Multiple platform build/check report for BioC 3.11 - CHECK report for gemini on tokay2

Package: gemini

Version: 1.2.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gemini.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings gemini_1.2.0.tar.gz

StartedAt: 2020-10-17 04:16:22 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 04:20:56 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 274.4 seconds

RetCode: 0

Status: OK

CheckDir: gemini.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gemini.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings gemini_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/gemini.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.2.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* 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  22.10   0.42   22.52
update_x_pb        9.14   0.06    9.22
update_tau_pb      7.98   0.05    8.03
gemini_initialize  5.51   0.05    5.56
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
gemini_inference  26.51   2.02   28.53
update_tau_pb      9.31   0.02    9.33
update_x_pb        8.75   0.03    8.78
gemini_initialize  6.21   0.07    6.28
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/gemini.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/gemini_1.2.0.tar.gz && rm -rf gemini.buildbin-libdir && mkdir gemini.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gemini.buildbin-libdir gemini_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL gemini_1.2.0.zip && rm gemini_1.2.0.tar.gz gemini_1.2.0.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 4075k    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 4075k  100 4075k    0     0  8880k      0 --:--:-- --:--:-- --:--:-- 8997k

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_1.2.0.zip
* DONE (gemini)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'gemini' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
== testthat results  ===========================================================
[ OK: 7 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
   8.64    0.51    9.14


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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")
== testthat results  ===========================================================
[ OK: 7 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
    9.4     0.5     9.9

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	3.17	0.06	3.23
gemini_calculate_lfc	0.45	0.08	0.54
gemini_create_input	0.25	0.13	0.37
gemini_inference	22.10	0.42	22.52
gemini_initialize	5.51	0.05	5.56
gemini_plot_mae	0.69	0.04	0.73
gemini_prepare_input	0.31	0.07	0.38
gemini_score	0.74	0.00	0.73
initialize_s	1.42	0.03	1.46
initialize_tau	2.20	0.04	2.25
initialize_x	4.44	0.08	4.52
initialize_y	0.93	0.03	0.97
pipe	0	0	0
update_mae	1.42	0.03	1.45
update_s_pb	1.88	0.02	1.89
update_tau_pb	7.98	0.05	8.03
update_x_pb	9.14	0.06	9.22
update_y_pb	2.63	0.02	2.64

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	3.06	0.05	3.17
gemini_calculate_lfc	0.39	0.01	0.40
gemini_create_input	0.41	0.08	0.49
gemini_inference	26.51	2.02	28.53
gemini_initialize	6.21	0.07	6.28
gemini_plot_mae	0.92	0.05	0.97
gemini_prepare_input	0.44	0.03	0.46
gemini_score	0.84	0.01	0.86
initialize_s	1.77	0.00	1.76
initialize_tau	1.86	0.01	1.88
initialize_x	3.80	0.04	3.82
initialize_y	0.81	0.03	0.85
pipe	0	0	0
update_mae	1.80	0.04	1.84
update_s_pb	2.45	0.00	2.45
update_tau_pb	9.31	0.02	9.33
update_x_pb	8.75	0.03	8.78
update_y_pb	3.55	0.03	3.58

CHECK report for gemini on tokay2

Summary

Command output

Installation output

Tests output

Example timings