Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-14 11:06:46 -0400 (Mon, 14 Mar 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4335 |
riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4061 |
palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4073 |
merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 311/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChromSCape 1.5.22 (landing page) Pacome Prompsy
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | ERROR | |||||||||
riesling1 | Windows Server 2019 Standard / x64 | OK | OK | ERROR | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
Package: ChromSCape |
Version: 1.5.22 |
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChromSCape.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChromSCape_1.5.22.tar.gz |
StartedAt: 2022-03-13 18:36:28 -0400 (Sun, 13 Mar 2022) |
EndedAt: 2022-03-13 18:47:45 -0400 (Sun, 13 Mar 2022) |
EllapsedTime: 676.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: ChromSCape.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ChromSCape.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ChromSCape_1.5.22.tar.gz ### ############################################################################## ############################################################################## * using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ChromSCape.Rcheck' * using R Under development (unstable) (2021-11-21 r81221) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'ChromSCape/DESCRIPTION' ... OK * this is package 'ChromSCape' version '1.5.22' * 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 5.9Mb sub-directories of 1Mb or more: data 1.3Mb 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 ... OK * 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' 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_coverage_BigWig: no visible binding for global variable 'score' 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_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' subset_bam_call_peaks: no visible binding for global variable 'merged_bam' Undefined global functions or variables: Fri_cyto Gain_or_Loss Gene V1 V2 absolute_value annot. cluster clusterConsensus cytoBand files_dir_list genes k merged_bam molecule ncells orientation run_tsne sample_id score total_counts * 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 ... OK * checking Rd \usage sections ... OK * 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 'D:/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) Found 'printf', possibly from 'printf' (C) 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' ... NOTE Files named as vignettes but with no recognized vignette engine: 'vignettes/PairedTag_Zhu_H3K4me1.Rmd' 'vignettes/scChIC_Ku_H3K4me3.Rmd' (Is a VignetteBuilder field missing?) * checking examples ... ERROR Running examples in 'ChromSCape-Ex.R' failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: differential_analysis_scExp > ### Title: Runs differential analysis between cell clusters > ### Aliases: differential_analysis_scExp > > ### ** Examples > > data("scExp") > scExp_cf = differential_analysis_scExp(scExp) Warning in .Internal(gc(verbose, reset, full)) : closing unused connection 15 (<-riesling1:11417) Warning in .Internal(gc(verbose, reset, full)) : closing unused connection 14 (<-riesling1:11417) Warning in .Internal(gc(verbose, reset, full)) : closing unused connection 13 (<-riesling1:11417) Warning in .Internal(gc(verbose, reset, full)) : closing unused connection 12 (<-riesling1:11417) Warning in .Internal(gc(verbose, reset, full)) : closing unused connection 11 (<-riesling1:11417) Warning in .Internal(gc(verbose, reset, full)) : closing unused connection 10 (<-riesling1:11417) Warning in .Internal(gc(verbose, reset, full)) : closing unused connection 9 (<-riesling1:11417) Warning in .Internal(gc(verbose, reset, full)) : closing unused connection 8 (<-riesling1:11417) Warning in .Internal(gc(verbose, reset, full)) : closing unused connection 7 (<-riesling1:11417) Warning in .Internal(gc(verbose, reset, full)) : closing unused connection 6 (<-riesling1:11417) Warning in .Internal(gc(verbose, reset, full)) : closing unused connection 5 (<-riesling1:11417) Warning in .Internal(gc(verbose, reset, full)) : closing unused connection 4 (<-riesling1:11417) Error in `[.data.frame`(res, , logFC.col) : undefined columns selected Calls: differential_analysis_scExp -> [ -> [.data.frame Execution halted * 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: 1 ERROR, 6 NOTEs See 'D:/biocbuild/bbs-3.15-bioc/meat/ChromSCape.Rcheck/00check.log' for details.
