Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-10-16 11:36:00 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 14:00:13 -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)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for ChromSCape on palomino3


To the developers/maintainers of the ChromSCape package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChromSCape.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: ChromSCape
Version: 1.10.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChromSCape.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ChromSCape_1.10.0.tar.gz
StartedAt: 2023-10-16 00:33:59 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 00:48:46 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 887.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChromSCape.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChromSCape.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings ChromSCape_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/ChromSCape.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 whether package 'ChromSCape' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    www    2.1Mb
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/ChromSCape/libs/x64/ChromSCape.dll':
  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 ... 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            51.89   0.79   52.84
get_pathway_mat_scExp                 39.47   3.12   42.66
plot_reduced_dim_scExp_CNA            26.10   0.34   26.47
get_most_variable_cyto                23.53   0.36   24.00
calculate_CNA                         22.51   1.13   23.69
calculate_logRatio_CNA                22.80   0.50   23.33
calculate_gain_or_loss                21.61   0.61   22.23
calculate_cyto_mat                    20.94   0.51   21.45
get_cyto_features                     20.45   0.43   20.94
num_cell_after_cor_filt_scExp         11.17   0.23   26.70
filter_correlated_cell_scExp          10.44   0.17   25.64
CompareedgeRGLM                       10.17   0.27   10.47
preprocessing_filtering_and_reduction  9.01   0.00    9.04
create_scDataset_raw                   7.50   0.39    7.92
import_scExp                           6.84   0.14    7.05
rebin_matrix                           6.19   0.02   21.35
differential_activation                5.58   0.17    5.75
CompareWilcox                          5.23   0.25   46.08
enrich_TF_ChEA3_scExp                  1.98   0.21    5.28
find_clusters_louvain_scExp            1.34   0.14    5.37
* 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, 5 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc/meat/ChromSCape.Rcheck/00check.log'
for details.



Installation output

ChromSCape.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL ChromSCape
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'ChromSCape' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c as_dist.cpp -o as_dist.o
g++ -std=gnu++17 -shared -s -static-libgcc -o ChromSCape.dll tmp.def RcppExports.o as_dist.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-ChromSCape/00new/ChromSCape/libs/x64
** 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
** 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 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 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")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 11 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
  40.04    2.82   73.82 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.000.030.03
CompareWilcox 5.23 0.2546.08
CompareedgeRGLM10.17 0.2710.47
annotToCol20.800.201.02
calculate_CNA22.51 1.1323.69
calculate_cyto_mat20.94 0.5121.45
calculate_gain_or_loss21.61 0.6122.23
calculate_logRatio_CNA22.80 0.5023.33
choose_cluster_scExp4.110.824.99
colors_scExp0.290.200.50
consensus_clustering_scExp3.440.443.89
correlation_and_hierarchical_clust_scExp0.470.140.61
create_project_folder000
create_scDataset_raw7.500.397.92
create_scExp0.750.030.78
define_feature0.190.020.21
detect_samples0.980.021.03
differential_activation5.580.175.75
differential_analysis_scExp2.800.172.97
enrich_TF_ChEA3_genes0.830.271.98
enrich_TF_ChEA3_scExp1.980.215.28
exclude_features_scExp0.780.000.78
feature_annotation_scExp1.860.051.93
filter_correlated_cell_scExp10.44 0.1725.64
filter_scExp0.920.020.93
find_clusters_louvain_scExp1.340.145.37
find_top_features0.340.190.54
gene_set_enrichment_analysis_scExp0.220.180.40
generate_analysis000
generate_coverage_tracks000
generate_report000
getExperimentNames0.270.130.39
getMainExperiment0.250.190.44
get_cyto_features20.45 0.4320.94
get_genomic_coordinates0.520.020.53
get_most_variable_cyto23.53 0.3624.00
get_pathway_mat_scExp39.47 3.1242.66
has_genomic_coordinates1.060.101.15
import_scExp6.840.147.05
inter_correlation_scExp0.470.150.62
intra_correlation_scExp0.340.130.47
launchApp000
normalize_scExp0.610.060.67
num_cell_after_QC_filt_scExp0.720.030.75
num_cell_after_cor_filt_scExp11.17 0.2326.70
num_cell_before_cor_filt_scExp0.270.130.39
num_cell_in_cluster_scExp0.450.110.58
num_cell_scExp0.570.000.56
plot_cluster_consensus_scExp1.170.191.36
plot_correlation_PCA_scExp1.170.231.41
plot_coverage_BigWig0.310.110.42
plot_differential_summary_scExp0.270.110.38
plot_differential_volcano_scExp0.370.220.59
plot_distribution_scExp0.470.140.61
plot_gain_or_loss_barplots51.89 0.7952.84
plot_heatmap_scExp0.350.160.50
plot_inter_correlation_scExp0.640.200.85
plot_intra_correlation_scExp0.680.160.84
plot_most_contributing_features0.540.160.70
plot_percent_active_feature_scExp2.060.202.29
plot_pie_most_contributing_chr0.360.120.48
plot_reduced_dim_scExp3.370.183.55
plot_reduced_dim_scExp_CNA26.10 0.3426.47
plot_top_TF_scExp0.570.130.70
plot_violin_feature_scExp2.320.092.40
preprocess_CPM0.610.030.65
preprocess_RPKM0.710.050.76
preprocess_TFIDF0.580.000.58
preprocess_TPM0.610.040.66
preprocess_feature_size_only0.770.020.78
preprocessing_filtering_and_reduction9.010.009.04
read_sparse_matrix000
rebin_matrix 6.19 0.0221.35
reduce_dims_scExp2.160.002.17
scExp1.230.141.37
subsample_scExp0.770.000.77
subset_bam_call_peaks000
summary_DA0.250.210.47
swapAltExp_sameColData0.260.160.42
table_enriched_genes_scExp0.250.140.39
wrapper_Signac_FeatureMatrix000