Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-18 12:05:19 -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 nebbiolo1


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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings ChromSCape_1.6.0.tar.gz
StartedAt: 2022-05-17 18:50:24 -0400 (Tue, 17 May 2022)
EndedAt: 2022-05-17 19:01:48 -0400 (Tue, 17 May 2022)
EllapsedTime: 683.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChromSCape.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:ChromSCape.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings ChromSCape_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/ChromSCape.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (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            49.949  0.759  50.709
calculate_CNA                         26.727  2.220  28.951
calculate_logRatio_CNA                24.252  0.688  24.944
calculate_gain_or_loss                23.446  0.776  24.223
calculate_cyto_mat                    23.033  0.879  23.914
plot_reduced_dim_scExp_CNA            23.089  0.196  23.285
get_most_variable_cyto                22.630  0.484  23.115
get_cyto_features                     20.438  0.584  21.023
filter_correlated_cell_scExp          11.654  0.922  12.523
num_cell_after_cor_filt_scExp         10.907  0.358  11.199
preprocessing_filtering_and_reduction  9.261  0.036   9.291
create_scDataset_raw                   7.749  0.408   8.156
import_scExp                           6.657  0.179   6.837
CompareWilcox                          6.129  0.478   6.005
differential_activation                6.032  0.080   6.113
enrich_TF_ChEA3_scExp                  1.161  0.057   7.448
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/ChromSCape.Rcheck/00check.log’
for details.



Installation output

ChromSCape.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL ChromSCape
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘ChromSCape’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c as_dist.cpp -o as_dist.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o ChromSCape.so RcppExports.o as_dist.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/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-pc-linux-gnu (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 
 39.422   2.317  41.472 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.0100.0000.009
CompareWilcox6.1290.4786.005
CompareedgeRGLM4.8040.1524.942
annotToCol21.0870.0441.131
calculate_CNA26.727 2.22028.951
calculate_cyto_mat23.033 0.87923.914
calculate_gain_or_loss23.446 0.77624.223
calculate_logRatio_CNA24.252 0.68824.944
choose_cluster_scExp3.6450.1323.771
colors_scExp0.3310.0000.331
consensus_clustering_scExp3.3650.1043.463
correlation_and_hierarchical_clust_scExp0.3460.0000.332
create_project_folder0.0020.0000.002
create_scDataset_raw7.7490.4088.156
create_scExp0.8030.0000.803
define_feature0.1690.0040.173
detect_samples1.1420.0081.088
differential_activation6.0320.0806.113
differential_analysis_scExp2.8650.0242.889
enrich_TF_ChEA3_genes0.5060.1442.427
enrich_TF_ChEA3_scExp1.1610.0577.448
exclude_features_scExp0.6960.0960.792
feature_annotation_scExp1.9210.1882.109
filter_correlated_cell_scExp11.654 0.92212.523
filter_scExp0.8650.0560.921
find_clusters_louvain_scExp0.5740.4490.646
find_top_features0.3830.0280.412
gene_set_enrichment_analysis_scExp0.2830.0000.284
generate_analysis000
generate_coverage_tracks000
generate_report000
getExperimentNames0.2510.0170.269
getMainExperiment0.2960.0190.316
get_cyto_features20.438 0.58421.023
get_genomic_coordinates0.5650.0240.590
get_most_variable_cyto22.630 0.48423.115
has_genomic_coordinates0.9480.0360.984
import_scExp6.6570.1796.837
inter_correlation_scExp0.4010.0080.409
intra_correlation_scExp0.3590.0040.363
launchApp0.0000.0010.000
normalize_scExp0.5880.0190.607
num_cell_after_QC_filt_scExp0.6690.0080.677
num_cell_after_cor_filt_scExp10.907 0.35811.199
num_cell_before_cor_filt_scExp0.2260.0040.231
num_cell_in_cluster_scExp0.5090.0050.506
num_cell_scExp0.5060.0430.550
plot_cluster_consensus_scExp0.8120.0720.884
plot_correlation_PCA_scExp0.8710.0040.874
plot_coverage_BigWig0.2140.0000.214
plot_differential_summary_scExp0.2400.0070.248
plot_differential_volcano_scExp0.3210.0090.328
plot_distribution_scExp0.4780.0000.478
plot_gain_or_loss_barplots49.949 0.75950.709
plot_heatmap_scExp0.3120.0000.313
plot_inter_correlation_scExp0.5110.0000.511
plot_intra_correlation_scExp0.4970.0000.497
plot_most_contributing_features0.4110.0040.416
plot_pie_most_contributing_chr0.3140.0160.329
plot_reduced_dim_scExp3.5910.0483.638
plot_reduced_dim_scExp_CNA23.089 0.19623.285
plot_top_TF_scExp0.4850.0080.493
plot_violin_feature_scExp2.2440.0522.296
preprocess_CPM0.5700.0320.602
preprocess_RPKM0.6180.0430.661
preprocess_TFIDF0.5900.0360.626
preprocess_TPM0.6340.0200.655
preprocess_feature_size_only0.6400.0280.668
preprocessing_filtering_and_reduction9.2610.0369.291
read_sparse_matrix0.0000.0000.001
rebin_matrix2.3660.0032.370
reduce_dims_scExp1.6210.0171.637
scExp1.3130.0111.325
subsample_scExp0.7980.0040.802
subset_bam_call_peaks0.0010.0000.000
summary_DA0.2540.0010.254
swapAltExp_sameColData0.3080.0110.320
table_enriched_genes_scExp0.2160.0000.216
wrapper_Signac_FeatureMatrix000