Solaiappan Manimaran
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/BatchQC |
| Branch: master |
| Last Commit: 8ee9568 |
| Last Changed Date: 2019-04-07 17:02:13 -0400 (Sun, 07 Apr 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:33:11 -0400 (Tue, 09 Apr 2019).
| Package 108/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BatchQC 1.11.3 Solaiappan Manimaran
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
| Package: BatchQC |
| Version: 1.11.3 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BatchQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BatchQC_1.11.3.tar.gz |
| StartedAt: 2019-04-08 23:23:11 -0400 (Mon, 08 Apr 2019) |
| EndedAt: 2019-04-08 23:25:59 -0400 (Mon, 08 Apr 2019) |
| EllapsedTime: 168.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BatchQC.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BatchQC.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BatchQC_1.11.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/BatchQC.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BatchQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BatchQC’ version ‘1.11.3’
* 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 ‘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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
batchQC 4.563 0.667 5.255
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/BatchQC.Rcheck/00check.log’
for details.
BatchQC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BatchQC ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘BatchQC’ ... ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (BatchQC)
BatchQC.Rcheck/tests/testthat.Rout
R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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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/usr/local/bin/pandoc +RTS -K512m -RTS batchqc_report.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output /Users/biocbuild/bbs-3.9-bioc/meat/BatchQC.Rcheck/tests/testthat/batchqc_report.html --email-obfuscation none --standalone --section-divs --table-of-contents --toc-depth 2 --template batchQC.html --highlight-style pygments --css /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rmarkdown/rmarkdown/templates/html_vignette/resources/vignette.css --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 FAILED: 0
>
> proc.time()
user system elapsed
12.741 1.106 13.936
BatchQC.Rcheck/BatchQC-Ex.timings
| name | user | system | elapsed | |
| batchQC | 4.563 | 0.667 | 5.255 | |
| batchQC_analyze | 0.259 | 0.015 | 0.274 | |
| batchQC_condition_adjusted | 0.041 | 0.016 | 0.059 | |
| batchQC_filter_genes | 0.055 | 0.005 | 0.059 | |
| batchQC_fsva_adjusted | 0.218 | 0.023 | 0.249 | |
| batchQC_num.sv | 0.115 | 0.006 | 0.123 | |
| batchQC_shapeVariation | 0.097 | 0.003 | 0.104 | |
| batchQC_sva | 0.189 | 0.009 | 0.198 | |
| batchQC_svregress_adjusted | 0.196 | 0.016 | 0.211 | |
| batchqc_circosplot | 0.135 | 0.004 | 0.139 | |
| batchqc_correlation | 0.221 | 0.002 | 0.226 | |
| batchqc_corscatter | 0.072 | 0.005 | 0.079 | |
| batchqc_explained_variation | 0.032 | 0.006 | 0.038 | |
| batchqc_heatmap | 0.218 | 0.003 | 0.224 | |
| batchqc_pc_explained_variation | 0.044 | 0.004 | 0.050 | |
| batchqc_pca | 0.038 | 0.012 | 0.051 | |
| batchqc_pca_svd | 0.216 | 0.004 | 0.223 | |
| batchtest | 0.075 | 0.013 | 0.091 | |
| combatPlot | 0.060 | 0.006 | 0.068 | |
| getShinyInput | 0.121 | 0.084 | 0.206 | |
| getShinyInputCombat | 0.000 | 0.000 | 0.001 | |
| getShinyInputOrig | 0.096 | 0.055 | 0.151 | |
| getShinyInputSVA | 0.000 | 0.001 | 0.000 | |
| getShinyInputSVAf | 0.000 | 0.000 | 0.001 | |
| getShinyInputSVAr | 0 | 0 | 0 | |
| gnormalize | 0.001 | 0.001 | 0.001 | |
| log2CPM | 0.064 | 0.014 | 0.079 | |
| plot_genewise_moments | 0.205 | 0.005 | 0.212 | |
| plot_samplewise_moments | 0.105 | 0.001 | 0.111 | |
| rnaseq_sim | 0.214 | 0.079 | 0.298 | |
| setShinyInput | 0 | 0 | 0 | |
| setShinyInputCombat | 0.000 | 0.000 | 0.001 | |
| setShinyInputOrig | 0.000 | 0.000 | 0.001 | |
| setShinyInputSVA | 0 | 0 | 0 | |
| setShinyInputSVAf | 0 | 0 | 0 | |
| setShinyInputSVAr | 0.001 | 0.000 | 0.001 | |