ChromSCape.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ChromSCape ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'ChromSCape' ... ** using staged installation ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c as_dist.cpp -o as_dist.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o ChromSCape.dll tmp.def RcppExports.o as_dist.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/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 converting help for package 'ChromSCape' finding HTML links ... done CompareWilcox html CompareedgeRGLM html DA_custom html DA_one_vs_rest_fun html DA_pairwise html H1proportion html annotToCol2 html annotation_from_merged_peaks html anocol_binary html anocol_categorical html bams_to_matrix_indexes html beds_to_matrix_indexes html calculate_CNA html calculate_cyto_mat html calculate_gain_or_loss html calculate_logRatio_CNA html call_macs2_merge_peaks html changeRange html check_correct_datamatrix html choose_cluster_scExp html choose_perplexity html col2hex html colors_scExp html combine_datamatrix html combine_enrichmentTests html concatenate_scBed_into_clusters html consensus_clustering_scExp html correlation_and_hierarchical_clust_scExp html count_coverage html create_project_folder html create_sample_name_mat html create_scDataset_raw html create_scExp html define_feature html detect_samples html differential_activation_scExp html differential_analysis_scExp html distPearson html enrichmentTest html exclude_features_scExp html feature_annotation_scExp html filter_correlated_cell_scExp html filter_genes_with_refined_peak_annotation html filter_scExp html find_top_features html gene_set_enrichment_analysis_scExp html generate_analysis html generate_count_matrix html generate_coverage_tracks html generate_feature_names html generate_report html getExperimentNames html getMainExperiment html get_color_dataframe_from_input html get_cyto_features html get_genomic_coordinates html get_most_variable_cyto html gg_fill_hue html groupMat html has_genomic_coordinates html hclustAnnotHeatmapPlot html hg38.GeneTSS html hg38.chromosomes html hg38.cytoBand html imageCol html import_count_input_files html import_scExp html index_peaks_barcodes_to_matrix_indexes html inter_correlation_scExp html intra_correlation_scExp html launchApp html load_MSIGdb html merge_MACS2_peaks html mm10.GeneTSS html mm10.chromosomes html mm10.cytoBand html normalize_scExp html num_cell_after_QC_filt_scExp html num_cell_after_cor_filt_scExp html num_cell_before_cor_filt_scExp html num_cell_in_cluster_scExp html num_cell_scExp html pca_irlba_for_sparseMatrix html peaks_to_bins html plot_cluster_consensus_scExp html plot_coverage_BigWig html plot_differential_H1_scExp html plot_differential_summary_scExp html plot_differential_volcano_scExp html plot_distribution_scExp html plot_gain_or_loss_barplots html plot_heatmap_scExp html plot_inter_correlation_scExp html plot_intra_correlation_scExp html plot_most_contributing_features html plot_pie_most_contributing_chr html plot_reduced_dim_scExp html plot_reduced_dim_scExp_CNA html preprocess_CPM html preprocess_RPKM html preprocess_TFIDF html preprocess_TPM html preprocess_feature_size_only html preprocessing_filtering_and_reduction html raw_counts_to_sparse_matrix html rawfile_ToBigWig html read_count_mat_with_separated_chr_start_end html read_sparse_matrix html reduce_dim_batch_correction html reduce_dims_scExp html remove_chr_M_fun html remove_non_canonical_fun html results_enrichmentTest html retrieve_top_bot_features_pca html run_pairwise_tests html run_tsne_scExp html scExp html separate_BAM_into_clusters html separator_count_mat html smoothBin html subsample_scExp html subset_bam_call_peaks html swapAltExp_sameColData html table_enriched_genes_scExp html warning_DA html warning_filter_correlated_cell_scExp html warning_plot_reduced_dim_scExp html warning_raw_counts_to_sparse_matrix html wrapper_Signac_FeatureMatrix html ** 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) Making 'packages.html' ... done
ChromSCape.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" Copyright (C) 2021 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 29.18 4.23 56.68
ChromSCape.Rcheck/ChromSCape-Ex.timings
name | user | system | elapsed | |
CompareWilcox | 4.08 | 0.11 | 38.47 | |
CompareedgeRGLM | 10.23 | 0.86 | 11.09 | |
annotToCol2 | 1.11 | 0.13 | 1.24 | |
calculate_CNA | 22.08 | 0.73 | 22.82 | |
calculate_cyto_mat | 21.17 | 0.28 | 21.47 | |
calculate_gain_or_loss | 18.98 | 0.24 | 19.22 | |
calculate_logRatio_CNA | 18.33 | 0.14 | 18.47 | |
choose_cluster_scExp | 2.97 | 1.22 | 4.19 | |
colors_scExp | 0.28 | 0.01 | 0.30 | |
consensus_clustering_scExp | 3.31 | 0.74 | 4.04 | |
correlation_and_hierarchical_clust_scExp | 0.22 | 0.01 | 0.24 | |
create_project_folder | 0 | 0 | 0 | |
create_scDataset_raw | 6.14 | 1.61 | 7.75 | |
create_scExp | 0.77 | 0.09 | 0.86 | |
define_feature | 0.17 | 0.00 | 0.17 | |
detect_samples | 0.95 | 0.06 | 0.96 | |
differential_activation_scExp | 0.32 | 0.14 | 135.92 | |