Pacome Prompsy
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/ChromSCape |
| git_branch: RELEASE_3_17 |
| git_last_commit: 541e6b7 |
| git_last_commit_date: 2023-04-25 11:23:20 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:37:59 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 339/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ChromSCape 1.10.0 (landing page) Pacome Prompsy
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the ChromSCape package: - 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. |
| Package: ChromSCape |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChromSCape_1.10.0.tar.gz |
| StartedAt: 2023-10-17 09:17:22 -0400 (Tue, 17 Oct 2023) |
| EndedAt: 2023-10-17 09:39:16 -0400 (Tue, 17 Oct 2023) |
| EllapsedTime: 1314.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ChromSCape.Rcheck |
| Warnings: 4 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChromSCape_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ChromSCape.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChromSCape/DESCRIPTION’ ... OK
* this is package ‘ChromSCape’ version ‘1.10.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ChromSCape’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' call not declared from: ‘dplyr’
'library' or 'require' call to ‘dplyr’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bams_to_matrix_indexes: no visible binding for global variable
‘files_dir_list’
enrich_TF_ChEA3_genes: no visible binding for global variable
‘CheA3_TF_nTargets’
filter_correlated_cell_scExp: no visible binding for global variable
‘run_tsne’
generate_analysis: no visible global function definition for ‘head’
generate_analysis: no visible binding for global variable ‘k’
generate_analysis: no visible binding for global variable
‘clusterConsensus’
get_most_variable_cyto: no visible binding for global variable
‘cytoBand’
get_most_variable_cyto: no visible binding for global variable
‘Fri_cyto’
num_cell_after_QC_filt_scExp: no visible binding for global variable
‘sample_id’
num_cell_after_QC_filt_scExp: no visible binding for global variable
‘total_counts’
num_cell_scExp: no visible binding for global variable ‘sample_id’
num_cell_scExp: no visible binding for global variable ‘total_counts’
plot_correlation_PCA_scExp: no visible binding for global variable
‘Component’
plot_coverage_BigWig: no visible binding for global variable ‘molecule’
plot_coverage_BigWig: no visible binding for global variable
‘orientation’
plot_coverage_BigWig: no visible binding for global variable ‘Gene’
plot_gain_or_loss_barplots: no visible binding for global variable
‘Gain_or_Loss’
plot_gain_or_loss_barplots: no visible binding for global variable
‘ncells’
plot_gain_or_loss_barplots: no visible binding for global variable
‘cytoBand’
plot_most_contributing_features: no visible binding for global variable
‘genes’
plot_percent_active_feature_scExp: no visible binding for global
variable ‘group’
plot_percent_active_feature_scExp: no visible binding for global
variable ‘percent_active’
plot_pie_most_contributing_chr: no visible binding for global variable
‘absolute_value’
plot_reduced_dim_scExp: no visible binding for global variable ‘V1’
plot_reduced_dim_scExp: no visible binding for global variable ‘V2’
plot_reduced_dim_scExp: no visible binding for global variable
‘cluster’
plot_top_TF_scExp: no visible binding for global variable ‘TF’
rebin_helper: no visible binding for global variable ‘new_row’
rebin_helper: no visible binding for global variable ‘origin_value’
rebin_matrix: no visible binding for global variable ‘group’
subset_bam_call_peaks: no visible binding for global variable
‘merged_bam’
Undefined global functions or variables:
CheA3_TF_nTargets Component Fri_cyto Gain_or_Loss Gene TF V1 V2
absolute_value cluster clusterConsensus cytoBand files_dir_list genes
group head k merged_bam molecule ncells new_row orientation
