Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-11-05 12:07 -0500 (Tue, 05 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4503
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4506
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1161/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mastR 1.6.0  (landing page)
Jinjin Chen
Snapshot Date: 2024-11-04 13:40 -0500 (Mon, 04 Nov 2024)
git_url: https://git.bioconductor.org/packages/mastR
git_branch: RELEASE_3_20
git_last_commit: 168917f
git_last_commit_date: 2024-10-29 11:20:15 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for mastR on lconway

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: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2024-11-05 00:18:09 -0500 (Tue, 05 Nov 2024)
EndedAt: 2024-11-05 00:30:20 -0500 (Tue, 05 Nov 2024)
EllapsedTime: 731.8 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/mastR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mastR/DESCRIPTION’ ... OK
* this is package ‘mastR’ version ‘1.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
plot_diagnostics 7.083  0.861   7.963
sig_gseaplot     6.906  0.926   7.617
get_panglao_sig  3.758  0.131  15.803
* 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: OK

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/4.4-x86_64/Resources/library’
* installing *source* package ‘mastR’ ...
** 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 (mastR)

Tests output

mastR.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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             2787         3348       3847   2869   1903
NotSig           2593         5434      10908  43672  45202
Up              44665        41263      35290   3504   2940
       NK-Others
Down          90
NotSig     49003
Up           952
       NK-Others
Down       29581
NotSig     17543
Up          2921
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             2787         3348       3847   2869   1903
NotSig           2593         5434      10908  43672  45202
Up              44665        41263      35290   3504   2940
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             2787         3348       3847   2869   1903
NotSig           2593         5434      10908  43672  45202
Up              44665        41263      35290   3504   2940
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4011         3946       3145   2696   2154
NotSig           1489         2688       4420   4995   6192
Up               4935         3801       2870   2744   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             4011         3946       3145   2696   2154
NotSig           1489         2688       4420   4995   6192
Up               4935         3801       2870   2744   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             4011         3946       3145   2696   2154
NotSig           1489         2688       4420   4995   6192
Up               4935         3801       2870   2744   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             4011         3946       3145   2696   2154
NotSig           1489         2688       4420   4995   6192
Up               4935         3801       2870   2744   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             4011         3946       3145   2696   2154
NotSig           1489         2688       4420   4995   6192
Up               4935         3801       2870   2744   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             4011         3946       3145   2696   2154
NotSig           1489         2688       4420   4995   6192
Up               4935         3801       2870   2744   2089
'select()' returned 1:many mapping between keys and columns
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       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             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       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             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4076         4049       3299   2894   2356
NotSig           1344         2476       4064   4565   5764
Up               4991         3886       3048   2952   2291
'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             4010         3945       3146   2693   2153
NotSig           1475         2678       4409   4984   6182
Up               4930         3792       2860   2738   2080
'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             4010         3945       3146   2693   2153
NotSig           1475         2678       4409   4984   6182
Up               4930         3792       2860   2738   2080
'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             4010         3945       3146   2693   2153
NotSig           1475         2678       4409   4984   6182
Up               4930         3792       2860   2738   2080
'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             4010         3945       3146   2693   2153
NotSig           1475         2678       4409   4984   6182
Up               4930         3792       2860   2738   2080
'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             4011         3944       3145   2695   2152
NotSig           1483         2684       4417   4990   6187
Up               4925         3791       2857   2734   2080
'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             4011         3944       3145   2695   2152
NotSig           1483         2684       4417   4990   6187
Up               4925         3791       2857   2734   2080
'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             4010         3945       3146   2693   2153
NotSig           1475         2678       4409   4984   6182
Up               4930         3792       2860   2738   2080
'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             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
[ FAIL 0 | WARN 28 | SKIP 0 | PASS 114 ]

[ FAIL 0 | WARN 28 | SKIP 0 | PASS 114 ]
> 
> proc.time()
   user  system elapsed 
191.985  15.158 223.760

Example timings

mastR.Rcheck/mastR-Ex.timings

nameusersystemelapsed
ccle_2_wide0.1170.0120.128
de_analysis2.0170.1022.124
filter_subset_sig2.8190.1622.985
get_de_table1.3540.0971.453
get_degs1.9970.1392.139
get_gsc_sig0.0120.0030.015
get_lm_sig0.0100.0070.017
get_panglao_sig 3.758 0.13115.803
gls2gsc0.0070.0030.009
gsc_plot0.6270.0550.684
list_panglao_organs0.0430.0100.454
list_panglao_types0.0480.0061.258
merge_markers0.0150.0060.021
pca_matrix_plot1.6660.0321.703
plot_diagnostics7.0830.8617.963
plot_mean_var1.5610.0761.641
process_data1.2120.0731.287
pseudo_sample_list0.0950.0010.095
pseudo_samples0.0320.0030.035
remove_bg_exp0.7380.0220.760
remove_bg_exp_mat0.7720.0560.829
select_sig1.3540.0951.452
sig_boxplot0.7600.0590.821
sig_gseaplot6.9060.9267.617
sig_heatmap2.0000.2232.228
sig_rankdensity_plot1.2340.0441.281
sig_scatter_plot1.2560.0801.339