) List of 5 $ eval : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ 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 : logi TRUE $ echo : logi FALSE $ message: logi FALSE "C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS batchqc_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc17606caa8fb.html --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.13-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" --standalone --section-divs --table-of-contents --toc-depth 2 --template batchQC.html --highlight-style pygments --css "C:/Users/biocbuild/bbs-3.13-bioc/R/library/rmarkdown/rmarkdown/templates/html_vignette/resources/vignette.css" --include-in-header "C:\Users\biocbuild\bbs-3.13-bioc\tmpdir\RtmpK6Gu7v\rmarkdown-str1760345570bc.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 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ] > > proc.time() user system elapsed 10.84 1.01 12.31 |
BatchQC.Rcheck/examples_i386/BatchQC-Ex.timings
|
BatchQC.Rcheck/examples_x64/BatchQC-Ex.timings
|