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This page was generated on 2024-06-11 14:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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: 2024-06-09 14:00 -0400 (Sun, 09 Jun 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
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 2024-06-10 03:14:02 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 03:17:48 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 226.4 seconds
RetCode: 0
Status:   OK  
CheckDir: ScreenR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 (2024-04-24)
* 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 40.790  0.560  41.350
plot_barcode_trend       40.475  0.560  41.035
compute_metrics          23.476  1.827  25.304
find_robust_zscore_hit   19.332  0.500  19.832
find_zscore_hit          19.404  0.396  19.800
* 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

##############################################################################
##############################################################################
###
### 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 (2024-04-24) -- "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 
 23.624   0.525  24.139 

Example timings

ScreenR.Rcheck/ScreenR-Ex.timings

nameusersystemelapsed
barcode_lost0.1260.0190.146
compute_data_table0.1910.0080.199
compute_explained_variance0.0190.0000.018
compute_metrics23.476 1.82725.304
compute_slope0.0410.0000.041
count_mapped_reads0.0320.0000.033
create_edger_obj0.0120.0080.019
create_screenr_object0.0350.0040.038
filter_by_slope0.1170.0030.121
filter_by_variance1.0990.0041.104
find_camera_hit1.1690.0051.173
find_common_hit0.0270.0000.026
find_roast_hit1.7290.0001.729
find_robust_zscore_hit19.332 0.50019.832
find_zscore_hit19.404 0.39619.800
get_annotation_table0.0130.0000.014
get_count_table0.0770.0000.077
get_data_table0.0260.0000.026
get_groups000
get_normalized_count_table0.0330.0030.037
get_replicates000
mapped_reads0.0570.0010.057
normalize_data0.040.000.04
plot_barcode_hit1.2220.0031.225
plot_barcode_lost0.3710.0000.371
plot_barcode_lost_for_gene1.2910.0011.291
plot_barcode_trend40.475 0.56041.035
plot_boxplot0.3180.0030.320
plot_common_hit0.220.000.22
plot_explained_variance0.3320.0000.332
plot_mapped_reads0.1720.0000.172
plot_mapped_reads_distribution1.4200.0041.424
plot_mds0.3710.0000.371
plot_trend1.5210.0121.533
plot_zscore_distribution40.79 0.5641.35
remove_all_zero_row0.0130.0000.012
set_annotation_table0.1210.0000.121
set_count_table0.1260.0000.126
set_data_table0.1420.0000.142
set_groups0.1240.0000.124
set_normalized_count_table0.1740.0000.173
set_replicates0.1510.0000.152