Multiple platform build/check report for BioC 3.14 - CHECK results for gemini 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: gemini

Version: 1.8.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gemini.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings gemini_1.8.0.tar.gz

StartedAt: 2022-04-12 20:05:31 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 20:10:05 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 274.0 seconds

RetCode: 0

Status: OK

CheckDir: gemini.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gemini.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings gemini_1.8.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/gemini.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 'gemini/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gemini' version '1.8.0'
* 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 'gemini' 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 ... NOTE
gemini_boxplot : <anonymous>: no visible binding for global variable
  '.'
gemini_boxplot: no visible binding for global variable '.'
gemini_boxplot : <anonymous>: no visible binding for global variable
  'gi'
gemini_boxplot : <anonymous>: no visible binding for global variable
  'hj'
gemini_boxplot: no visible binding for global variable 'label'
gemini_boxplot: no visible binding for global variable 'y'
gemini_calculate_lfc: no visible binding for global variable '.'
update_s_pb: no visible binding for global variable '.'
update_tau_pb: no visible binding for global variable '.'
Undefined global functions or variables:
  . gi hj label y
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
gemini_inference 18.09   1.16   19.25
update_tau_pb     7.34   0.02    7.36
update_x_pb       7.27   0.04    7.32
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
gemini_inference  22.39   0.07   22.48
update_tau_pb     10.04   0.03   10.09
update_x_pb        8.41   0.02    8.42
gemini_initialize  5.34   0.06    5.41
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/gemini.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/gemini_1.8.0.tar.gz && rm -rf gemini.buildbin-libdir && mkdir gemini.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gemini.buildbin-libdir gemini_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL gemini_1.8.0.zip && rm gemini_1.8.0.tar.gz gemini_1.8.0.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
  2 4075k    2 91587    0     0   458k      0  0:00:08 --:--:--  0:00:08  458k
 41 4075k   41 1676k    0     0  1378k      0  0:00:02  0:00:01  0:00:01 1378k
100 4075k  100 4075k    0     0  1870k      0  0:00:02  0:00:02 --:--:-- 1871k

install for i386

* installing *source* package 'gemini' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gemini'
    finding HTML links ... done
    Input                                   html  
    Model                                   html  
    Sgene2Pguides_hash                      html  
    Sguide2Pguides_hash                     html  
    compound                                html  
    counts                                  html  
    dot-median_normalize                    html  
    gemini_boxplot                          html  
    gemini_calculate_lfc                    html  
    gemini_create_input                     html  
    gemini_inference                        html  
    gemini_initialize                       html  
    gemini_parallelization                  html  
    gemini_plot_mae                         html  
    gemini_prepare_input                    html  
    gemini_score                            html  
    guide.annotation                        html  
    initialize_s                            html  
    initialize_tau                          html  
    initialize_x                            html  
    initialize_y                            html  
    pipe                                    html  
    sample.replicate.annotation             html  
    update_mae                              html  
    update_s_pb                             html  
    update_tau_pb                           html  
    update_x_pb                             html  
    update_y_pb                             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 'gemini' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'gemini' as gemini_1.8.0.zip
* DONE (gemini)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'gemini' 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(gemini)
> 
> test_check("gemini")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
   7.78    0.46    8.21


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(gemini)
> 
> test_check("gemini")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
   7.26    0.37    7.62

name	user	system	elapsed
Sgene2Pguides_hash	0	0	0
Sguide2Pguides_hash	0	0	0
compound	0	0	0
dot-median_normalize	0	0	0
gemini_boxplot	2.16	0.08	2.23
gemini_calculate_lfc	0.36	0.01	0.38
gemini_create_input	0.28	0.06	0.34
gemini_inference	18.09	1.16	19.25
gemini_initialize	4.83	0.00	4.83
gemini_plot_mae	0.71	0.03	0.74
gemini_prepare_input	0.29	0.02	0.31
gemini_score	0.63	0.01	0.64
initialize_s	1.17	0.03	1.20
initialize_tau	1.58	0.03	1.61
initialize_x	2.67	0.02	2.69
initialize_y	0.52	0.02	0.54
pipe	0	0	0
update_mae	0.83	0.01	0.84
update_s_pb	1.55	0.00	1.55
update_tau_pb	7.34	0.02	7.36
update_x_pb	7.27	0.04	7.32
update_y_pb	2.76	0.04	2.80

name	user	system	elapsed
Sgene2Pguides_hash	0	0	0
Sguide2Pguides_hash	0	0	0
compound	0	0	0
dot-median_normalize	0	0	0
gemini_boxplot	3.08	0.06	3.14
gemini_calculate_lfc	0.47	0.02	0.48
gemini_create_input	0.47	0.07	0.55
gemini_inference	22.39	0.07	22.48
gemini_initialize	5.34	0.06	5.41
gemini_plot_mae	0.71	0.03	0.75
gemini_prepare_input	0.44	0.02	0.46
gemini_score	0.71	0.01	0.71
initialize_s	1.40	0.01	1.42
initialize_tau	1.86	0.00	1.86
initialize_x	3.44	0.03	3.47
initialize_y	0.81	0.02	0.83
pipe	0	0	0
update_mae	1.44	0.00	1.44
update_s_pb	1.95	0.03	1.98
update_tau_pb	10.04	0.03	10.09
update_x_pb	8.41	0.02	8.42
update_y_pb	4.14	0.01	4.16

CHECK results for gemini on tokay2

Summary

Command output

Installation output

Tests output

Example timings