Pacome Prompsy
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/ChromSCape |
| Branch: RELEASE_3_12 |
| Last Commit: c84df0d |
| Last Changed Date: 2020-10-27 12:02:02 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:30:14 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the ChromSCape package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 298/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChromSCape 1.0.0 (landing page) Pacome Prompsy
| 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: ChromSCape |
| Version: 1.0.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChromSCape.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ChromSCape_1.0.0.tar.gz |
| StartedAt: 2021-05-06 01:25:06 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 01:37:26 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 740.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ChromSCape.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ChromSCape.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings ChromSCape_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/ChromSCape.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ChromSCape/DESCRIPTION' ... OK
* this is package 'ChromSCape' version '1.0.0'
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'ChromSCape' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CompareedgeRGLM 16.48 0.43 16.93
filter_scExp 16.83 0.06 16.89
differential_analysis_scExp 11.50 0.57 12.07
create_scDataset_raw 10.28 0.93 11.21
consensus_clustering_scExp 6.58 0.11 6.69
import_scExp 6.50 0.05 6.54
choose_cluster_scExp 6.00 0.16 6.16
CompareWilcox 5.35 0.07 5.40
num_cell_after_QC_filt_scExp 5.30 0.12 5.43
reduce_dims_scExp 4.95 0.08 5.03
peaks_to_bins 3.73 0.12 6.03
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
filter_scExp 15.96 0.06 16.03
CompareedgeRGLM 14.72 0.22 14.94
create_scDataset_raw 9.80 0.49 10.28
differential_analysis_scExp 9.11 0.04 9.14
import_scExp 7.51 0.04 7.57
num_cell_after_QC_filt_scExp 6.41 0.05 6.46
CompareWilcox 6.17 0.03 6.20
reduce_dims_scExp 6.01 0.02 6.28
peaks_to_bins 4.94 0.15 7.59
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
'C:/Users/biocbuild/bbs-3.12-bioc/meat/ChromSCape.Rcheck/00check.log'
for details.
ChromSCape.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/ChromSCape_1.0.0.tar.gz && rm -rf ChromSCape.buildbin-libdir && mkdir ChromSCape.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ChromSCape.buildbin-libdir ChromSCape_1.0.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL ChromSCape_1.0.0.zip && rm ChromSCape_1.0.0.tar.gz ChromSCape_1.0.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 2737k 100 2737k 0 0 53.8M 0 --:--:-- --:--:-- --:--:-- 54.5M
install for i386
* installing *source* package 'ChromSCape' ...
** 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 'ChromSCape'
finding HTML links ... done
CompareWilcox html
CompareedgeRGLM html
DA_one_vs_rest_fun html
DA_pairwise html
H1proportion html
annotToCol2 html
annotation_from_merged_peaks html
anocol_binary html
anocol_categorical html
bams_to_matrix_indexes html
beds_to_matrix_indexes html
call_macs2_merge_peaks html
changeRange html
check_correct_datamatrix html
choose_cluster_scExp html
choose_perplexity html
col2hex html
colors_scExp html
combine_datamatrix html
combine_enrichmentTests html
consensus_clustering_scExp html
correlation_and_hierarchical_clust_scExp
html
create_sample_name_mat html
create_scDataset_raw html
create_scExp html
define_feature html
detect_samples html
differential_analysis_scExp html
distPearson html
enrichmentTest html
exclude_features_scExp html
feature_annotation_scExp html
filter_correlated_cell_scExp html
filter_genes_with_refined_peak_annotation
html
filter_scExp html
gene_set_enrichment_analysis_scExp html
generate_count_matrix html
generate_feature_names html
get_color_dataframe_from_input html
get_genomic_coordinates html
gg_fill_hue html
groupMat html
has_genomic_coordinates html
hclustAnnotHeatmapPlot html
hg38.GeneTSS html
hg38.chromosomes html
imageCol html
import_count_input_files html
import_scExp html
index_peaks_barcodes_to_matrix_indexes
html
launchApp html
load_MSIGdb html
merge_MACS2_peaks html
mm10.GeneTSS html
mm10.chromosomes html
normalize_scExp html
num_cell_after_QC_filt_scExp html
num_cell_after_cor_filt_scExp html
num_cell_before_cor_filt_scExp html
num_cell_in_cluster_scExp html
num_cell_scExp html
pca_irlba_for_sparseMatrix html
peaks_to_bins html
plot_cluster_consensus_scExp html
plot_differential_H1_scExp html
plot_differential_summary_scExp html
plot_differential_volcano_scExp html
plot_distribution_scExp html
plot_heatmap_scExp html
plot_reduced_dim_scExp html
preprocess_CPM html
preprocess_RPKM html
preprocess_TPM html
preprocess_feature_size_only html
raw_counts_to_feature_count_files html
read_count_mat_with_separated_chr_start_end
html
reduce_dim_batch_correction html
reduce_dims_scExp html
remove_chr_M_fun html
remove_non_canonical_fun html
results_enrichmentTest html
run_pairwise_tests html
run_tsne_scExp html
scExp html
separate_BAM_into_clusters html
separator_count_mat html
subsample_scExp html
subset_bam_call_peaks html
table_enriched_genes_scExp html
warning_DA html
warning_filter_correlated_cell_scExp html
warning_plot_reduced_dim_scExp html
warning_raw_counts_to_feature_count_files
html
** 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
install for x64
* installing *source* package 'ChromSCape' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ChromSCape' as ChromSCape_1.0.0.zip
* DONE (ChromSCape)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'ChromSCape' successfully unpacked and MD5 sums checked
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ChromSCape.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(ChromSCape)
>
> test_check("ChromSCape")
Read the 285 x 50 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000
Computing input similarities...
