Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-18 12:07:55 -0400 (Wed, 18 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4379
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4154
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4220
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

CHECK results for ChromSCape on merida1


To the developers/maintainers of the ChromSCape package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 321/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ChromSCape 1.6.0  (landing page)
Pacome Prompsy
Snapshot Date: 2022-05-17 13:55:01 -0400 (Tue, 17 May 2022)
git_url: https://git.bioconductor.org/packages/ChromSCape
git_branch: RELEASE_3_15
git_last_commit: f0f1527
git_last_commit_date: 2022-04-26 12:09:05 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 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 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: ChromSCape
Version: 1.6.0
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_1.6.0.tar.gz
StartedAt: 2022-05-18 00:18:35 -0400 (Wed, 18 May 2022)
EndedAt: 2022-05-18 00:38:55 -0400 (Wed, 18 May 2022)
EllapsedTime: 1219.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChromSCape.Rcheck
Warnings: 3

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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/ChromSCape.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChromSCape/DESCRIPTION’ ... OK
* this is package ‘ChromSCape’ version ‘1.6.0’
* 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
* 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 dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘GenomeInfoDb’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
CompareWilcox: no visible binding for global variable ‘annot.’
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 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’
rawfile_ToBigWig: no visible binding for global variable ‘filename’
rebin_matrix: no visible global function definition for ‘head’
rebin_matrix: no visible binding for global variable ‘new_row’
rebin_matrix: no visible binding for global variable ‘origin_value’
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 annot. cluster clusterConsensus cytoBand filename
  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 'count_coverage':
count_coverage
  Code: function(input, format = "BAM", bins, canonical_chr,
                 n_smoothBin = 5, ref = "hg38", read_size = 101,
                 original_bins = NULL)
  Docs: function(filename, format = "BAM", bins, canonical_chr,
                 n_smoothBin = 5, ref = "hg38", read_size = 101)
  Argument names in code not in docs:
    input original_bins
  Argument names in docs not in code:
    filename
  Mismatches in argument names:
    Position: 1 Code: input Docs: filename

Codoc mismatches from documentation object 'find_clusters_louvain_scExp':
find_clusters_louvain_scExp
  Code: function(scExp, k = 10, resolution = 1, use.dimred = "PCA",
                 type = c("rank", "number", "jaccard")[3], BPPARAM =
                 BiocParallel::bpparam())
  Docs: function(scExp, k = 10, use.dimred = "PCA", type = c("rank",
                 "number", "jaccard")[3], BPPARAM =
                 BiocParallel::bpparam())
  Argument names in code not in docs:
    resolution
  Mismatches in argument names:
    Position: 3 Code: resolution Docs: use.dimred
    Position: 4 Code: use.dimred Docs: type
    Position: 5 Code: type Docs: BPPARAM

Codoc mismatches from documentation object 'generate_coverage_tracks':
generate_coverage_tracks
  Code: function(scExp_cf, input, odir, format = "scBED", ref_genome =
                 c("hg38", "mm10")[1], bin_width = 150, n_smoothBin =
                 5, read_size = 101, progress = NULL)
  Docs: function(scExp_cf, input, odir, input_type = "scBED",
                 ref_genome = c("hg38", "mm10")[1], bin_width = 150,
                 n_smoothBin = 5, read_size = 101, progress = NULL)
  Argument names in code not in docs:
    format
  Argument names in docs not in code:
    input_type
  Mismatches in argument names:
    Position: 4 Code: format Docs: input_type

Codoc mismatches from documentation object 'rawfile_ToBigWig':
rawfile_ToBigWig
  Code: function(input, BigWig_filename, format = "BAM", bin_width =
                 150, n_smoothBin = 5, ref = "hg38", read_size = 101,
                 original_bins = NULL)
  Docs: function(input, BigWig_filename, format = "BAM", bin_width =
                 150, n_smoothBin = 5, ref = "hg38", read_size = 101)
  Argument names in code not in docs:
    original_bins

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'generate_coverage_tracks'
  ‘input_type’

