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).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" | 4380 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" | 4156 |
merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.0 (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 |
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. |
Package 321/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChromSCape 1.6.0 (landing page) Pacome Prompsy
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
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 |
############################################################################## ############################################################################## ### ### 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.
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)
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
ChromSCape.Rcheck/ChromSCape-Ex.timings
name | user | system | elapsed | |
CheA3_TF_nTargets | 0.01 | 0.00 | 0.01 | |
CompareWilcox | 4.92 | 0.16 | 51.22 | |
CompareedgeRGLM | 11.92 | 0.21 | 12.14 | |
annotToCol2 | 1.06 | 0.24 | 1.29 | |
calculate_CNA | 27.43 | 1.09 | 28.52 | |
calculate_cyto_mat | 28.64 | 0.60 | 29.23 | |
calculate_gain_or_loss | 27.37 | 0.57 | 27.96 | |
calculate_logRatio_CNA | 25.50 | 0.77 | 26.28 | |
choose_cluster_scExp | 4.46 | 0.91 | 5.36 | |
colors_scExp | 0.31 | 0.11 | 0.42 | |
consensus_clustering_scExp | 3.32 | 0.40 | 3.74 | |
correlation_and_hierarchical_clust_scExp | 0.46 | 0.08 | 0.55 | |
create_project_folder | 0.00 | 0.00 | 0.01 | |
create_scDataset_raw | 7.99 | 0.39 | 8.38 | |
create_scExp | 0.84 | 0.03 | 0.87 | |
define_feature | 0.27 | 0.00 | 0.27 | |
detect_samples | 1.05 | 0.03 | 1.06 | |
differential_activation | 6.39 | 0.14 | 6.53 | |
differential_analysis_scExp | 2.76 | 0.19 | 2.95 | |
enrich_TF_ChEA3_genes | 0.89 | 0.20 | 2.63 | |
enrich_TF_ChEA3_scExp | 2.02 | 0.19 | 8.36 | |
exclude_features_scExp | 0.86 | 0.05 | 0.90 | |
feature_annotation_scExp | 2.04 | 0.08 | 2.13 | |
filter_correlated_cell_scExp | 11.24 | 0.15 | 27.58 | |
filter_scExp | 1.03 | 0.02 | 1.04 | |
find_clusters_louvain_scExp | 1.37 | 0.20 | 8.32 | |
find_top_features | 0.40 | 0.08 | 0.47 | |
gene_set_enrichment_analysis_scExp | 0.21 | 0.11 | 0.32 | |
generate_analysis | 0 | 0 | 0 | |
generate_coverage_tracks | 0 | 0 | 0 | |
generate_report | 0 | 0 | 0 | |
getExperimentNames | 0.32 | 0.12 | 0.44 | |
getMainExperiment | 0.43 | 0.15 | 0.58 | |
get_cyto_features | 23.71 | 0.39 | 24.09 | |
get_genomic_coordinates | 0.75 | 0.04 | 0.80 | |
get_most_variable_cyto | 27.29 | 0.30 | 27.62 | |
has_genomic_coordinates | 0.99 | 0.06 | 1.05 | |
import_scExp | 6.80 | 0.05 | 6.85 | |
inter_correlation_scExp | 0.60 | 0.11 | 0.71 | |
intra_correlation_scExp | 0.54 | 0.16 | 0.69 | |
launchApp | 0 | 0 | 0 | |
normalize_scExp | 0.87 | 0.05 | 0.92 | |
num_cell_after_QC_filt_scExp | 0.99 | 0.03 | 1.01 | |
num_cell_after_cor_filt_scExp | 11.42 | 0.14 | 27.46 | |
num_cell_before_cor_filt_scExp | 0.29 | 0.16 | 0.45 | |
num_cell_in_cluster_scExp | 0.60 | 0.14 | 0.75 | |
num_cell_scExp | 0.83 | 0.00 | 0.83 | |
plot_cluster_consensus_scExp | 1.11 | 0.11 | 1.22 | |
plot_correlation_PCA_scExp | 1.04 | 0.17 | 1.22 | |
plot_coverage_BigWig | 0.27 | 0.20 | 0.47 | |
plot_differential_summary_scExp | 0.25 | 0.19 | 0.43 | |
plot_differential_volcano_scExp | 0.36 | 0.14 | 0.50 | |
plot_distribution_scExp | 0.54 | 0.10 | 0.64 | |
plot_gain_or_loss_barplots | 58.08 | 0.70 | 58.80 | |
plot_heatmap_scExp | 0.35 | 0.08 | 0.42 | |
plot_inter_correlation_scExp | 0.56 | 0.06 | 0.62 | |
plot_intra_correlation_scExp | 0.48 | 0.14 | 0.63 | |
plot_most_contributing_features | 0.49 | 0.17 | 0.66 | |
plot_pie_most_contributing_chr | 0.33 | 0.08 | 0.41 | |
plot_reduced_dim_scExp | 4.68 | 0.20 | 4.90 | |
plot_reduced_dim_scExp_CNA | 28.03 | 0.30 | 28.33 | |
plot_top_TF_scExp | 0.57 | 0.19 | 0.75 | |
plot_violin_feature_scExp | 3.23 | 0.17 | 3.41 | |
preprocess_CPM | 0.61 | 0.04 | 0.65 | |
preprocess_RPKM | 0.64 | 0.04 | 0.67 | |
preprocess_TFIDF | 0.63 | 0.01 | 0.65 | |
preprocess_TPM | 0.73 | 0.08 | 0.81 | |
preprocess_feature_size_only | 0.88 | 0.01 | 0.89 | |
preprocessing_filtering_and_reduction | 8.82 | 0.08 | 9.00 | |
read_sparse_matrix | 0 | 0 | 0 | |
rebin_matrix | 2.25 | 0.00 | 2.25 | |
reduce_dims_scExp | 2.13 | 0.00 | 2.12 | |
scExp | 1.80 | 0.10 | 1.91 | |
subsample_scExp | 0.75 | 0.03 | 0.78 | |
subset_bam_call_peaks | 0.01 | 0.00 | 0.02 | |
summary_DA | 0.20 | 0.17 | 0.37 | |
swapAltExp_sameColData | 0.38 | 0.06 | 0.44 | |
table_enriched_genes_scExp | 0.26 | 0.16 | 0.42 | |
wrapper_Signac_FeatureMatrix | 0 | 0 | 0 | |