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This page was generated on 2023-11-02 11:41:15 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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 1896/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ScreenR 1.4.0  (landing page)
Emanuel Michele Soda
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/ScreenR
git_branch: RELEASE_3_18
git_last_commit: 36bfecb
git_last_commit_date: 2023-10-24 11:42:29 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  

CHECK results for ScreenR on kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: ScreenR
Version: 1.4.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ScreenR_1.4.0.tar.gz
StartedAt: 2023-11-02 14:12:00 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 14:16:57 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 296.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: ScreenR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ScreenR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ScreenR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ScreenR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ScreenR’ version ‘1.4.0’
* 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 R 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 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 ... 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ScreenR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_zscore_distribution
> ### Title: Plot distribution Z-score
> ### Aliases: plot_zscore_distribution
> 
> ### ** Examples
> 
> object <- get0("object", envir = asNamespace("ScreenR"))
> 
> table1 <- compute_metrics(object,
+     control = "TRT", treatment = "Time3",
+     day = "Time3"
+ )
> 
> table2 <- compute_metrics(object,
+     control = "TRT", treatment = "Time4",
+     day = "Time4"
+ )
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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 ERROR
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/ScreenR.Rcheck/00check.log’
for details.


Installation output

ScreenR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL ScreenR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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(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 
 35.477   1.037  36.765 

Example timings

ScreenR.Rcheck/ScreenR-Ex.timings

nameusersystemelapsed
barcode_lost0.2030.0160.219
compute_data_table0.3050.0120.318
compute_explained_variance0.0370.0000.038
compute_metrics34.841 1.39736.307
compute_slope0.0730.0000.074
count_mapped_reads0.0640.0000.065
create_edger_obj0.0400.0000.041
create_screenr_object0.0680.0010.068
filter_by_slope0.1990.0000.199
filter_by_variance1.5320.0031.538
find_camera_hit1.6860.0051.693
find_common_hit0.0410.0000.042
find_roast_hit2.5120.0072.523
find_robust_zscore_hit27.585 0.44028.073
find_zscore_hit28.564 0.32728.943
get_annotation_table0.0220.0000.022
get_count_table0.1050.0000.104
get_data_table0.040.000.04
get_groups000
get_normalized_count_table0.0670.0000.067
get_replicates000
mapped_reads0.0860.0040.090
normalize_data0.0590.0040.063
plot_barcode_hit1.8850.0001.889
plot_barcode_lost0.4960.0040.501
plot_barcode_lost_for_gene2.1370.0162.157
plot_barcode_trend58.020 0.54758.677
plot_boxplot0.5510.0000.552
plot_common_hit0.4840.0000.487
plot_explained_variance0.4820.0000.483
plot_mapped_reads0.2530.0040.258
plot_mapped_reads_distribution2.8000.0322.837
plot_mds0.5360.0000.537
plot_trend2.0120.0242.040