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This page was generated on 2025-10-23 12:06 -0400 (Thu, 23 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4894
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4684
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4629
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1197/2355HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mastR 1.9.1  (landing page)
Jinjin Chen
Snapshot Date: 2025-10-22 13:45 -0400 (Wed, 22 Oct 2025)
git_url: https://git.bioconductor.org/packages/mastR
git_branch: devel
git_last_commit: 50e1100
git_last_commit_date: 2025-06-30 23:19:16 -0400 (Mon, 30 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    NA  

CHECK results for mastR on kjohnson3

To the developers/maintainers of the mastR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mastR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: mastR
Version: 1.9.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mastR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mastR_1.9.1.tar.gz
StartedAt: 2025-10-22 20:31:18 -0400 (Wed, 22 Oct 2025)
EndedAt: 2025-10-22 20:35:23 -0400 (Wed, 22 Oct 2025)
EllapsedTime: 245.0 seconds
RetCode: 0
Status:   OK  
CheckDir: mastR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mastR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mastR_1.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/mastR.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mastR/DESCRIPTION’ ... OK
* this is package ‘mastR’ version ‘1.9.1’
* 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 ‘mastR’ 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 code 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'DEGs_Group.Rd':
  ‘[limma:ebayes]{limma::treat()}’

Non-topic package-anchored link(s) in Rd file 'DEGs_RP.Rd':
  ‘[limma:ebayes]{limma::treat()}’

Non-topic package-anchored link(s) in Rd file 'de_analysis.Rd':
  ‘[limma:ebayes]{limma::treat()}’

Non-topic package-anchored link(s) in Rd file 'process_data.Rd':
  ‘[limma:ebayes]{limma::treat()}’

Non-topic package-anchored link(s) in Rd file 'select_sig.Rd':
  ‘[limma:ebayes]{limma::treat()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
get_panglao_sig  1.6  0.057    6.33
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.22-bioc/meat/mastR.Rcheck/00check.log’
for details.

Installation output

mastR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL mastR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘mastR’ ...
** this is package ‘mastR’ version ‘1.9.1’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (mastR)

Tests output

mastR.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(mastR)

> 
> test_check("mastR")
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             2794         3366       3888   2947   1955
NotSig           2465         5052      10779  43514  45073
Up              44786        41627      35378   3584   3017
       NK-Others
Down         107
NotSig     48972
Up           966
       NK-Others
Down       29581
NotSig     17543
Up          2921
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             2794         3366       3888   2947   1955
NotSig           2465         5052      10779  43514  45073
Up              44786        41627      35378   3584   3017
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             2794         3366       3888   2947   1955
NotSig           2465         5052      10779  43514  45073
Up              44786        41627      35378   3584   3017
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4013         3946       3149   2701   2154
NotSig           1482         2687       4412   4986   6192
Up               4940         3802       2874   2748   2089
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4013         3946       3149   2701   2154
NotSig           1482         2687       4412   4986   6192
Up               4940         3802       2874   2748   2089
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4013         3946       3149   2701   2154
NotSig           1482         2687       4412   4986   6192
Up               4940         3802       2874   2748   2089
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4013         3946       3149   2701   2154
NotSig           1482         2687       4412   4986   6192
Up               4940         3802       2874   2748   2089
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4013         3946       3149   2701   2154
NotSig           1482         2687       4412   4986   6192
Up               4940         3802       2874   2748   2089
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4013         3946       3149   2701   2154
NotSig           1482         2687       4412   4986   6192
Up               4940         3802       2874   2748   2089
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3943       3147   2697   2154
NotSig           1471         2680       4400   4980   6178
Up               4929         3788       2864   2734   2079
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3943       3147   2697   2154
NotSig           1471         2680       4400   4980   6178
Up               4929         3788       2864   2734   2079
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             3056         2843       2174   1824   1444
NotSig           1246         2669       4189   4576   5527
Up               3926         2716       1865   1828   1257
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3943       3147   2697   2154
NotSig           1471         2680       4400   4980   6178
Up               4929         3788       2864   2734   2079
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3943       3147   2697   2154
NotSig           1471         2680       4400   4980   6178
Up               4929         3788       2864   2734   2079
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3943       3147   2697   2154
NotSig           1471         2680       4400   4980   6178
Up               4929         3788       2864   2734   2079
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3943       3147   2697   2154
NotSig           1471         2680       4400   4980   6178
Up               4929         3788       2864   2734   2079
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3943       3147   2697   2154
NotSig           1471         2680       4400   4980   6178
Up               4929         3788       2864   2734   2079
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             3629         3510       2668   2189   1728
NotSig           1957         3500       5403   5947   7039
Up               4714         3290       2229   2164   1533
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3943       3147   2697   2154
NotSig           1471         2680       4400   4980   6178
Up               4929         3788       2864   2734   2079
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3943       3147   2697   2154
NotSig           1471         2680       4400   4980   6178
Up               4929         3788       2864   2734   2079
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3943       3147   2697   2154
NotSig           1471         2680       4400   4980   6178
Up               4929         3788       2864   2734   2079
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3943       3147   2697   2154
NotSig           1471         2680       4400   4980   6178
Up               4929         3788       2864   2734   2079
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4079         4050       3299   2891   2350
NotSig           1340         2476       4065   4569   5769
Up               4992         3885       3047   2951   2292
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
All samples in sig_data are used!
All samples in bg_data are used!
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
see ?depmap and browseVignettes('depmap') for documentation
loading from cache
see ?depmap and browseVignettes('depmap') for documentation
loading from cache
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4012         3944       3148   2697   2153
NotSig           1472         2679       4402   4978   6179
Up               4931         3792       2865   2740   2083
'select()' returned 1:many mapping between keys and columns