origin_value percent_active run_tsne sample_id total_counts
Consider adding
importFrom("utils", "head")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: raw_counts_to_sparse_matrix.Rd:6-8: Dropping empty section \source
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'generate_analysis':
generate_analysis
Code: function(input_data_folder, analysis_name = "Analysis_1",
output_directory = "./", input_data_type = c("scBED",
"DenseMatrix", "SparseMatrix", "scBAM")[1],
feature_count_on = c("bins", "genebody", "peaks")[1],
feature_count_parameter = 50000, rebin_sparse_matrix =
FALSE, ref_genome = c("hg38", "mm10")[1], run =
c("filter", "CNA", "cluster", "consensus", "coverage",
"DA", "GSA", "report")[c(1, 3, 5, 6, 7, 8)],
min_reads_per_cell = 1000, max_quantile_read_per_cell
= 99, n_top_features = 40000, norm_type = "CPM",
subsample_n = NULL, exclude_regions = NULL, n_clust =
NULL, corr_threshold = 99, percent_correlation = 1,
maxK = 10, qval.th = 0.1, logFC.th = 1,
enrichment_qval = 0.1, doBatchCorr = FALSE, batch_sels
= NULL, control_samples_CNA = NULL, genes_to_plot =
c("Krt8", "Krt5", "Tgfb1", "Foxq1", "Cdkn2b",
"Cdkn2a", "chr7:15000000-20000000"))
Docs: function(input_data_folder, analysis_name = "Analysis_1",
output_directory = "./", input_data_type = c("scBED",
"DenseMatrix", "SparseMatrix", "scBAM")[1],
rebin_sparse_matrix = FALSE, feature_count_on =
c("bins", "genebody", "peaks")[1],
feature_count_parameter = 50000, ref_genome =
c("hg38", "mm10")[1], run = c("filter", "CNA",
"cluster", "consensus", "peak_call", "coverage", "DA",
"GSA", "report")[c(1, 3, 6, 7, 8, 9)],
min_reads_per_cell = 1000, max_quantile_read_per_cell
= 99, n_top_features = 40000, norm_type = "CPM",
subsample_n = NULL, exclude_regions = NULL, n_clust =
NULL, corr_threshold = 99, percent_correlation = 1,
maxK = 10, qval.th = 0.1, logFC.th = 1,
enrichment_qval = 0.1, doBatchCorr = FALSE, batch_sels
= NULL, control_samples_CNA = NULL, genes_to_plot =
c("Krt8", "Krt5", "Tgfb1", "Foxq1", "Cdkn2b",
"Cdkn2a", "chr7:15000000-20000000"))
Mismatches in argument names:
Position: 5 Code: feature_count_on Docs: rebin_sparse_matrix
Position: 6 Code: feature_count_parameter Docs: feature_count_on
Position: 7 Code: rebin_sparse_matrix Docs: feature_count_parameter
Mismatches in argument default values:
Name: 'run'
Code: c("filter", "CNA", "cluster", "consensus", "coverage", "DA",
"GSA", "report")[c(1, 3, 5, 6, 7, 8)]
Docs: c("filter", "CNA", "cluster", "consensus", "peak_call", "coverage",
"DA", "GSA", "report")[c(1, 3, 6, 7, 8, 9)]
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'rebin_matrix'
‘rebin_function’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning: 'as(<matrix>, "dspMatrix")' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_gain_or_loss_barplots 59.739 0.664 92.380
get_pathway_mat_scExp 43.840 2.722 71.176
calculate_CNA 29.058 2.034 51.689
calculate_cyto_mat 28.183 0.818 44.732
plot_reduced_dim_scExp_CNA 28.630 0.305 42.429
calculate_gain_or_loss 27.673 0.702 41.575
calculate_logRatio_CNA 27.042 0.823 42.323
get_most_variable_cyto 27.129 0.348 42.220
get_cyto_features 25.245 0.362 37.638
num_cell_after_cor_filt_scExp 9.382 0.368 14.175
filter_correlated_cell_scExp 8.709 0.359 13.630
preprocessing_filtering_and_reduction 8.107 0.133 12.639
create_scDataset_raw 6.650 0.474 11.027
differential_activation 6.197 0.166 11.236
CompareedgeRGLM 6.128 0.227 13.692
import_scExp 5.902 0.116 8.683
CompareWilcox 5.384 0.439 12.587
rebin_matrix 5.481 0.075 33.529
plot_reduced_dim_scExp 4.255 0.067 6.561
choose_cluster_scExp 3.700 0.240 6.043
consensus_clustering_scExp 3.289 0.212 5.369
differential_analysis_scExp 3.208 0.042 5.681
enrich_TF_ChEA3_scExp 1.234 0.074 6.566
enrich_TF_ChEA3_genes 0.635 0.161 8.562
* 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: 4 WARNINGs, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/ChromSCape.Rcheck/00check.log’
for details.
