| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:50 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 | ||||
|
To the developers/maintainers of the ScreenR package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1799/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ScreenR 1.1.0 (landing page) Emanuel Michele Soda
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: ScreenR |
| Version: 1.1.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ScreenR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ScreenR_1.1.0.tar.gz |
| StartedAt: 2022-12-29 03:22:51 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 03:32:56 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 605.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ScreenR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ScreenR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ScreenR_1.1.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/ScreenR.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server 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 '1.1.0'
* 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 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_barcode_trend 193.55 6.15 199.83
plot_zscore_distribution 107.66 7.30 114.97
find_zscore_hit 82.25 3.28 85.54
find_robust_zscore_hit 46.64 1.67 48.31
compute_metrics 39.84 1.34 41.20
plot_trend 9.29 0.27 9.58
find_roast_hit 7.80 0.48 8.29
* 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: OK
ScreenR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL ScreenR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-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) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 251 | SKIP 0 | PASS 64 ]
[ FAIL 0 | WARN 251 | SKIP 0 | PASS 64 ]
>
> proc.time()
user system elapsed
24.12 1.59 25.76
ScreenR.Rcheck/ScreenR-Ex.timings
| name | user | system | elapsed | |
| barcode_lost | 0.16 | 0.00 | 0.15 | |
| compute_data_table | 0.19 | 0.02 | 0.20 | |
| compute_explained_variance | 0.02 | 0.00 | 0.02 | |
| compute_metrics | 39.84 | 1.34 | 41.20 | |
| compute_slope | 0.09 | 0.00 | 0.09 | |
| count_mapped_reads | 0.07 | 0.00 | 0.07 | |
| create_edger_obj | 0.03 | 0.00 | 0.03 | |
| create_screenr_object | 0.05 | 0.00 | 0.04 | |
| filter_by_slope | 0.31 | 0.00 | 0.32 | |
| filter_by_variance | 3.51 | 0.08 | 3.59 | |
| find_camera_hit | 3.88 | 0.05 | 3.92 | |
| find_common_hit | 0.06 | 0.00 | 0.06 | |
| find_roast_hit | 7.80 | 0.48 | 8.29 | |
| find_robust_zscore_hit | 46.64 | 1.67 | 48.31 | |
| find_zscore_hit | 82.25 | 3.28 | 85.54 | |
| get_annotation_table | 0.01 | 0.00 | 0.02 | |
| get_count_table | 0.14 | 0.05 | 0.22 | |
| 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 | 0.10 | 0.00 | 0.09 | |
| normalize_data | 0.04 | 0.00 | 0.05 | |
| plot_barcode_hit | 2.97 | 0.06 | 3.03 | |
| plot_barcode_lost | 2.21 | 0.08 | 2.28 | |
| plot_barcode_lost_for_gene | 1.34 | 0.02 | 1.36 | |
| plot_barcode_trend | 193.55 | 6.15 | 199.83 | |
| plot_boxplot | 0.93 | 0.00 | 0.94 | |
| plot_common_hit | 0.21 | 0.02 | 0.25 | |
| plot_explained_variance | 0.43 | 0.00 | 0.43 | |
| plot_mapped_reads | 0.22 | 0.00 | 0.22 | |
| plot_mapped_reads_distribution | 2.82 | 0.01 | 2.83 | |
| plot_mds | 0.78 | 0.00 | 0.78 | |
| plot_trend | 9.29 | 0.27 | 9.58 | |
| plot_zscore_distribution | 107.66 | 7.30 | 114.97 | |
| remove_all_zero_row | 0.03 | 0.00 | 0.03 | |
| set_annotation_table | 0.19 | 0.00 | 0.19 | |
| set_count_table | 0.12 | 0.00 | 0.12 | |
| set_data_table | 0.14 | 0.00 | 0.14 | |
| set_groups | 0.16 | 0.01 | 0.17 | |
| set_normalized_count_table | 0.2 | 0.0 | 0.2 | |
| set_replicates | 0.16 | 0.02 | 0.17 | |