Multiple platform build/check report for BioC 3.12 - CHECK report for gemini on tokay1

Package: gemini

Version: 1.4.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gemini.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings gemini_1.4.0.tar.gz

StartedAt: 2021-05-06 02:59:20 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 03:03:52 -0400 (Thu, 06 May 2021)

EllapsedTime: 272.3 seconds

RetCode: 1

Status: ERROR

CheckDir: gemini.Rcheck

Warnings: NA

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:gemini.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings gemini_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/gemini.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.4.0'
* 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  20.16   0.47   20.63
update_tau_pb     10.33   0.89   11.22
update_x_pb        9.37   0.02    9.39
gemini_initialize  7.14   0.08    7.22
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
gemini_inference  21.38   0.01   21.42
update_tau_pb      8.78   0.01    8.79
update_x_pb        7.68   0.10    7.77
gemini_initialize  4.98   0.04    5.03
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(gemini)
  > 
  > test_check("gemini")
  == Failed tests ================================================================
  -- Failure (test_data.R:31:5): Input object is reproducible --------------------
  `Input.new` not equal to `Input`.
  Component "sample.annot": Attributes: < Component "row.names": Mean relative difference: 0.5454545 >
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
** running tests for arch 'x64' ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(gemini)
  > 
  > test_check("gemini")
  == Failed tests ================================================================
  -- Failure (test_data.R:31:5): Input object is reproducible --------------------
  `Input.new` not equal to `Input`.
  Component "sample.annot": Attributes: < Component "row.names": Mean relative difference: 0.5454545 >
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
* 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 ERRORs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/gemini.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/gemini_1.4.0.tar.gz && rm -rf gemini.buildbin-libdir && mkdir gemini.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=gemini.buildbin-libdir gemini_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL gemini_1.4.0.zip && rm gemini_1.4.0.tar.gz gemini_1.4.0.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
100 4075k  100 4075k    0     0  47.4M      0 --:--:-- --:--:-- --:--:-- 47.9M

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_1.4.0.zip
* DONE (gemini)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'gemini' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(gemini)
> 
> test_check("gemini")
== Failed tests ================================================================
-- Failure (test_data.R:31:5): Input object is reproducible --------------------
`Input.new` not equal to `Input`.
Component "sample.annot": Attributes: < Component "row.names": Mean relative difference: 0.5454545 >

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
Error: Test failures
Execution halted


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(gemini)
> 
> test_check("gemini")
== Failed tests ================================================================
-- Failure (test_data.R:31:5): Input object is reproducible --------------------
`Input.new` not equal to `Input`.
Component "sample.annot": Attributes: < Component "row.names": Mean relative difference: 0.5454545 >

[ FAIL 1 | WARN 0 | SKIP 0 | PASS 6 ]
Error: Test failures
Execution halted

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	4.64	0.15	4.82
gemini_calculate_lfc	0.59	0.05	0.64
gemini_create_input	0.47	0.14	0.61
gemini_inference	20.16	0.47	20.63
gemini_initialize	7.14	0.08	7.22
gemini_plot_mae	1.16	0.00	1.16
gemini_prepare_input	0.56	0.03	0.59
gemini_score	0.74	0.03	0.77
initialize_s	2.01	0.03	2.05
initialize_tau	3.35	0.05	3.39
initialize_x	4.65	0.03	4.68
initialize_y	1.00	0.06	1.07
pipe	0	0	0
update_mae	1.77	0.02	1.78
update_s_pb	2.56	0.03	2.59
update_tau_pb	10.33	0.89	11.22
update_x_pb	9.37	0.02	9.39
update_y_pb	4.33	0.03	4.36

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	2.82	0.06	2.87
gemini_calculate_lfc	0.34	0.03	0.38
gemini_create_input	0.28	0.08	0.36
gemini_inference	21.38	0.01	21.42
gemini_initialize	4.98	0.04	5.03
gemini_plot_mae	0.61	0.00	0.61
gemini_prepare_input	0.30	0.01	0.31
gemini_score	0.57	0.03	0.61
initialize_s	1.22	0.00	1.22
initialize_tau	1.88	0.02	1.89
initialize_x	2.81	0.03	2.85
initialize_y	0.55	0.02	0.56
pipe	0	0	0
update_mae	1.22	0.06	1.28
update_s_pb	1.54	0.00	1.55
update_tau_pb	8.78	0.01	8.79
update_x_pb	7.68	0.10	7.77
update_y_pb	2.81	0.01	2.83

CHECK report for gemini on tokay1

Summary

Command output

Installation output

Tests output

Example timings