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This page was generated on 2024-12-23 11:43 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4372
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 2131/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tidytof 1.1.0  (landing page)
Timothy Keyes
Snapshot Date: 2024-12-22 13:40 -0500 (Sun, 22 Dec 2024)
git_url: https://git.bioconductor.org/packages/tidytof
git_branch: devel
git_last_commit: 3ca5f4a
git_last_commit_date: 2024-10-29 11:33:26 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for tidytof on palomino7

To the developers/maintainers of the tidytof package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/tidytof.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: tidytof
Version: 1.1.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tidytof.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings tidytof_1.1.0.tar.gz
StartedAt: 2024-12-23 05:36:27 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 05:44:46 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 498.8 seconds
RetCode: 0
Status:   OK  
CheckDir: tidytof.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:tidytof.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings tidytof_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/tidytof.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'tidytof/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'tidytof' 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 whether package 'tidytof' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
* 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 code 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 R/sysdata.rda ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/tidytof/libs/x64/tidytof.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
tof_assess_clusters_knn 9.28   0.05    9.33
tof_cluster_flowsom     6.08   0.16    6.32
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'spelling.R'
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  'E:/biocbuild/bbs-3.21-bioc/meat/tidytof.Rcheck/00check.log'
for details.


Installation output

tidytof.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL tidytof
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'tidytof' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign   -c code.cpp -o code.o
g++ -std=gnu++17 -shared -s -static-libgcc -o tidytof.dll tmp.def RcppExports.o code.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-tidytof/00new/tidytof/libs/x64
** 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 (tidytof)

Tests output

tidytof.Rcheck/tests/spelling.Rout


R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> if (requireNamespace("spelling", quietly = TRUE)) {
+     spelling::spell_check_test(
+         vignettes = TRUE, error = FALSE,
+         skip_on_cran = TRUE
+     )
+ }
NULL
> 
> proc.time()
   user  system elapsed 
   0.23    0.00    0.26 

tidytof.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> Sys.setenv(R_TESTS="")
> library(testthat)
> library(tidytof)

Attaching package: 'tidytof'

The following object is masked from 'package:testthat':

    matches

> test_check("tidytof")

Attaching package: 'dplyr'

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'purrr'

The following object is masked from 'package:testthat':

    is_null


Attaching package: 'tidyr'

The following object is masked from 'package:testthat':

    matches

Loading required namespace: diffcyt

Attaching package: 'readr'

The following objects are masked from 'package:testthat':

    edition_get, local_edition

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 709 ]
> 
> proc.time()
   user  system elapsed 
 254.37    6.64  259.06 

Example timings

tidytof.Rcheck/tidytof-Ex.timings

nameusersystemelapsed
as_SingleCellExperiment000
as_flowFrame000
as_flowSet000
as_seurat000
as_tof_tbl0.050.030.08
make_flowcore_annotated_data_frame000
reexports000
rev_asinh000
tidytof_example_data000
tof_analyze_abundance000
tof_analyze_abundance_diffcyt000
tof_analyze_abundance_glmm000
tof_analyze_abundance_ttest000
tof_analyze_expression000
tof_analyze_expression_diffcyt000
tof_analyze_expression_lmm000
tof_analyze_expression_ttest000
tof_annotate_clusters0.110.020.12
tof_apply_classifier000
tof_assess_channels0.110.000.11
tof_assess_clusters_distance0.440.110.55
tof_assess_clusters_entropy0.690.030.71
tof_assess_clusters_knn9.280.059.33
tof_assess_flow_rate0.910.031.14
tof_assess_flow_rate_tibble0.20.00.2
tof_assess_model0.490.000.49
tof_batch_correct000
tof_batch_correct_quantile000
tof_batch_correct_quantile_tibble000
tof_batch_correct_rescale000
tof_calculate_flow_rate0.020.000.02
tof_cluster0.510.060.58
tof_cluster_ddpr0.20.00.2
tof_cluster_flowsom6.080.166.32
tof_cluster_kmeans0.030.000.03
tof_cluster_phenograph1.890.031.92
tof_cosine_dist000
tof_create_grid0.050.000.05
tof_downsample0.140.000.14
tof_downsample_constant0.060.000.06
tof_downsample_density0.530.010.55
tof_downsample_prop0.080.000.08
tof_estimate_density0.380.000.39
tof_extract_central_tendency0.150.000.15
tof_extract_emd1.020.131.17
tof_extract_features0.630.030.66
tof_extract_jsd1.030.221.26
tof_extract_proportion0.160.000.16
tof_extract_threshold0.180.000.19
tof_find_knn0.290.110.39
tof_generate_palette000
tof_get_model_mixture0.320.000.32
tof_get_model_outcomes0.320.000.32
tof_get_model_penalty0.250.000.25
tof_get_model_training_data0.370.000.37
tof_get_model_type0.330.000.33
tof_get_model_x0.250.000.25
tof_get_model_y0.310.000.31
tof_get_panel0.060.000.06
tof_log_rank_test000
tof_make_knn_graph000
tof_make_roc_curve0.380.000.41
tof_metacluster0.720.040.77
tof_metacluster_consensus0.370.050.42
tof_metacluster_flowsom0.970.091.06
tof_metacluster_hierarchical0.080.000.08
tof_metacluster_kmeans0.080.000.08
tof_metacluster_phenograph0.110.000.11
tof_plot_cells_density0.030.000.03
tof_plot_cells_embedding3.720.023.73
tof_plot_cells_layout3.170.023.19
tof_plot_cells_scatter000
tof_plot_clusters_heatmap0.060.000.06
tof_plot_clusters_mst0.190.000.19
tof_plot_clusters_volcano0.050.000.05
tof_plot_model0.560.000.56
tof_plot_sample_features0.10.00.1
tof_plot_sample_heatmap0.050.000.05
tof_postprocess0.10.00.1
tof_predict0.290.000.29
tof_preprocess0.20.00.2
tof_read_data0.090.010.11
tof_reduce_dimensions2.550.022.84
tof_reduce_pca0.200.010.22
tof_reduce_tsne1.160.031.19
tof_reduce_umap3.950.034.11
tof_set_panel0.080.000.08
tof_spade_density0.50.00.5
tof_split_data0.050.000.04
tof_split_tidytof_reduced_dimensions000
tof_train_model1.820.041.86
tof_transform0.120.010.14
tof_upsample0.20.00.2
tof_upsample_distance0.470.000.47
tof_upsample_neighbor0.060.000.06
tof_write_data000
tof_write_fcs000
where000