using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4012         3944       3148   2697   2153
NotSig           1472         2679       4402   4978   6179
Up               4931         3792       2865   2740   2083
'select()' returned 1:many mapping between keys and columns
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4012         3944       3148   2697   2153
NotSig           1472         2679       4402   4978   6179
Up               4931         3792       2865   2740   2083
'select()' returned 1:many mapping between keys and columns
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4012         3944       3148   2697   2153
NotSig           1472         2679       4402   4978   6179
Up               4931         3792       2865   2740   2083
'select()' returned 1:many mapping between keys and columns
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4013         3944       3145   2698   2152
NotSig           1476         2682       4412   4984   6184
Up               4930         3793       2862   2737   2083
'select()' returned 1:many mapping between keys and columns
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4013         3944       3145   2698   2152
NotSig           1476         2682       4412   4984   6184
Up               4930         3793       2862   2737   2083
'select()' returned 1:many mapping between keys and columns
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4012         3944       3148   2697   2153
NotSig           1472         2679       4402   4978   6179
Up               4931         3792       2865   2740   2083
'select()' returned 1:many mapping between keys and columns
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
'select()' returned 1:many mapping between keys and columns
Gene KIR2DL2 is not in data.
Gene KIR2DL5A is not in data.
Gene KIR2DS2 is not in data.
Gene KIR2DS5 is not in data.
Gene KLRA1P is not in data.
Gene LOC653757 is not in data.
Gene MGC24103 is not in data.
Gene TRDC is not in data.
Gene CCL4 is not in data.
Gene CCL5 is not in data.

The automatically generated colors map from the 1^st and 99^th of the
values in the matrix. There are outliers in the matrix whose patterns
might be hidden by this color mapping. You can manually set the color
to `col` argument.

Use `suppressMessages()` to turn off this message.
'select()' returned 1:many mapping between keys and columns
Gene CCL4 is not in data.
Gene CCL5 is not in data.

The automatically generated colors map from the 1^st and 99^th of the
values in the matrix. There are outliers in the matrix whose patterns
might be hidden by this color mapping. You can manually set the color
to `col` argument.

Use `suppressMessages()` to turn off this message.
'select()' returned 1:many mapping between keys and columns
Gene CCL4 is not in data.
Gene CCL5 is not in data.

The automatically generated colors map from the 1^st and 99^th of the
values in the matrix. There are outliers in the matrix whose patterns
might be hidden by this color mapping. You can manually set the color
to `col` argument.

Use `suppressMessages()` to turn off this message.
'select()' returned 1:many mapping between keys and columns
Gene CCL4 is not in data.
Gene CCL5 is not in data.

The automatically generated colors map from the 1^st and 99^th of the
values in the matrix. There are outliers in the matrix whose patterns
might be hidden by this color mapping. You can manually set the color
to `col` argument.

