Kent Riemondy
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/clustifyr |
| git_branch: master |
| git_last_commit: f0341a1 |
| git_last_commit_date: 2022-03-09 14:11:06 -0400 (Wed, 09 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:12 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 clustifyr package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/clustifyr.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 342/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| clustifyr 1.7.3 (landing page) Kent Riemondy
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: clustifyr |
| Version: 1.7.3 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clustifyr.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings clustifyr_1.7.3.tar.gz |
| StartedAt: 2022-03-17 18:45:07 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:49:43 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 276.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: clustifyr.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clustifyr.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings clustifyr_1.7.3.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/clustifyr.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'clustifyr/DESCRIPTION' ... OK * this is package 'clustifyr' version '1.7.3' * 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 'clustifyr' 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 ... NOTE assess_rank_bias : <anonymous>: no visible binding for '<<-' assignment to 'res3' assess_rank_bias: no visible binding for global variable 'res3' average_clusters : <anonymous>: no visible binding for global variable 'pbmc_matrix_small' Undefined global functions or variables: pbmc_matrix_small res3 * 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 LazyData ... 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 'D:/biocbuild/bbs-3.15-bioc/meat/clustifyr.Rcheck/00check.log' for details.
clustifyr.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL clustifyr
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'clustifyr' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'clustifyr'
finding HTML links ... done
append_genes html
assess_rank_bias html
assign_ident html
average_clusters html
binarize_expr html
build_atlas html
calc_distance html
calc_similarity html
calculate_pathway_gsea html
call_consensus html
call_to_metadata html
cbmc_m html
cbmc_ref html
check_raw_counts html
clustify html
clustify_lists html
clustify_nudge html
clustifyr-package html
clustifyr_methods html
collapse_to_cluster html
compare_lists html
cor_to_call html
cor_to_call_rank html
cor_to_call_topn html
cosine html
downrefs html
downsample_matrix html
feature_select_PCA html
file_marker_parse html
find_rank_bias html
gene_pct html
gene_pct_markerm html
get_best_match_matrix html
get_best_str html
get_common_elements html
get_similarity html
get_ucsc_reference html
get_unique_column html
get_vargenes html
gmt_to_list html
human_genes_10x html
insert_meta_object html
kl_divergence html
make_comb_ref html
marker_select html
matrixize_markers html
mouse_genes_10x html
not_pretty_palette html
object_data html
object_loc_lookup html
object_ref html
overcluster html
overcluster_test html
parse_loc_object html
pbmc_markers html
pbmc_markers_M3Drop html
pbmc_matrix_small html
pbmc_meta html
pbmc_vargenes html
percent_clusters html
permute_similarity html
plot_best_call html
plot_call html
plot_cor html
plot_cor_heatmap html
plot_dims html
plot_gene html
plot_pathway_gsea html
plot_rank_bias html
pos_neg_marker html
pos_neg_select html
pretty_palette html
pretty_palette2 html
pretty_palette_ramp_d html
query_rank_bias html
ref_feature_select html
ref_marker_select html
reverse_marker_matrix html
run_clustifyr_app html
run_gsea html
s_small html
s_small3 html
sce_small html
seurat_meta html
seurat_ref html
vector_similarity html
write_meta html
*** 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 (clustifyr)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'DEFormats' is missing or broken
done
clustifyr.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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(clustifyr)
>
> test_check("clustifyr")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 172 ]
>
> proc.time()
user system elapsed
101.31 9.00 110.34
clustifyr.Rcheck/clustifyr-Ex.timings
| name | user | system | elapsed | |
| append_genes | 0.04 | 0.01 | 0.05 | |
| assess_rank_bias | 0 | 0 | 0 | |
| average_clusters | 0.49 | 0.00 | 0.49 | |
| binarize_expr | 0.01 | 0.03 | 0.04 | |
| build_atlas | 0.05 | 0.03 | 0.08 | |
| calc_distance | 0.01 | 0.00 | 0.02 | |
| calculate_pathway_gsea | 1.89 | 0.07 | 1.95 | |
| call_consensus | 0.18 | 0.03 | 0.20 | |
| call_to_metadata | 0.15 | 0.06 | 0.22 | |
| check_raw_counts | 0.91 | 0.11 | 1.02 | |
| clustify | 0.17 | 0.00 | 0.17 | |
| clustify_lists | 0.06 | 0.00 | 0.06 | |
| clustify_nudge | 0.39 | 0.01 | 0.40 | |
| clustifyr_methods | 0 | 0 | 0 | |
| collapse_to_cluster | 0.88 | 0.08 | 0.96 | |
| compare_lists | 0.09 | 0.03 | 0.12 | |
| cor_to_call | 0.06 | 0.00 | 0.06 | |
| cor_to_call_rank | 0.06 | 0.00 | 0.06 | |
| cor_to_call_topn | 0.07 | 0.00 | 0.07 | |
| downsample_matrix | 0.07 | 0.00 | 0.07 | |
| feature_select_PCA | 0.02 | 0.00 | 0.02 | |
| file_marker_parse | 0 | 0 | 0 | |
| find_rank_bias | 0.01 | 0.03 | 0.05 | |
| gene_pct_markerm | 0.24 | 0.00 | 0.23 | |
| get_ucsc_reference | 0 | 0 | 0 | |
| get_vargenes | 0 | 0 | 0 | |
| gmt_to_list | 0.22 | 0.02 | 0.25 | |
| insert_meta_object | 0 | 0 | 0 | |
| make_comb_ref | 0.00 | 0.01 | 0.02 | |
| marker_select | 0.01 | 0.00 | 0.01 | |
| matrixize_markers | 0.03 | 0.00 | 0.03 | |
| object_data | 0.04 | 0.00 | 0.03 | |
| object_ref | 0 | 0 | 0 | |
| overcluster | 1.18 | 0.36 | 1.55 | |
| overcluster_test | 0.86 | 0.02 | 0.88 | |
| parse_loc_object | 0 | 0 | 0 | |
| plot_best_call | 0.41 | 0.11 | 0.51 | |
| plot_cor | 0.45 | 0.01 | 0.47 | |
| plot_cor_heatmap | 0.58 | 0.03 | 0.61 | |
| plot_dims | 0.22 | 0.00 | 0.22 | |
| plot_gene | 0.33 | 0.02 | 0.34 | |
| plot_pathway_gsea | 2.54 | 0.02 | 2.57 | |
| plot_rank_bias | 0 | 0 | 0 | |
| pos_neg_marker | 0.02 | 0.00 | 0.01 | |
| pos_neg_select | 0.03 | 0.01 | 0.05 | |
| query_rank_bias | 0.03 | 0.00 | 0.03 | |
| ref_feature_select | 0.03 | 0.02 | 0.05 | |
| ref_marker_select | 0.11 | 0.00 | 0.11 | |
| reverse_marker_matrix | 0 | 0 | 0 | |
| run_clustifyr_app | 0 | 0 | 0 | |
| seurat_meta | 0 | 0 | 0 | |
| seurat_ref | 0 | 0 | 0 | |
| write_meta | 0.08 | 0.00 | 0.08 | |