Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-03-27 11:36:32 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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

Package 375/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clustifyr 1.14.0  (landing page)
Kent Riemondy
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/clustifyr
git_branch: RELEASE_3_18
git_last_commit: de3d2df
git_last_commit_date: 2023-10-24 11:19:27 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for clustifyr on palomino4


To the developers/maintainers of the clustifyr package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: clustifyr
Version: 1.14.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clustifyr.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings clustifyr_1.14.0.tar.gz
StartedAt: 2024-03-25 23:30:55 -0400 (Mon, 25 Mar 2024)
EndedAt: 2024-03-25 23:43:45 -0400 (Mon, 25 Mar 2024)
EllapsedTime: 769.4 seconds
RetCode: 0
Status:   OK  
CheckDir: clustifyr.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:clustifyr.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings clustifyr_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/clustifyr.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'clustifyr/DESCRIPTION' ... OK
* this is package 'clustifyr' version '1.14.0'
* 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 '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
gmt_to_list: no visible global function definition for 'read.csv'
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
* 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
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
plot_pathway_gsea      18.02   0.21   18.25
calculate_pathway_gsea 15.00   0.04   15.08
* 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
  'F:/biocbuild/bbs-3.18-bioc/meat/clustifyr.Rcheck/00check.log'
for details.



Installation output

clustifyr.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL clustifyr
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-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
*** 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)

Tests output

clustifyr.Rcheck/tests/testthat.Rout


R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 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")

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[ FAIL 0 | WARN 7 | SKIP 0 | PASS 176 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 176 ]
> 
> proc.time()
   user  system elapsed 
 500.54    5.53  507.71 

Example timings

clustifyr.Rcheck/clustifyr-Ex.timings

nameusersystemelapsed
append_genes0.690.000.68
assess_rank_bias000
average_clusters0.080.000.08
binarize_expr0.090.000.09
build_atlas0.740.020.75
calc_distance000
calculate_pathway_gsea15.00 0.0415.08
call_consensus0.310.040.34
call_to_metadata0.270.200.47
check_raw_counts0.810.010.83
clustify0.160.000.16
clustify_lists0.060.020.07
clustify_nudge0.580.020.61
clustifyr_methods000
collapse_to_cluster0.650.070.74
compare_lists0.860.020.87
cor_to_call0.080.000.08
cor_to_call_rank0.090.000.09
cor_to_call_topn0.090.000.09
downsample_matrix0.050.000.05
feature_select_PCA0.020.000.02
file_marker_parse0.000.000.01
find_rank_bias0.030.010.05
gene_pct_markerm0.390.000.39
get_ucsc_reference000
get_vargenes000
gmt_to_list0.060.000.06
insert_meta_object000
make_comb_ref0.020.000.02
marker_select0.010.000.01
matrixize_markers0.030.000.03
object_data0.050.000.05
object_ref0.020.000.02
overcluster1.340.051.39
overcluster_test1.780.061.84
parse_loc_object000
plot_best_call0.560.050.61
plot_cor0.770.020.80
plot_cor_heatmap1.340.501.42
plot_dims0.420.230.37
plot_gene0.750.170.71
plot_pathway_gsea18.02 0.2118.25
plot_rank_bias0.020.000.01
pos_neg_marker000
pos_neg_select0.090.000.10
query_rank_bias0.060.000.06
ref_feature_select0.050.010.06
ref_marker_select0.260.000.27
reverse_marker_matrix000
run_clustifyr_app000
seurat_meta000
seurat_ref000
write_meta0.120.000.13