Symmetrizing...
Done in 0.09 seconds!
Learning embedding...
Iteration 50: error is 69.898844 (50 iterations in 0.09 seconds)
Iteration 100: error is 69.553466 (50 iterations in 0.08 seconds)
Iteration 150: error is 68.635999 (50 iterations in 0.09 seconds)
Iteration 200: error is 69.985188 (50 iterations in 0.08 seconds)
Iteration 250: error is 72.869613 (50 iterations in 0.08 seconds)
Iteration 300: error is 2.279092 (50 iterations in 0.09 seconds)
Iteration 350: error is 2.077542 (50 iterations in 0.08 seconds)
Iteration 400: error is 1.748012 (50 iterations in 0.08 seconds)
Iteration 450: error is 1.717981 (50 iterations in 0.09 seconds)
Iteration 500: error is 1.684500 (50 iterations in 0.09 seconds)
Iteration 550: error is 1.648475 (50 iterations in 0.09 seconds)
Iteration 600: error is 1.600328 (50 iterations in 0.09 seconds)
Iteration 650: error is 1.562537 (50 iterations in 0.09 seconds)
Iteration 700: error is 1.553019 (50 iterations in 0.08 seconds)
Iteration 750: error is 1.539536 (50 iterations in 0.08 seconds)
Iteration 800: error is 1.534533 (50 iterations in 0.08 seconds)
Iteration 850: error is 1.532796 (50 iterations in 0.08 seconds)
Iteration 900: error is 1.530459 (50 iterations in 0.09 seconds)
Iteration 950: error is 1.529834 (50 iterations in 0.11 seconds)
Iteration 1000: error is 1.528450 (50 iterations in 0.08 seconds)
Fitting performed in 1.73 seconds.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
>
> proc.time()
user system elapsed
33.14 4.32 37.46
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ChromSCape.Rcheck/tests_x64/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-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(ChromSCape)
>
> test_check("ChromSCape")
Read the 285 x 50 data matrix successfully!
OpenMP is working. 1 threads.
Using no_dims = 2, perplexity = 30.000000, and theta = 0.000000
Computing input similarities...
Symmetrizing...
Done in 0.08 seconds!
Learning embedding...
Iteration 50: error is 69.898844 (50 iterations in 0.03 seconds)
Iteration 100: error is 69.553466 (50 iterations in 0.05 seconds)
Iteration 150: error is 68.635999 (50 iterations in 0.05 seconds)
Iteration 200: error is 69.985188 (50 iterations in 0.05 seconds)
Iteration 250: error is 72.869613 (50 iterations in 0.03 seconds)
Iteration 300: error is 2.279092 (50 iterations in 0.03 seconds)
Iteration 350: error is 2.077542 (50 iterations in 0.03 seconds)
Iteration 400: error is 1.748012 (50 iterations in 0.03 seconds)
Iteration 450: error is 1.717981 (50 iterations in 0.05 seconds)
Iteration 500: error is 1.684500 (50 iterations in 0.05 seconds)
Iteration 550: error is 1.648475 (50 iterations in 0.05 seconds)
Iteration 600: error is 1.600328 (50 iterations in 0.05 seconds)
Iteration 650: error is 1.562537 (50 iterations in 0.03 seconds)
Iteration 700: error is 1.553019 (50 iterations in 0.03 seconds)
Iteration 750: error is 1.539536 (50 iterations in 0.05 seconds)
Iteration 800: error is 1.534533 (50 iterations in 0.05 seconds)
Iteration 850: error is 1.532796 (50 iterations in 0.03 seconds)
Iteration 900: error is 1.530459 (50 iterations in 0.03 seconds)
Iteration 950: error is 1.529834 (50 iterations in 0.03 seconds)
Iteration 1000: error is 1.528450 (50 iterations in 0.05 seconds)
Fitting performed in 0.78 seconds.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
>
> proc.time()
user system elapsed
31.76 1.28 33.03
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ChromSCape.Rcheck/examples_i386/ChromSCape-Ex.timings
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ChromSCape.Rcheck/examples_x64/ChromSCape-Ex.timings
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