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This page was generated on 2022-01-19 13:06:38 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4328
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4077
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4138
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 gemini on tokay2


To the developers/maintainers of the gemini package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gemini.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 713/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gemini 1.8.0  (landing page)
Sidharth Jain
Snapshot Date: 2022-01-18 01:55:07 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/gemini
git_branch: RELEASE_3_14
git_last_commit: fb7a7eb
git_last_commit_date: 2021-10-26 12:52:55 -0500 (Tue, 26 Oct 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: 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: 2022-01-18 19:56:20 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 20:00:23 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 242.6 seconds
RetCode: 0
Status:   OK  
CheckDir: gemini.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/gemini.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 '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 16.81   0.87   17.69
update_tau_pb     7.67   0.86    8.53
update_x_pb       6.89   0.00    6.89
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
gemini_inference  21.36   0.05   21.40
update_tau_pb      8.44   0.02    8.45
update_x_pb        7.42   0.00    7.42
gemini_initialize  5.48   0.03    5.52
* 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.



Installation output

gemini.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 22 4075k   22  913k    0     0  1858k      0  0:00:02 --:--:--  0:00:02 1857k
100 4075k  100 4075k    0     0  2874k      0  0:00:01  0:00:01 --:--:-- 2876k

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

Tests output

gemini.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(gemini)
> 
> test_check("gemini")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
   7.18    0.43    7.60 

gemini.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(gemini)
> 
> test_check("gemini")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
   7.93    0.45    8.39 

Example timings

gemini.Rcheck/examples_i386/gemini-Ex.timings

nameusersystemelapsed
Sgene2Pguides_hash000
Sguide2Pguides_hash000
compound000
dot-median_normalize000
gemini_boxplot2.110.112.25
gemini_calculate_lfc0.310.020.33
gemini_create_input0.250.050.29
gemini_inference16.81 0.8717.69
gemini_initialize4.420.094.52
gemini_plot_mae0.660.050.70
gemini_prepare_input0.330.020.34
gemini_score0.690.010.71
initialize_s1.750.051.79
initialize_tau1.760.051.81
initialize_x2.810.002.82
initialize_y0.710.060.76
pipe000
update_mae1.310.011.33
update_s_pb1.720.051.78
update_tau_pb7.670.868.53
update_x_pb6.890.006.89
update_y_pb2.440.032.47

gemini.Rcheck/examples_x64/gemini-Ex.timings

nameusersystemelapsed
Sgene2Pguides_hash000
Sguide2Pguides_hash000
compound000
dot-median_normalize000
gemini_boxplot2.660.092.75
gemini_calculate_lfc0.340.000.34
gemini_create_input0.240.080.32
gemini_inference21.36 0.0521.40
gemini_initialize5.480.035.52
gemini_plot_mae0.640.010.65
gemini_prepare_input0.310.000.32
gemini_score0.720.000.71
initialize_s1.350.041.38
initialize_tau1.930.031.97
initialize_x3.130.013.14
initialize_y0.700.020.72
pipe000
update_mae1.390.011.42
update_s_pb1.860.051.91
update_tau_pb8.440.028.45
update_x_pb7.420.007.42
update_y_pb3.030.013.05