Multiple platform build/check report for BioC 3.14 - CHECK results for MicrobiomeProfiler on tokay2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	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*

Package: MicrobiomeProfiler

Version: 1.0.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MicrobiomeProfiler.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MicrobiomeProfiler_1.0.0.tar.gz

StartedAt: 2022-04-12 22:50:45 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 22:54:59 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 253.7 seconds

RetCode: 0

Status: OK

CheckDir: MicrobiomeProfiler.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MicrobiomeProfiler.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings MicrobiomeProfiler_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/MicrobiomeProfiler.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MicrobiomeProfiler/DESCRIPTION' ... OK
* this is package 'MicrobiomeProfiler' version '1.0.0'
* 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 whether package 'MicrobiomeProfiler' 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
** running examples for arch 'x64' ... OK
* 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

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/MicrobiomeProfiler_1.0.0.tar.gz && rm -rf MicrobiomeProfiler.buildbin-libdir && mkdir MicrobiomeProfiler.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MicrobiomeProfiler.buildbin-libdir MicrobiomeProfiler_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL MicrobiomeProfiler_1.0.0.zip && rm MicrobiomeProfiler_1.0.0.tar.gz MicrobiomeProfiler_1.0.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  840k  100  840k    0     0   894k      0 --:--:-- --:--:-- --:--:--  893k

install for i386

* installing *source* package 'MicrobiomeProfiler' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MicrobiomeProfiler'
    finding HTML links ... done
    MicrobiomeProfiler-package              html  
    Psoriasis_data                          html  
    Rat_data                                html  
    bitr_smpdb                              html  
    enrichCOG                               html  
    enrichHMDB                              html  
    enrichKO                                html  
    enrichMBKEGG                            html  
    enrichMDA                               html  
    enrichSMPDB                             html  
    microbiota_taxlist                      html  
    run_MicrobiomeProfiler                  html  
** 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 'MicrobiomeProfiler' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MicrobiomeProfiler' as MicrobiomeProfiler_1.0.0.zip
* DONE (MicrobiomeProfiler)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'MicrobiomeProfiler' successfully unpacked and MD5 sums checked


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(MicrobiomeProfiler)

> test_check("MicrobiomeProfiler")
--> No gene can be mapped....
--> Expected input gene ID: K01774,K10703,K15634,K14756,K07514,K19660
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: COG0423,COG0013,COG2451,COG0082,COG0116,COG0293
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 836,1506,283168,29387,1380,41200
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: PW_C000981,PW_C001034,PW_C001144,PW_C000031,PW_C001099,PW_C001420
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: C05747,C00229,C00083,C01101,C05345,C00154
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: HMDB0001451,HMDB0001096,HMDB0001206,HMDB0001967,HMDB0000272,HMDB0000119
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> 
> proc.time()
   user  system elapsed 
   9.09    0.75    9.84


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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(MicrobiomeProfiler)

> test_check("MicrobiomeProfiler")
--> No gene can be mapped....
--> Expected input gene ID: K17468,K02745,K01959,K01629,K05308,K05305
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: COG0016,COG2502,COG1269,COG0367,COG1190,COG1383
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: 729,1506,846,35783,216851,41200
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: PW_C000035,PW_C000862,PW_C000105,PW_C001316,PW_C001034,PW_C000046
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: C00795,C00794,C00111,C00489,C00311,C05259
--> return NULL...
--> No gene can be mapped....
--> Expected input gene ID: HMDB0000123,HMDB0001268,HMDB0000064,HMDB0001491,HMDB0000300,HMDB0000243
--> return NULL...
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 13 ]
> 
> 
> proc.time()
   user  system elapsed 
  10.53    0.32   10.84

name	user	system	elapsed
Psoriasis_data	0.02	0.00	0.02
Rat_data	0	0	0
bitr_smpdb	0.08	0.02	0.10
enrichCOG	0.03	0.00	0.03
enrichHMDB	0.11	0.01	0.12
enrichKO	0.31	0.03	0.35
enrichMBKEGG	0.16	0.00	0.15
enrichMDA	0.11	0.00	0.11
enrichSMPDB	0.09	0.00	0.10
microbiota_taxlist	0.02	0.00	0.01
run_MicrobiomeProfiler	0	0	0

name	user	system	elapsed
Psoriasis_data	0.00	0.02	0.02
Rat_data	0	0	0
bitr_smpdb	0.08	0.00	0.08
enrichCOG	0.06	0.00	0.06
enrichHMDB	0.11	0.00	0.11
enrichKO	0.31	0.00	0.32
enrichMBKEGG	0.16	0.00	0.15
enrichMDA	0.09	0.00	0.10
enrichSMPDB	0.11	0.00	0.11
microbiota_taxlist	0	0	0
run_MicrobiomeProfiler	0	0	0

CHECK results for MicrobiomeProfiler on tokay2

Summary

Command output

Installation output

Tests output

Example timings