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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                         user system elapsed
plot_gain_or_loss_barplots            101.941  0.460 106.885
plot_reduced_dim_scExp_CNA             49.636  0.219  53.671
calculate_CNA                          47.592  1.538  49.190
calculate_gain_or_loss                 48.123  0.540  50.461
calculate_cyto_mat                     46.594  0.528  48.973
get_most_variable_cyto                 45.890  0.187  47.468
calculate_logRatio_CNA                 44.414  0.486  44.960
get_cyto_features                      43.252  0.544  43.901
num_cell_after_cor_filt_scExp          11.457  0.528  12.488
filter_correlated_cell_scExp           11.305  0.615  11.929
preprocessing_filtering_and_reduction  11.181  0.099  11.855
differential_activation                11.065  0.046  11.124
create_scDataset_raw                   10.079  0.598  10.692
CompareedgeRGLM                         9.669  0.479  10.161
plot_reduced_dim_scExp                  8.579  0.080   9.383
CompareWilcox                           7.085  1.180   6.100
import_scExp                            7.090  0.126   7.577
choose_cluster_scExp                    6.102  0.931   7.053
consensus_clustering_scExp              6.129  0.574   6.729
differential_analysis_scExp             5.782  0.035   5.832
plot_violin_feature_scExp               5.236  0.036   5.726
enrich_TF_ChEA3_scExp                   1.979  0.098   8.355
* 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: 3 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/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/4.2/Resources/library’
* installing *source* package ‘ChromSCape’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c as_dist.cpp -o as_dist.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.2/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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
 58.183   3.856  64.554 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.0150.0020.016
CompareWilcox7.0851.1806.100
CompareedgeRGLM 9.669 0.47910.161
annotToCol22.2260.1052.335
calculate_CNA47.592 1.53849.190
calculate_cyto_mat46.594 0.52848.973
calculate_gain_or_loss48.123 0.54050.461
calculate_logRatio_CNA44.414 0.48644.960
choose_cluster_scExp6.1020.9317.053
colors_scExp0.6380.0090.647
consensus_clustering_scExp6.1290.5746.729
correlation_and_hierarchical_clust_scExp0.6180.0070.625
create_project_folder0.0020.0020.004
create_scDataset_raw10.079 0.59810.692
create_scExp1.3240.0131.337
define_feature0.3160.0090.325
detect_samples1.1440.0791.223
differential_activation11.065 0.04611.124
differential_analysis_scExp5.7820.0355.832
enrich_TF_ChEA3_genes0.9360.1032.667
enrich_TF_ChEA3_scExp1.9790.0988.355
exclude_features_scExp1.3950.0071.405
feature_annotation_scExp3.4150.0833.503
filter_correlated_cell_scExp11.305 0.61511.929
filter_scExp1.7800.0641.846
find_clusters_louvain_scExp1.0470.6671.104
find_top_features0.6590.0430.704
gene_set_enrichment_analysis_scExp0.4190.0120.431
generate_analysis000
generate_coverage_tracks000
generate_report000
getExperimentNames0.4560.0200.476
getMainExperiment0.5430.0260.570
get_cyto_features43.252 0.54443.901
get_genomic_coordinates1.1880.0341.224
get_most_variable_cyto45.890 0.18747.468
has_genomic_coordinates2.0820.0392.206
import_scExp7.0900.1267.577
inter_correlation_scExp0.8310.0190.858
intra_correlation_scExp0.7280.0160.777
launchApp0.0000.0010.000
normalize_scExp1.2940.0231.350
num_cell_after_QC_filt_scExp1.4490.0511.604
num_cell_after_cor_filt_scExp11.457 0.52812.488
num_cell_before_cor_filt_scExp0.4040.0130.440
num_cell_in_cluster_scExp1.0610.0191.143
num_cell_scExp1.1960.0441.312
plot_cluster_consensus_scExp1.8500.1282.075
plot_correlation_PCA_scExp1.8090.0221.917
plot_coverage_BigWig0.4010.0150.432
plot_differential_summary_scExp0.4650.0130.502
plot_differential_volcano_scExp0.5690.0150.617
plot_distribution_scExp1.0070.0111.060
plot_gain_or_loss_barplots101.941 0.460106.885
plot_heatmap_scExp0.6460.0190.673
plot_inter_correlation_scExp1.0940.0151.169
plot_intra_correlation_scExp1.0760.0211.248
plot_most_contributing_features0.8310.0120.893
plot_pie_most_contributing_chr0.6050.0200.662
plot_reduced_dim_scExp8.5790.0809.383
plot_reduced_dim_scExp_CNA49.636 0.21953.671
plot_top_TF_scExp0.8910.0151.006
plot_violin_feature_scExp5.2360.0365.726
preprocess_CPM1.3250.0381.493
preprocess_RPKM1.3300.0201.402
preprocess_TFIDF1.2720.0221.360
preprocess_TPM1.3350.0531.482
preprocess_feature_size_only1.2540.0181.330
preprocessing_filtering_and_reduction11.181 0.09911.855
read_sparse_matrix0.0000.0010.000
rebin_matrix2.7580.0222.996
reduce_dims_scExp3.7400.0294.129
scExp2.7100.0332.959
subsample_scExp1.7550.0101.839
subset_bam_call_peaks000
summary_DA0.4290.0050.437
swapAltExp_sameColData0.6140.0110.668
table_enriched_genes_scExp0.3920.0210.417
wrapper_Signac_FeatureMatrix0.0010.0000.001