Back to Mac ARM64 build report for BioC 3.17
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This page was generated on 2023-10-20 09:37:59 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (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 339/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.10.0  (landing page)
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)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for ChromSCape on kjohnson2


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.

raw results


Summary

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

Command output

##############################################################################
##############################################################################
###
### 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.



Installation output

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)

Tests output

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 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.0100.0030.013
CompareWilcox 5.384 0.43912.587
CompareedgeRGLM 6.128 0.22713.692
annotToCol21.1770.0812.959
calculate_CNA29.058 2.03451.689
calculate_cyto_mat28.183 0.81844.732
calculate_gain_or_loss27.673 0.70241.575
calculate_logRatio_CNA27.042 0.82342.323
choose_cluster_scExp3.7000.2406.043
colors_scExp0.4360.0080.672
consensus_clustering_scExp3.2890.2125.369
correlation_and_hierarchical_clust_scExp0.4270.0070.667
create_project_folder0.0020.0020.005
create_scDataset_raw 6.650 0.47411.027
create_scExp0.8230.0231.597
define_feature0.1820.0100.337
detect_samples1.0460.0942.083
differential_activation 6.197 0.16611.236
differential_analysis_scExp3.2080.0425.681
enrich_TF_ChEA3_genes0.6350.1618.562
enrich_TF_ChEA3_scExp1.2340.0746.566
exclude_features_scExp0.8250.0211.474
feature_annotation_scExp2.1420.0693.910
filter_correlated_cell_scExp 8.709 0.35913.630
filter_scExp1.0380.0311.602
find_clusters_louvain_scExp0.5350.1480.999
find_top_features0.4630.0370.719
gene_set_enrichment_analysis_scExp0.3090.0080.477
generate_analysis0.0000.0010.000
generate_coverage_tracks0.0000.0000.001
generate_report000
getExperimentNames0.3350.0100.534
getMainExperiment0.3750.0160.593
get_cyto_features25.245 0.36237.638
get_genomic_coordinates0.6940.0221.095
get_most_variable_cyto27.129 0.34842.220
get_pathway_mat_scExp43.840 2.72271.176
has_genomic_coordinates1.2470.1362.041
import_scExp5.9020.1168.683
inter_correlation_scExp0.5540.0250.742
intra_correlation_scExp0.4750.0170.622
launchApp000
normalize_scExp0.7520.0321.001
num_cell_after_QC_filt_scExp0.8430.0431.119
num_cell_after_cor_filt_scExp 9.382 0.36814.175
num_cell_before_cor_filt_scExp0.3070.0120.480
num_cell_in_cluster_scExp0.6320.0150.988
num_cell_scExp0.6410.0231.007
plot_cluster_consensus_scExp1.2610.0752.055
plot_correlation_PCA_scExp1.1390.0191.776
plot_coverage_BigWig0.3530.0090.548
plot_differential_summary_scExp0.3860.0080.601
plot_differential_volcano_scExp0.4130.0120.638
plot_distribution_scExp0.5670.0130.892
plot_gain_or_loss_barplots59.739 0.66492.380
plot_heatmap_scExp0.4200.0200.654
plot_inter_correlation_scExp0.7140.0131.094
plot_intra_correlation_scExp0.7320.0161.101
plot_most_contributing_features0.6300.0180.972
plot_percent_active_feature_scExp2.1930.0363.118
plot_pie_most_contributing_chr0.4530.0160.701
plot_reduced_dim_scExp4.2550.0676.561
plot_reduced_dim_scExp_CNA28.630 0.30542.429
plot_top_TF_scExp0.6610.0231.043
plot_violin_feature_scExp2.2980.0463.587
preprocess_CPM0.7030.0341.126
preprocess_RPKM0.7720.0571.272
preprocess_TFIDF0.7390.0341.192
preprocess_TPM0.8040.0501.292
preprocess_feature_size_only0.7120.0331.139
preprocessing_filtering_and_reduction 8.107 0.13312.639
read_sparse_matrix000
rebin_matrix 5.481 0.07533.529
reduce_dims_scExp2.0980.0323.211
scExp1.2970.0362.048
subsample_scExp1.0450.0211.632
subset_bam_call_peaks000
summary_DA0.3580.0120.547
swapAltExp_sameColData0.4590.0090.703
table_enriched_genes_scExp0.3410.0070.537
wrapper_Signac_FeatureMatrix0.0010.0000.000