Back to Multiple platform build/check report for BioC 3.14
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-18 12:03:36 -0400 (Mon, 18 Oct 2021).

CHECK results for BatchQC on nebbiolo2

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.

raw results

Package 123/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BatchQC 1.21.0  (landing page)
Solaiappan Manimaran
Snapshot Date: 2021-10-17 14:50:03 -0400 (Sun, 17 Oct 2021)
git_url: https://git.bioconductor.org/packages/BatchQC
git_branch: master
git_last_commit: 31e710c
git_last_commit_date: 2021-05-19 12:19:44 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BatchQC
Version: 1.21.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BatchQC.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BatchQC_1.21.0.tar.gz
StartedAt: 2021-10-17 19:09:07 -0400 (Sun, 17 Oct 2021)
EndedAt: 2021-10-17 19:11:49 -0400 (Sun, 17 Oct 2021)
EllapsedTime: 161.8 seconds
RetCode: 0
Status:   OK  
CheckDir: BatchQC.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BatchQC.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BatchQC_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/BatchQC.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.21.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/BatchQC.Rcheck/00check.log’
for details.



Installation output

BatchQC.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL BatchQC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘BatchQC’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BatchQC)

Tests output

BatchQC.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(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

/usr/bin/pandoc +RTS -K512m -RTS batchqc_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /home/biocbuild/bbs-3.14-bioc/meat/BatchQC.Rcheck/tests/testthat/batchqc_report.html --lua-filter /home/biocbuild/bbs-3.14-bioc/R/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.14-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 /home/biocbuild/bbs-3.14-bioc/R/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

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
 10.742   0.730  11.470 

Example timings

BatchQC.Rcheck/BatchQC-Ex.timings

nameusersystemelapsed
batchQC2.5040.1262.642
batchQC_analyze0.1510.0000.151
batchQC_condition_adjusted0.0240.0000.024
batchQC_filter_genes0.0340.0000.033
batchQC_fsva_adjusted0.1230.0080.130
batchQC_num.sv0.0780.0000.078
batchQC_shapeVariation0.0430.0000.044
batchQC_sva0.1360.0000.137
batchQC_svregress_adjusted0.1240.0040.129
batchqc_circosplot0.0660.0000.066
batchqc_correlation0.1340.0000.133
batchqc_corscatter0.0340.0000.034
batchqc_explained_variation0.0280.0000.027
batchqc_heatmap0.1030.0080.111
batchqc_pc_explained_variation0.0360.0000.035
batchqc_pca0.0180.0070.026
batchqc_pca_svd0.1110.0010.111
batchtest0.0460.0040.050
combatPlot0.0310.0000.031
getShinyInput0.0320.0240.055
getShinyInputCombat000
getShinyInputOrig0.0280.0150.043
getShinyInputSVA000
getShinyInputSVAf000
getShinyInputSVAr000
gnormalize0.0000.0000.001
log2CPM0.0360.0040.041
plot_genewise_moments0.090.000.09
plot_samplewise_moments0.0670.0000.066
rnaseq_sim0.1440.0190.163
setShinyInput000
setShinyInputCombat000
setShinyInputOrig000
setShinyInputSVA000
setShinyInputSVAf0.0010.0000.000
setShinyInputSVAr000