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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 780/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gemini 1.21.0  (landing page)
Sidharth Jain
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/gemini
git_branch: devel
git_last_commit: 22ea9ce
git_last_commit_date: 2024-10-29 10:38:26 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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
kjohnson3macOS 13.7.1 Ventura / arm64  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 nebbiolo1

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: 1.21.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:gemini.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings gemini_1.21.0.tar.gz
StartedAt: 2024-12-23 22:14:40 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 22:17:00 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 140.2 seconds
RetCode: 0
Status:   OK  
CheckDir: gemini.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:gemini.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings gemini_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/gemini.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘gemini/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gemini’ version ‘1.21.0’
* 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 for sufficient/correct file permissions ... 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 loading without being on the library search path ... 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 17.375  0.693  18.084
update_tau_pb     8.127  0.035   8.164
update_x_pb       6.903  0.066   6.975
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/gemini.Rcheck/00check.log’
for details.


Installation output

gemini.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL gemini
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-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) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  6.353   0.329   6.674 

Example timings

gemini.Rcheck/gemini-Ex.timings

nameusersystemelapsed
Sgene2Pguides_hash0.0000.0010.000
Sguide2Pguides_hash0.0000.0000.001
compound0.0000.0000.001
dot-median_normalize000
gemini_boxplot1.8680.0551.924
gemini_calculate_lfc0.3180.0070.326
gemini_create_input0.2160.0010.218
gemini_inference17.375 0.69318.084
gemini_initialize3.8920.0423.934
gemini_plot_mae0.6190.0340.653
gemini_prepare_input0.2820.0050.288
gemini_score0.5910.0100.601
initialize_s1.0240.0251.049
initialize_tau1.2480.0071.254
initialize_x2.3580.0132.371
initialize_y0.5480.0050.553
pipe000
update_mae0.8700.0030.874
update_s_pb1.5340.0011.536
update_tau_pb8.1270.0358.164
update_x_pb6.9030.0666.975
update_y_pb2.3070.0022.310