| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:31 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1840/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ScreenR 1.1.0 (landing page) Emanuel Michele Soda
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ||||||||||
| Package: ScreenR |
| Version: 1.1.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ScreenR_1.1.0.tar.gz |
| StartedAt: 2023-04-11 23:24:52 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 23:28:30 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 218.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ScreenR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:ScreenR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings ScreenR_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/ScreenR.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* 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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_zscore_distribution 38.327 0.432 38.804
plot_barcode_trend 37.085 0.560 37.645
compute_metrics 22.059 1.488 23.547
find_zscore_hit 18.249 0.219 18.469
find_robust_zscore_hit 17.982 0.461 18.441
* 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 ...
‘Analysis_Example.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
ScreenR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL ScreenR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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)
ScreenR.Rcheck/tests/testthat.Rout
R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
24.454 0.756 25.194
ScreenR.Rcheck/ScreenR-Ex.timings
| name | user | system | elapsed | |
| barcode_lost | 0.166 | 0.007 | 0.174 | |
| compute_data_table | 0.212 | 0.008 | 0.220 | |
| compute_explained_variance | 0.018 | 0.007 | 0.026 | |
| compute_metrics | 22.059 | 1.488 | 23.547 | |
| compute_slope | 0.064 | 0.000 | 0.064 | |
| count_mapped_reads | 0.049 | 0.001 | 0.050 | |
| create_edger_obj | 0.029 | 0.000 | 0.029 | |
| create_screenr_object | 0.048 | 0.000 | 0.048 | |
| filter_by_slope | 0.127 | 0.003 | 0.131 | |
| filter_by_variance | 1.114 | 0.005 | 1.119 | |
| find_camera_hit | 1.202 | 0.003 | 1.206 | |
| find_common_hit | 0.035 | 0.001 | 0.034 | |
| find_roast_hit | 1.835 | 0.015 | 1.851 | |
| find_robust_zscore_hit | 17.982 | 0.461 | 18.441 | |
| find_zscore_hit | 18.249 | 0.219 | 18.469 | |
| get_annotation_table | 0.015 | 0.001 | 0.015 | |
| get_count_table | 0.078 | 0.003 | 0.082 | |
| get_data_table | 0.029 | 0.000 | 0.029 | |
| get_groups | 0.001 | 0.001 | 0.001 | |
| get_normalized_count_table | 0.047 | 0.000 | 0.047 | |
| get_replicates | 0 | 0 | 0 | |
| mapped_reads | 0.064 | 0.000 | 0.064 | |
| normalize_data | 0.046 | 0.000 | 0.046 | |
| plot_barcode_hit | 1.236 | 0.007 | 1.244 | |
| plot_barcode_lost | 0.354 | 0.000 | 0.354 | |
| plot_barcode_lost_for_gene | 1.355 | 0.008 | 1.363 | |
| plot_barcode_trend | 37.085 | 0.560 | 37.645 | |
| plot_boxplot | 0.381 | 0.000 | 0.382 | |
| plot_common_hit | 0.239 | 0.000 | 0.239 | |
| plot_explained_variance | 0.381 | 0.000 | 0.382 | |
| plot_mapped_reads | 0.196 | 0.000 | 0.196 | |
| plot_mapped_reads_distribution | 2.177 | 0.016 | 2.192 | |
| plot_mds | 0.393 | 0.000 | 0.392 | |
| plot_trend | 1.469 | 0.015 | 1.484 | |
| plot_zscore_distribution | 38.327 | 0.432 | 38.804 | |
| remove_all_zero_row | 0.017 | 0.000 | 0.017 | |
| set_annotation_table | 0.16 | 0.00 | 0.16 | |
| set_count_table | 0.134 | 0.000 | 0.134 | |
| set_data_table | 0.139 | 0.000 | 0.140 | |
| set_groups | 0.139 | 0.004 | 0.143 | |
| set_normalized_count_table | 0.189 | 0.000 | 0.190 | |
| set_replicates | 0.141 | 0.000 | 0.140 | |