Use `suppressMessages()` to turn off this message.
'select()' returned 1:many mapping between keys and columns
Gene CCL4 is not in data.
Gene CCL5 is not in data.

The automatically generated colors map from the 1^st and 99^th of the
values in the matrix. There are outliers in the matrix whose patterns
might be hidden by this color mapping. You can manually set the color
to `col` argument.

Use `suppressMessages()` to turn off this message.
'select()' returned 1:many mapping between keys and columns
Gene KIR2DL2 is not in data.
Gene KIR2DL5A is not in data.
Gene KIR2DS2 is not in data.
Gene KIR2DS5 is not in data.
Gene KLRA1P is not in data.
Gene LOC653757 is not in data.
Gene MGC24103 is not in data.
Gene TRDC is not in data.
Gene CCL4 is not in data.
Gene CCL5 is not in data.

The automatically generated colors map from the 1^st and 99^th of the
values in the matrix. There are outliers in the matrix whose patterns
might be hidden by this color mapping. You can manually set the color
to `col` argument.

Use `suppressMessages()` to turn off this message.
'select()' returned 1:many mapping between keys and columns
Gene CCL4 is not in data.
Gene CCL5 is not in data.

The automatically generated colors map from the 1^st and 99^th of the
values in the matrix. There are outliers in the matrix whose patterns
might be hidden by this color mapping. You can manually set the color
to `col` argument.

Use `suppressMessages()` to turn off this message.
'select()' returned 1:many mapping between keys and columns
Gene KIR2DL2 is not in data.
Gene KIR2DL5A is not in data.
Gene KIR2DS2 is not in data.
Gene KIR2DS5 is not in data.
Gene KLRA1P is not in data.
Gene LOC653757 is not in data.
Gene MGC24103 is not in data.
Gene TRDC is not in data.
Gene CCL4 is not in data.
Gene CCL5 is not in data.

The automatically generated colors map from the 1^st and 99^th of the
values in the matrix. There are outliers in the matrix whose patterns
might be hidden by this color mapping. You can manually set the color
to `col` argument.

Use `suppressMessages()` to turn off this message.
'select()' returned 1:many mapping between keys and columns
Gene CCL4 is not in data.
Gene CCL5 is not in data.

The automatically generated colors map from the 1^st and 99^th of the
values in the matrix. There are outliers in the matrix whose patterns
might be hidden by this color mapping. You can manually set the color
to `col` argument.

Use `suppressMessages()` to turn off this message.
'select()' returned 1:many mapping between keys and columns
Gene CCL4 is not in data.
Gene CCL5 is not in data.

'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3943       3147   2697   2154
NotSig           1471         2680       4400   4980   6178
Up               4929         3788       2864   2734   2079
[ FAIL 0 | WARN 64 | SKIP 0 | PASS 114 ]

[ FAIL 0 | WARN 64 | SKIP 0 | PASS 114 ]
> 
> proc.time()
   user  system elapsed 
 94.528   8.521 111.301

Example timings

mastR.Rcheck/mastR-Ex.timings

nameusersystemelapsed
ccle_2_wide0.0730.0040.078
de_analysis1.0030.0411.053
filter_subset_sig1.4260.0641.497
get_de_table0.6160.0340.650
get_degs1.0020.0551.057
get_gsc_sig0.0070.0010.007
get_lm_sig0.0040.0010.005
get_panglao_sig1.6000.0576.330
gls2gsc0.0030.0010.005
gsc_plot0.3370.0060.343
list_panglao_organs0.0230.0030.411
list_panglao_types0.0240.0041.064
merge_markers0.0070.0010.008
pca_matrix_plot0.9850.0111.004
plot_diagnostics3.2390.3243.586
plot_mean_var0.8400.0600.901
process_data0.5790.0370.616
pseudo_sample_list0.0490.0010.050
pseudo_samples0.0330.0020.035
remove_bg_exp0.3700.0110.381
remove_bg_exp_mat0.7870.0300.818
select_sig0.6200.0500.673
sig_boxplot0.3630.0110.380
sig_gseaplot3.8010.6194.312
sig_heatmap0.9380.1341.073
sig_rankdensity_plot0.6160.0300.647
sig_scatter_plot0.6360.0480.685