Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-14 13:06:43 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4327
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4076
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4137
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

CHECK results for microbiomeMarker on tokay2


To the developers/maintainers of the microbiomeMarker package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/microbiomeMarker.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 1144/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
microbiomeMarker 1.0.1  (landing page)
Yang Cao
Snapshot Date: 2022-01-13 01:55:04 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/microbiomeMarker
git_branch: RELEASE_3_14
git_last_commit: d4852b9
git_last_commit_date: 2021-11-08 03:46:16 -0500 (Mon, 08 Nov 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: microbiomeMarker
Version: 1.0.1
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:microbiomeMarker.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings microbiomeMarker_1.0.1.tar.gz
StartedAt: 2022-01-13 22:26:58 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 22:38:42 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 703.8 seconds
RetCode: 0
Status:   OK  
CheckDir: microbiomeMarker.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:microbiomeMarker.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings microbiomeMarker_1.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/microbiomeMarker.Rcheck'
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'microbiomeMarker/DESCRIPTION' ... OK
* this is package 'microbiomeMarker' version '1.0.1'
* 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 whether package 'microbiomeMarker' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... 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 R/sysdata.rda ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
run_aldex      9.34   1.29   10.75
run_deseq2     9.13   0.00    9.15
run_ancombc    7.33   0.04    7.36
plot_cladogram 6.69   0.19    6.88
run_lefse      6.03   0.10    6.16
plot_heatmap   5.41   0.25    5.65
plot_sl_roc    5.14   0.08    5.22
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
run_deseq2        11.94   0.00   11.97
plot_cladogram    11.65   0.17   11.83
run_aldex          8.95   0.88    9.86
run_lefse          9.17   0.13    9.39
run_ancombc        9.00   0.01    9.03
plot_sl_roc        8.38   0.14    8.52
plot_heatmap       6.10   0.09    6.18
run_metagenomeseq  5.78   0.02    5.79
plot_abundance     5.22   0.00    5.22
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

microbiomeMarker.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/microbiomeMarker_1.0.1.tar.gz && rm -rf microbiomeMarker.buildbin-libdir && mkdir microbiomeMarker.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=microbiomeMarker.buildbin-libdir microbiomeMarker_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL microbiomeMarker_1.0.1.zip && rm microbiomeMarker_1.0.1.tar.gz microbiomeMarker_1.0.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1544k  100 1544k    0     0  2443k      0 --:--:-- --:--:-- --:--:-- 2448k

install for i386

* installing *source* package 'microbiomeMarker' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'microbiomeMarker'
    finding HTML links ... done
    abundances-methods                      html  
    finding level-2 HTML links ... done

    aggregate_taxa                          html  
    assign-marker_table                     html  
    assign-otu_table                        html  
    data-caporaso                           html  
    data-cid_ying                           html  
    data-ecam                               html  
    data-enterotypes_arumugam               html  
    data-kostic_crc                         html  
    data-oxygen                             html  
    data-pediatric_ibd                      html  
    data-spontaneous_colitis                html  
    effect_size-plot                        html  
    extract-methods                         html  
    extract_posthoc_res                     html  
    get_treedata_phyloseq                   html  
    import_dada2                            html  
    import_qiime2                           html  
    marker_table-class                      html  
    marker_table-methods                    html  
    microbiomeMarker-class                  html  
    microbiomeMarker-package                html  
    microbiomeMarker                        html  
    nmarker-methods                         html  
    normalize-methods                       html  
    phyloseq2DESeq2                         html  
    phyloseq2edgeR                          html  
    phyloseq2metagenomeSeq                  html  
    plot_abundance                          html  
    plot_cladogram                          html  
    plot_heatmap                            html  
    plot_postHocTest                        html  
    plot_sl_roc                             html  
    postHocTest-class                       html  
    postHocTest                             html  
    reexports                               html  
    run_aldex                               html  
    run_ancom                               html  
    run_ancombc                             html  
    run_deseq2                              html  
    run_edger                               html  
    run_lefse                               html  
    run_limma_voom                          html  
    run_marker                              html  
    run_metagenomeseq                       html  
    run_posthoc_test                        html  
    run_simple_stat                         html  
    run_sl                                  html  
    run_test_multiple_groups                html  
    run_test_two_groups                     html  
    subset_marker                           html  
    summarize_taxa                          html  
    transform_abundances                    html  
*** 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

install for x64

* installing *source* package 'microbiomeMarker' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'microbiomeMarker' as microbiomeMarker_1.0.1.zip
* DONE (microbiomeMarker)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'microbiomeMarker' successfully unpacked and MD5 sums checked