ChromSCape.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChromSCape ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘ChromSCape’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c as_dist.cpp -o as_dist.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o ChromSCape.so RcppExports.o as_dist.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-ChromSCape/00new/ChromSCape/libs ** R ** data ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ChromSCape)
ChromSCape.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 11 ]
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 11 ]
>
> proc.time()
user system elapsed
39.871 2.072 64.004
ChromSCape.Rcheck/ChromSCape-Ex.timings
| name | user | system | elapsed | |
| CheA3_TF_nTargets | 0.010 | 0.003 | 0.013 | |
| CompareWilcox | 5.384 | 0.439 | 12.587 | |
| CompareedgeRGLM | 6.128 | 0.227 | 13.692 | |
| annotToCol2 | 1.177 | 0.081 | 2.959 | |
| calculate_CNA | 29.058 | 2.034 | 51.689 | |
| calculate_cyto_mat | 28.183 | 0.818 | 44.732 | |
| calculate_gain_or_loss | 27.673 | 0.702 | 41.575 | |
| calculate_logRatio_CNA | 27.042 | 0.823 | 42.323 | |
| choose_cluster_scExp | 3.700 | 0.240 | 6.043 | |
| colors_scExp | 0.436 | 0.008 | 0.672 | |
| consensus_clustering_scExp | 3.289 | 0.212 | 5.369 | |
| correlation_and_hierarchical_clust_scExp | 0.427 | 0.007 | 0.667 | |
| create_project_folder | 0.002 | 0.002 | 0.005 | |
| create_scDataset_raw | 6.650 | 0.474 | 11.027 | |
| create_scExp | 0.823 | 0.023 | 1.597 | |
| define_feature | 0.182 | 0.010 | 0.337 | |
| detect_samples | 1.046 | 0.094 | 2.083 | |
| differential_activation | 6.197 | 0.166 | 11.236 | |
| differential_analysis_scExp | 3.208 | 0.042 | 5.681 | |
| enrich_TF_ChEA3_genes | 0.635 | 0.161 | 8.562 | |
| enrich_TF_ChEA3_scExp | 1.234 | 0.074 | 6.566 | |
| exclude_features_scExp | 0.825 | 0.021 | 1.474 | |
| feature_annotation_scExp | 2.142 | 0.069 | 3.910 | |
| filter_correlated_cell_scExp | 8.709 | 0.359 | 13.630 | |
| filter_scExp | 1.038 | 0.031 | 1.602 | |
| find_clusters_louvain_scExp | 0.535 | 0.148 | 0.999 | |
| find_top_features | 0.463 | 0.037 | 0.719 | |
| gene_set_enrichment_analysis_scExp | 0.309 | 0.008 | 0.477 | |
| generate_analysis | 0.000 | 0.001 | 0.000 | |
| generate_coverage_tracks | 0.000 | 0.000 | 0.001 | |
| generate_report | 0 | 0 | 0 | |
| getExperimentNames | 0.335 | 0.010 | 0.534 | |
| getMainExperiment | 0.375 | 0.016 | 0.593 | |
| get_cyto_features | 25.245 | 0.362 | 37.638 | |
