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This page was generated on 2024-03-28 11:37:44 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 788/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gemini 1.17.0  (landing page)
Sidharth Jain
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/gemini
git_branch: devel
git_last_commit: 4d8ab9f
git_last_commit_date: 2023-10-24 11:15:03 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for gemini on palomino3


To the developers/maintainers of the gemini package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: gemini
Version: 1.17.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gemini.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings gemini_1.17.0.tar.gz
StartedAt: 2024-03-28 02:16:32 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 02:19:36 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 184.2 seconds
RetCode: 0
Status:   OK  
CheckDir: gemini.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gemini.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings gemini_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/gemini.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'gemini/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gemini' version '1.17.0'
* 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 ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 ... NOTE
checkRd: (-1) gemini_initialize.Rd:81-83: Lost braces
    81 | \strong{Use of negative control}{
       |                                 ^
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
gemini_inference  22.60   4.24   26.83
update_tau_pb     10.91   1.98   12.89
update_x_pb        8.61   1.90   10.51
gemini_initialize  5.42   0.17    5.59
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/gemini.Rcheck/00check.log'
for details.


Installation output

gemini.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL gemini
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'gemini' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (gemini)

Tests output

gemini.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 3 | SKIP 0 | PASS 7 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 7 ]
> 
> proc.time()
   user  system elapsed 
   7.28    0.98    8.28 

Example timings

gemini.Rcheck/gemini-Ex.timings

nameusersystemelapsed
Sgene2Pguides_hash0.000.020.02
Sguide2Pguides_hash000
compound000
dot-median_normalize000
gemini_boxplot1.760.081.84
gemini_calculate_lfc0.280.060.35
gemini_create_input0.230.200.44
gemini_inference22.60 4.2426.83
gemini_initialize5.420.175.59
gemini_plot_mae0.840.060.91
gemini_prepare_input0.500.020.52
gemini_score0.860.050.90
initialize_s1.380.071.45
initialize_tau1.530.071.60
initialize_x3.040.123.17
initialize_y0.600.090.69
pipe000
update_mae1.110.111.22
update_s_pb1.840.162.00
update_tau_pb10.91 1.9812.89
update_x_pb 8.61 1.9010.51
update_y_pb2.970.203.17