Tests output

microbiomeMarker.Rcheck/tests_i386/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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

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

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

> library(testthat)
> library(microbiomeMarker)
> 
> test_check("microbiomeMarker")
== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 11 | SKIP 1 | PASS 194 ]
> 
> proc.time()
   user  system elapsed 
  73.37    3.64   77.20 

microbiomeMarker.Rcheck/tests_x64/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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

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

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

> library(testthat)
> library(microbiomeMarker)
> 
> test_check("microbiomeMarker")
== Skipped tests ===============================================================
* empty test (1)

[ FAIL 0 | WARN 11 | SKIP 1 | PASS 194 ]
> 
> proc.time()
   user  system elapsed 
  72.26    2.29   74.54 

Example timings

microbiomeMarker.Rcheck/examples_i386/microbiomeMarker-Ex.timings

nameusersystemelapsed
abundances-methods0.120.000.12
aggregate_taxa0.380.010.39
assign-marker_table2.880.433.30
effect_size-plot2.780.012.79
extract_posthoc_res0.090.030.13
import_dada20.150.030.17
import_qiime20.350.110.83
marker_table-methods2.800.002.79
microbiomeMarker0.020.000.02
nmarker-methods000
normalize-methods0.120.000.12
phyloseq2DESeq20.610.000.61
phyloseq2edgeR0.160.020.18
phyloseq2metagenomeSeq0.120.030.15
plot_abundance3.250.003.25
plot_cladogram6.690.196.88
plot_heatmap5.410.255.65
plot_postHocTest0.890.010.91
plot_sl_roc5.140.085.22
postHocTest0.060.020.08
run_aldex 9.34 1.2910.75
run_ancom000
run_ancombc7.330.047.36
run_deseq29.130.009.15
run_edger2.970.003.00
run_lefse6.030.106.16
run_limma_voom2.590.022.61
run_metagenomeseq3.310.003.31
run_posthoc_test0.610.000.61
run_simple_stat3.420.023.44
run_sl2.410.012.42
run_test_multiple_groups2.890.002.89
run_test_two_groups3.200.023.22
subset_marker2.660.012.67
summarize_taxa0.330.020.34
transform_abundances0.160.000.16

microbiomeMarker.Rcheck/examples_x64/microbiomeMarker-Ex.timings

nameusersystemelapsed
abundances-methods0.170.030.21
aggregate_taxa1.390.041.43
assign-marker_table3.470.053.51
effect_size-plot3.530.003.54
extract_posthoc_res0.110.030.14
import_dada20.070.000.08
import_qiime20.220.060.28
marker_table-methods3.30.03.3
microbiomeMarker0.020.000.02
nmarker-methods000
normalize-methods0.110.020.12
phyloseq2DESeq20.860.020.88
phyloseq2edgeR0.140.010.16
phyloseq2metagenomeSeq0.190.020.20
plot_abundance5.220.005.22
plot_cladogram11.65 0.1711.83
plot_heatmap6.100.096.18
plot_postHocTest1.180.001.19
plot_sl_roc8.380.148.52
postHocTest0.140.000.14
run_aldex8.950.889.86
run_ancom000
run_ancombc9.000.019.03
run_deseq211.94 0.0011.97
run_edger4.500.054.55
run_lefse9.170.139.39
run_limma_voom3.760.013.80
run_metagenomeseq5.780.025.79
run_posthoc_test0.940.000.94
run_simple_stat3.220.003.22
run_sl3.170.003.18
run_test_multiple_groups3.670.003.67
run_test_two_groups3.920.003.97
subset_marker2.770.022.78
summarize_taxa0.510.000.52
transform_abundances0.210.030.23