Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-05-27 12:06:19 -0400 (Fri, 27 May 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 palomino3


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: 2022-05-26 13:55:15 -0400 (Thu, 26 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: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChromSCape.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChromSCape_1.6.0.tar.gz
StartedAt: 2022-05-26 22:35:16 -0400 (Thu, 26 May 2022)
EndedAt: 2022-05-26 22:50:15 -0400 (Thu, 26 May 2022)
EllapsedTime: 899.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: ChromSCape.Rcheck
Warnings: 3

Command output

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


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/ChromSCape.Rcheck'
* using R version 4.2.0 (2022-04-22 ucrt)
* using platform: x86_64-w64-mingw32 (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 whether package 'ChromSCape' can be installed ... OK
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.15-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. 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                       user system elapsed
plot_gain_or_loss_barplots            58.08   0.70   58.80
calculate_cyto_mat                    28.64   0.60   29.23
calculate_CNA                         27.43   1.09   28.52
plot_reduced_dim_scExp_CNA            28.03   0.30   28.33
calculate_gain_or_loss                27.37   0.57   27.96
get_most_variable_cyto                27.29   0.30   27.62
calculate_logRatio_CNA                25.50   0.77   26.28
get_cyto_features                     23.71   0.39   24.09
CompareedgeRGLM                       11.92   0.21   12.14
num_cell_after_cor_filt_scExp         11.42   0.14   27.46
filter_correlated_cell_scExp          11.24   0.15   27.58
preprocessing_filtering_and_reduction  8.82   0.08    9.00
create_scDataset_raw                   7.99   0.39    8.38
import_scExp                           6.80   0.05    6.85
differential_activation                6.39   0.14    6.53
choose_cluster_scExp                   4.46   0.91    5.36
CompareWilcox                          4.92   0.16   51.22
enrich_TF_ChEA3_scExp                  2.02   0.19    8.36
find_clusters_louvain_scExp            1.37   0.20    8.32
* 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, 5 NOTEs
See
  'F:/biocbuild/bbs-3.15-bioc/meat/ChromSCape.Rcheck/00check.log'
for details.



Installation output

ChromSCape.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ChromSCape
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'ChromSCape' ...
** using staged installation
** libs
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c as_dist.cpp -o as_dist.o
g++ -std=gnu++11 -shared -s -static-libgcc -o ChromSCape.dll tmp.def RcppExports.o as_dist.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-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 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
  39.29    3.14   74.07 

Example timings

ChromSCape.Rcheck/ChromSCape-Ex.timings

nameusersystemelapsed
CheA3_TF_nTargets0.010.000.01
CompareWilcox 4.92 0.1651.22
CompareedgeRGLM11.92 0.2112.14
annotToCol21.060.241.29
calculate_CNA27.43 1.0928.52
calculate_cyto_mat28.64 0.6029.23
calculate_gain_or_loss27.37 0.5727.96
calculate_logRatio_CNA25.50 0.7726.28
choose_cluster_scExp4.460.915.36
colors_scExp0.310.110.42
consensus_clustering_scExp3.320.403.74
correlation_and_hierarchical_clust_scExp0.460.080.55
create_project_folder0.000.000.01
create_scDataset_raw7.990.398.38
create_scExp0.840.030.87
define_feature0.270.000.27
detect_samples1.050.031.06
differential_activation6.390.146.53
differential_analysis_scExp2.760.192.95
enrich_TF_ChEA3_genes0.890.202.63
enrich_TF_ChEA3_scExp2.020.198.36
exclude_features_scExp0.860.050.90
feature_annotation_scExp2.040.082.13
filter_correlated_cell_scExp11.24 0.1527.58
filter_scExp1.030.021.04
find_clusters_louvain_scExp1.370.208.32
find_top_features0.400.080.47
gene_set_enrichment_analysis_scExp0.210.110.32
generate_analysis000
generate_coverage_tracks000
generate_report000
getExperimentNames0.320.120.44
getMainExperiment0.430.150.58
get_cyto_features23.71 0.3924.09
get_genomic_coordinates0.750.040.80
get_most_variable_cyto27.29 0.3027.62
has_genomic_coordinates0.990.061.05
import_scExp6.800.056.85
inter_correlation_scExp0.600.110.71
intra_correlation_scExp0.540.160.69
launchApp000
normalize_scExp0.870.050.92
num_cell_after_QC_filt_scExp0.990.031.01
num_cell_after_cor_filt_scExp11.42 0.1427.46
num_cell_before_cor_filt_scExp0.290.160.45
num_cell_in_cluster_scExp0.600.140.75
num_cell_scExp0.830.000.83
plot_cluster_consensus_scExp1.110.111.22
plot_correlation_PCA_scExp1.040.171.22
plot_coverage_BigWig0.270.200.47
plot_differential_summary_scExp0.250.190.43
plot_differential_volcano_scExp0.360.140.50
plot_distribution_scExp0.540.100.64
plot_gain_or_loss_barplots58.08 0.7058.80
plot_heatmap_scExp0.350.080.42
plot_inter_correlation_scExp0.560.060.62
plot_intra_correlation_scExp0.480.140.63
plot_most_contributing_features0.490.170.66
plot_pie_most_contributing_chr0.330.080.41
plot_reduced_dim_scExp4.680.204.90
plot_reduced_dim_scExp_CNA28.03 0.3028.33
plot_top_TF_scExp0.570.190.75
plot_violin_feature_scExp3.230.173.41
preprocess_CPM0.610.040.65
preprocess_RPKM0.640.040.67
preprocess_TFIDF0.630.010.65
preprocess_TPM0.730.080.81
preprocess_feature_size_only0.880.010.89
preprocessing_filtering_and_reduction8.820.089.00
read_sparse_matrix000
rebin_matrix2.250.002.25
reduce_dims_scExp2.130.002.12
scExp1.800.101.91
subsample_scExp0.750.030.78
subset_bam_call_peaks0.010.000.02
summary_DA0.200.170.37
swapAltExp_sameColData0.380.060.44
table_enriched_genes_scExp0.260.160.42
wrapper_Signac_FeatureMatrix000