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This page was generated on 2024-05-04 11:37:10 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1917/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ScreenR 1.6.0  (landing page)
Emanuel Michele Soda
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/ScreenR
git_branch: RELEASE_3_19
git_last_commit: ecb0863
git_last_commit_date: 2024-04-30 11:43:04 -0400 (Tue, 30 Apr 2024)
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  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for ScreenR on nebbiolo1


To the developers/maintainers of the ScreenR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ScreenR.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: ScreenR
Version: 1.6.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ScreenR_1.6.0.tar.gz
StartedAt: 2024-05-04 03:29:39 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 03:33:24 -0400 (Sat, 04 May 2024)
EllapsedTime: 225.3 seconds
RetCode: 0
Status:   OK  
CheckDir: ScreenR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings ScreenR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/ScreenR.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ScreenR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ScreenR’ version ‘1.6.0’
* 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 ‘ScreenR’ 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 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) annotation_table.Rd:25: Lost braces
    25 |                  \url{https://cellecta.com/}{cellecta}}
       |                                             ^
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'compute_camera.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'select_number_barcode.Rd':
  ‘...’

Documented arguments not in \usage in Rd file 'unique_gene_symbols.Rd':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
plot_zscore_distribution 40.320  0.532  40.853
plot_barcode_trend       40.206  0.608  40.814
compute_metrics          23.162  1.463  24.628
find_robust_zscore_hit   19.513  0.492  20.006
find_zscore_hit          19.388  0.228  19.616
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/ScreenR.Rcheck/00check.log’
for details.


Installation output

ScreenR.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL ScreenR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘ScreenR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (ScreenR)

Tests output

ScreenR.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
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(ScreenR)

Welcome to ScreenR
--------------------------

See ?ScreenR for a list of
available functions.

Enjoy!

> 
> test_check("ScreenR")
ScreenR count table containing:
 5320 rows
 15 columns
ScreenR annotation table containing:
 5320 rows
 5 columns
ScreenR normalized count table containing:
 5320 rows
 15 columns
ScreenR normalized data table containing:
 74480 rows
 9 columns
ScreenR annotation table containing:
 5320 rows
 5 columns
ScreenR annotation table containing:
 5320 rows
 5 columns
ScreenR count table containing:
 5320 rows
 15 columns
ScreenR count table containing:
 5320 rows
 15 columns
ScreenR normalized count table containing:
 5320 rows
 15 columns
ScreenR normalized count table containing:
 5320 rows
 15 columns
ScreenR normalized data table containing:
 74480 rows
 9 columns
ScreenR normalized data table containing:
 74480 rows
 9 columns
Using classic mode.
[ FAIL 0 | WARN 253 | SKIP 0 | PASS 64 ]

[ FAIL 0 | WARN 253 | SKIP 0 | PASS 64 ]
> 
> proc.time()
   user  system elapsed 
 23.662   0.525  24.175 

Example timings

ScreenR.Rcheck/ScreenR-Ex.timings

nameusersystemelapsed
barcode_lost0.1320.0160.148
compute_data_table0.2030.0000.202
compute_explained_variance0.0190.0000.018
compute_metrics23.162 1.46324.628
compute_slope0.0370.0030.042
count_mapped_reads0.0360.0000.036
create_edger_obj0.0210.0000.021
create_screenr_object0.0420.0000.043
filter_by_slope0.1190.0000.120
filter_by_variance1.1210.0151.137
find_camera_hit1.1760.0041.180
find_common_hit0.0380.0010.038
find_roast_hit1.7260.0071.734
find_robust_zscore_hit19.513 0.49220.006
find_zscore_hit19.388 0.22819.616
get_annotation_table0.0140.0000.014
get_count_table0.0740.0040.077
get_data_table0.030.000.03
get_groups0.0010.0000.001
get_normalized_count_table0.0370.0000.038
get_replicates000
mapped_reads0.0450.0000.045
normalize_data0.0410.0000.040
plot_barcode_hit1.2290.0081.236
plot_barcode_lost0.3560.0000.357
plot_barcode_lost_for_gene1.2360.0001.236
plot_barcode_trend40.206 0.60840.814
plot_boxplot0.2970.0040.301
plot_common_hit0.2080.0000.208
plot_explained_variance0.3040.0000.304
plot_mapped_reads0.1660.0000.166
plot_mapped_reads_distribution1.4010.0041.405
plot_mds0.3650.0040.368
plot_trend1.3340.0001.334
plot_zscore_distribution40.320 0.53240.853
remove_all_zero_row0.0120.0080.020
set_annotation_table0.1420.0000.141
set_count_table0.1240.0040.128
set_data_table0.1380.0000.138
set_groups0.1400.0000.141
set_normalized_count_table0.1910.0000.192
set_replicates0.1370.0000.137