| get_genomic_coordinates | 0.694 | 0.022 | 1.095 | |
| get_most_variable_cyto | 27.129 | 0.348 | 42.220 | |
| get_pathway_mat_scExp | 43.840 | 2.722 | 71.176 | |
| has_genomic_coordinates | 1.247 | 0.136 | 2.041 | |
| import_scExp | 5.902 | 0.116 | 8.683 | |
| inter_correlation_scExp | 0.554 | 0.025 | 0.742 | |
| intra_correlation_scExp | 0.475 | 0.017 | 0.622 | |
| launchApp | 0 | 0 | 0 | |
| normalize_scExp | 0.752 | 0.032 | 1.001 | |
| num_cell_after_QC_filt_scExp | 0.843 | 0.043 | 1.119 | |
| num_cell_after_cor_filt_scExp | 9.382 | 0.368 | 14.175 | |
| num_cell_before_cor_filt_scExp | 0.307 | 0.012 | 0.480 | |
| num_cell_in_cluster_scExp | 0.632 | 0.015 | 0.988 | |
| num_cell_scExp | 0.641 | 0.023 | 1.007 | |
| plot_cluster_consensus_scExp | 1.261 | 0.075 | 2.055 | |
| plot_correlation_PCA_scExp | 1.139 | 0.019 | 1.776 | |
| plot_coverage_BigWig | 0.353 | 0.009 | 0.548 | |
| plot_differential_summary_scExp | 0.386 | 0.008 | 0.601 | |
| plot_differential_volcano_scExp | 0.413 | 0.012 | 0.638 | |
| plot_distribution_scExp | 0.567 | 0.013 | 0.892 | |
| plot_gain_or_loss_barplots | 59.739 | 0.664 | 92.380 | |
| plot_heatmap_scExp | 0.420 | 0.020 | 0.654 | |
| plot_inter_correlation_scExp | 0.714 | 0.013 | 1.094 | |
| plot_intra_correlation_scExp | 0.732 | 0.016 | 1.101 | |
| plot_most_contributing_features | 0.630 | 0.018 | 0.972 | |
| plot_percent_active_feature_scExp | 2.193 | 0.036 | 3.118 | |
| plot_pie_most_contributing_chr | 0.453 | 0.016 | 0.701 | |
| plot_reduced_dim_scExp | 4.255 | 0.067 | 6.561 | |
| plot_reduced_dim_scExp_CNA | 28.630 | 0.305 | 42.429 | |
| plot_top_TF_scExp | 0.661 | 0.023 | 1.043 | |
| plot_violin_feature_scExp | 2.298 | 0.046 | 3.587 | |
| preprocess_CPM | 0.703 | 0.034 | 1.126 | |
| preprocess_RPKM | 0.772 | 0.057 | 1.272 | |
| preprocess_TFIDF | 0.739 | 0.034 | 1.192 | |
| preprocess_TPM | 0.804 | 0.050 | 1.292 | |
| preprocess_feature_size_only | 0.712 | 0.033 | 1.139 | |
| preprocessing_filtering_and_reduction | 8.107 | 0.133 | 12.639 | |
| read_sparse_matrix | 0 | 0 | 0 | |
| rebin_matrix | 5.481 | 0.075 | 33.529 | |
| reduce_dims_scExp | 2.098 | 0.032 | 3.211 | |
| scExp | 1.297 | 0.036 | 2.048 | |
| subsample_scExp | 1.045 | 0.021 | 1.632 | |
| subset_bam_call_peaks | 0 | 0 | 0 | |
| summary_DA | 0.358 | 0.012 | 0.547 | |
| swapAltExp_sameColData | 0.459 | 0.009 | 0.703 | |
| table_enriched_genes_scExp | 0.341 | 0.007 | 0.537 | |
| wrapper_Signac_FeatureMatrix | 0.001 | 0.000 | 0.000 | |