Emanuel Michele Soda
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/ScreenR |
| git_branch: devel |
| git_last_commit: f8f8e19 |
| git_last_commit_date: 2023-10-24 11:42:30 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:38:29 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R 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 1894/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ScreenR 1.5.0 (landing page) Emanuel Michele Soda
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. |
| Package: ScreenR |
| Version: 1.5.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ScreenR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ScreenR_1.5.0.tar.gz |
| StartedAt: 2024-03-28 06:28:08 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 06:33:38 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 329.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ScreenR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ScreenR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings ScreenR_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/ScreenR.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 'ScreenR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ScreenR' version '1.5.0'
* 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 '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 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 56.55 8.77 65.07
plot_barcode_trend 49.49 5.85 55.12
compute_metrics 28.17 1.50 29.75
find_zscore_hit 26.75 2.53 29.19
find_robust_zscore_hit 25.22 3.94 29.06
* 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: 2 NOTEs
See
'F:/biocbuild/bbs-3.19-bioc/meat/ScreenR.Rcheck/00check.log'
for details.
ScreenR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL ScreenR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.19-bioc/R/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)
ScreenR.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(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
32.12 2.64 34.73
ScreenR.Rcheck/ScreenR-Ex.timings
| name | user | system | elapsed | |
| barcode_lost | 0.09 | 0.05 | 0.14 | |
| compute_data_table | 0.27 | 0.01 | 0.28 | |
| compute_explained_variance | 0.03 | 0.00 | 0.03 | |
| compute_metrics | 28.17 | 1.50 | 29.75 | |
| compute_slope | 0.07 | 0.00 | 0.07 | |
| count_mapped_reads | 0.06 | 0.00 | 0.06 | |
| create_edger_obj | 0.03 | 0.00 | 0.03 | |
| create_screenr_object | 0.06 | 0.00 | 0.06 | |
| filter_by_slope | 0.18 | 0.03 | 0.20 | |
| filter_by_variance | 1.71 | 0.03 | 1.75 | |
| find_camera_hit | 2.08 | 0.06 | 2.14 | |
| find_common_hit | 0.05 | 0.00 | 0.04 | |
| find_roast_hit | 2.50 | 0.06 | 2.57 | |
| find_robust_zscore_hit | 25.22 | 3.94 | 29.06 | |
| find_zscore_hit | 26.75 | 2.53 | 29.19 | |
| get_annotation_table | 0.03 | 0.00 | 0.03 | |
| get_count_table | 0.12 | 0.11 | 0.23 | |
| get_data_table | 0.04 | 0.00 | 0.03 | |
| get_groups | 0 | 0 | 0 | |
| get_normalized_count_table | 0.04 | 0.00 | 0.05 | |
| get_replicates | 0 | 0 | 0 | |
| mapped_reads | 0.08 | 0.00 | 0.08 | |
| normalize_data | 0.08 | 0.00 | 0.08 | |
| plot_barcode_hit | 1.81 | 0.17 | 1.98 | |
| plot_barcode_lost | 0.83 | 0.05 | 0.88 | |
| plot_barcode_lost_for_gene | 1.42 | 0.04 | 1.47 | |
| plot_barcode_trend | 49.49 | 5.85 | 55.12 | |
| plot_boxplot | 0.37 | 0.01 | 0.39 | |
| plot_common_hit | 0.27 | 0.00 | 0.28 | |
| plot_explained_variance | 1.01 | 0.05 | 1.07 | |
| plot_mapped_reads | 0.38 | 0.00 | 0.37 | |
| plot_mapped_reads_distribution | 2.09 | 0.03 | 2.13 | |
| plot_mds | 0.74 | 0.00 | 0.74 | |
| plot_trend | 2.26 | 0.48 | 2.75 | |
| plot_zscore_distribution | 56.55 | 8.77 | 65.07 | |
| remove_all_zero_row | 0.01 | 0.00 | 0.02 | |
| set_annotation_table | 0.19 | 0.00 | 0.19 | |
| set_count_table | 0.2 | 0.0 | 0.2 | |
| set_data_table | 0.21 | 0.01 | 0.22 | |
| set_groups | 0.19 | 0.00 | 0.20 | |
| set_normalized_count_table | 0.25 | 0.00 | 0.25 | |
| set_replicates | 0.18 | 0.00 | 0.19 | |