Andrea Calabria
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/ISAnalytics |
| Branch: RELEASE_3_12 |
| Last Commit: a1014e7 |
| Last Changed Date: 2021-04-08 08:11:42 -0400 (Thu, 08 Apr 2021) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:35:24 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the ISAnalytics package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 913/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ISAnalytics 1.0.11 (landing page) Andrea Calabria
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ISAnalytics |
| Version: 1.0.11 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ISAnalytics_1.0.11.tar.gz |
| StartedAt: 2021-05-06 02:56:47 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 03:00:15 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 208.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ISAnalytics.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ISAnalytics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ISAnalytics_1.0.11.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/ISAnalytics.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ISAnalytics/DESCRIPTION’ ... OK
* this is package ‘ISAnalytics’ version ‘1.0.11’
* 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 ‘ISAnalytics’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
remove_collisions 31.656 1.796 10.357
realign_after_collisions 31.692 1.736 10.361
CIS_grubbs 6.341 0.521 6.345
CIS_volcano_plot 6.084 0.535 6.129
* 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
ISAnalytics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ISAnalytics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘ISAnalytics’ ... ** using staged installation ** R ** 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 (ISAnalytics)
ISAnalytics.Rcheck/tests/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(ISAnalytics)
Loading required package: magrittr
Attaching package: 'magrittr'
The following objects are masked from 'package:testthat':
equals, is_less_than, not
>
> test_check("ISAnalytics")
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
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Identifying collisions...
Processing collisions...
Finished! You provided a single sequence count as matrix, to re-align other related matrices see ?realign_after_collisions
Duplicates found for some files
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Some files are missing and will be ignored
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Some files are missing and will be ignored
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Some files are missing and will be ignored
Some files are missing and will be ignored
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Duplicates found for some files: in automatic mode duplicates are not preserved - use interactive mode for more accurate file selection
Some files are missing and will be ignored
Some files are missing and will be ignored
adding: tmp/RtmpBaSMEI/file7c234c417472.tsv (deflated 43%)
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 742 ]
>
> proc.time()
user system elapsed
144.478 16.052 86.178
ISAnalytics.Rcheck/ISAnalytics-Ex.timings
| name | user | system | elapsed | |
| CIS_grubbs | 6.341 | 0.521 | 6.345 | |
| CIS_volcano_plot | 6.084 | 0.535 | 6.129 | |
| aggregate_metadata | 0.190 | 0.022 | 0.212 | |
| aggregate_values_by_key | 1.277 | 0.441 | 1.138 | |
| annotation_IS_vars | 0.000 | 0.000 | 0.001 | |
| as_sparse_matrix | 0.819 | 1.054 | 0.731 | |
| association_file_columns | 0.001 | 0.001 | 0.002 | |
| clinical_relevant_suspicious_genes | 0.021 | 0.003 | 0.025 | |
| comparison_matrix | 1.011 | 0.348 | 1.107 | |
| compute_abundance | 1.023 | 1.128 | 0.861 | |
| compute_near_integrations | 1.687 | 2.062 | 1.393 | |
| cumulative_count_union | 1.253 | 0.560 | 1.178 | |
| date_columns_coll | 0 | 0 | 0 | |
| date_formats | 0.001 | 0.000 | 0.000 | |
| default_stats | 1.248 | 0.086 | 1.339 | |
| generate_Vispa2_launch_AF | 0.152 | 0.017 | 0.170 | |
| generate_blank_association_file | 0.007 | 0.001 | 0.006 | |
| import_association_file | 0.141 | 0.023 | 0.164 | |
| import_parallel_Vispa2Matrices_auto | 1.148 | 0.422 | 1.099 | |
| import_parallel_Vispa2Matrices_interactive | 0.000 | 0.001 | 0.000 | |
| import_single_Vispa2Matrix | 0.963 | 1.104 | 0.835 | |
| known_clinical_oncogenes | 0.015 | 0.005 | 0.019 | |
| mandatory_IS_vars | 0 | 0 | 0 | |
| matching_options | 0 | 0 | 0 | |
| quantification_types | 0.001 | 0.000 | 0.000 | |
| realign_after_collisions | 31.692 | 1.736 | 10.361 | |
| reduced_AF_columns | 0.001 | 0.001 | 0.001 | |
| remove_collisions | 31.656 | 1.796 | 10.357 | |
| sample_statistics | 1.230 | 0.396 | 1.175 | |
| separate_quant_matrices | 1.092 | 0.392 | 0.986 | |
| threshold_filter | 0.020 | 0.003 | 0.023 | |
| top_integrations | 0.054 | 0.006 | 0.061 | |
| unzip_file_system | 0.006 | 0.018 | 0.023 | |