Ariane L. Moore
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/GeneAccord |
| Branch: RELEASE_3_10 |
| Last Commit: ad6ab9d |
| Last Changed Date: 2019-10-29 13:11:18 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:14:34 -0400 (Wed, 15 Apr 2020).
| Package 646/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GeneAccord 1.4.0 Ariane L. Moore
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: GeneAccord |
| Version: 1.4.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GeneAccord.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GeneAccord_1.4.0.tar.gz |
| StartedAt: 2020-04-15 05:56:19 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 05:58:30 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 130.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GeneAccord.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GeneAccord.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GeneAccord_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/GeneAccord.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneAccord/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneAccord’ 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 ‘GeneAccord’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 10.0Mb
sub-directories of 1Mb or more:
data 3.0Mb
extdata 6.6Mb
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* 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 NOTE
See
‘/home/biocbuild/bbs-3.10-bioc/meat/GeneAccord.Rcheck/00check.log’
for details.
GeneAccord.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL GeneAccord ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘GeneAccord’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (GeneAccord)
GeneAccord.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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("assertthat")
>
> library("GeneAccord")
> # "When R CMD check runs tests, it sets R_TESTS. When the tests
> # themeselves run R CMD xxxx, as is the case with the tests in
> # devtools, having R_TESTS set causes errors because it confuses
> # the R subprocesses. Unsetting it here avoids those problems.
> #"R_TESTS" = "" "
> Sys.setenv("R_TESTS" = "")
>
> test_check("GeneAccord")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 27 | SKIPPED: 6 | WARNINGS: 0 | FAILED: 0 ]
>
>
> proc.time()
user system elapsed
15.116 0.160 15.384
GeneAccord.Rcheck/GeneAccord-Ex.timings
| name | user | system | elapsed | |
| GeneAccord | 2.232 | 0.008 | 2.252 | |
| build_null_test_statistic | 2.040 | 0.000 | 2.049 | |
| compute_rates_clon_excl | 0.248 | 0.000 | 0.250 | |
| compute_test_stat_avg_rate | 0.044 | 0.000 | 0.041 | |
| convert_ensembl_to_reactome_pw_tbl | 0.460 | 0.008 | 0.471 | |
| create_ensembl_gene_tbl_hg | 0.000 | 0.000 | 0.001 | |
| create_tbl_ent_clones | 0.072 | 0.000 | 0.101 | |
| create_tbl_tree_collection | 0.456 | 0.000 | 0.668 | |
| ecdf_lr_test_clon_excl_avg_rate | 0.680 | 0.000 | 0.709 | |
| ensembl_to_hgnc | 0 | 0 | 0 | |
| ensembl_to_reactome | 0.024 | 0.000 | 0.024 | |
| extract_num_clones_tbl | 0.036 | 0.000 | 0.035 | |
| generate_ecdf_test_stat | 0.620 | 0.004 | 0.624 | |
| generate_test_stat_hist | 0.964 | 0.000 | 0.991 | |
| get_hist_clon_excl | 0.696 | 0.000 | 0.702 | |
| get_hist_clon_excl_this_pat_this_pair | 0.024 | 0.000 | 0.044 | |
| get_rate_diff_branch_ent_pair | 0.408 | 0.000 | 0.470 | |
| heatmap_clones_gene_pat | 0.940 | 0.000 | 0.963 | |
| hgnc_to_ensembl | 0 | 0 | 0 | |
| is_diff_branch_ent_pair | 0.012 | 0.000 | 0.011 | |
| map_pairs_to_hgnc_symbols | 0 | 0 | 0 | |
| merge_clones_identical_ents | 0.052 | 0.000 | 0.051 | |
| pairs_in_patients_hist | 0.040 | 0.000 | 0.041 | |
| plot_ecdf_test_stat | 0.240 | 0.000 | 0.241 | |
| plot_rates_clon_excl | 0.292 | 0.000 | 0.292 | |
| take_pairs_and_get_patients | 0.168 | 0.000 | 0.167 | |
| vis_pval_distr_num_pat | 0.040 | 0.000 | 0.041 | |
| write_res_pairs_to_disk | 0.012 | 0.000 | 0.011 | |