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).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.0 (2022-04-22) -- "Vigorous Calisthenics" | 4379 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" | 4154 |
merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.0 (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 |
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: /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 |
############################################################################## ############################################################################## ### ### 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.
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)
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
ChromSCape.Rcheck/ChromSCape-Ex.timings
name | user | system | elapsed | |
CheA3_TF_nTargets | 0.010 | 0.000 | 0.009 | |
CompareWilcox | 6.129 | 0.478 | 6.005 | |
CompareedgeRGLM | 4.804 | 0.152 | 4.942 | |
annotToCol2 | 1.087 | 0.044 | 1.131 | |
calculate_CNA | 26.727 | 2.220 | 28.951 | |
calculate_cyto_mat | 23.033 | 0.879 | 23.914 | |
calculate_gain_or_loss | 23.446 | 0.776 | 24.223 | |
calculate_logRatio_CNA | 24.252 | 0.688 | 24.944 | |
choose_cluster_scExp | 3.645 | 0.132 | 3.771 | |
colors_scExp | 0.331 | 0.000 | 0.331 | |
consensus_clustering_scExp | 3.365 | 0.104 | 3.463 | |
correlation_and_hierarchical_clust_scExp | 0.346 | 0.000 | 0.332 | |
create_project_folder | 0.002 | 0.000 | 0.002 | |
create_scDataset_raw | 7.749 | 0.408 | 8.156 | |
create_scExp | 0.803 | 0.000 | 0.803 | |
define_feature | 0.169 | 0.004 | 0.173 | |
detect_samples | 1.142 | 0.008 | 1.088 | |
differential_activation | 6.032 | 0.080 | 6.113 | |
differential_analysis_scExp | 2.865 | 0.024 | 2.889 | |
enrich_TF_ChEA3_genes | 0.506 | 0.144 | 2.427 | |
enrich_TF_ChEA3_scExp | 1.161 | 0.057 | 7.448 | |
exclude_features_scExp | 0.696 | 0.096 | 0.792 | |
feature_annotation_scExp | 1.921 | 0.188 | 2.109 | |
filter_correlated_cell_scExp | 11.654 | 0.922 | 12.523 | |
filter_scExp | 0.865 | 0.056 | 0.921 | |
find_clusters_louvain_scExp | 0.574 | 0.449 | 0.646 | |
find_top_features | 0.383 | 0.028 | 0.412 | |
gene_set_enrichment_analysis_scExp | 0.283 | 0.000 | 0.284 | |
generate_analysis | 0 | 0 | 0 | |
generate_coverage_tracks | 0 | 0 | 0 | |
generate_report | 0 | 0 | 0 | |
getExperimentNames | 0.251 | 0.017 | 0.269 | |
getMainExperiment | 0.296 | 0.019 | 0.316 | |
get_cyto_features | 20.438 | 0.584 | 21.023 | |
get_genomic_coordinates | 0.565 | 0.024 | 0.590 | |
get_most_variable_cyto | 22.630 | 0.484 | 23.115 | |
has_genomic_coordinates | 0.948 | 0.036 | 0.984 | |
import_scExp | 6.657 | 0.179 | 6.837 | |
inter_correlation_scExp | 0.401 | 0.008 | 0.409 | |
intra_correlation_scExp | 0.359 | 0.004 | 0.363 | |
launchApp | 0.000 | 0.001 | 0.000 | |
normalize_scExp | 0.588 | 0.019 | 0.607 | |
num_cell_after_QC_filt_scExp | 0.669 | 0.008 | 0.677 | |
num_cell_after_cor_filt_scExp | 10.907 | 0.358 | 11.199 | |
num_cell_before_cor_filt_scExp | 0.226 | 0.004 | 0.231 | |
num_cell_in_cluster_scExp | 0.509 | 0.005 | 0.506 | |
num_cell_scExp | 0.506 | 0.043 | 0.550 | |
plot_cluster_consensus_scExp | 0.812 | 0.072 | 0.884 | |
plot_correlation_PCA_scExp | 0.871 | 0.004 | 0.874 | |
plot_coverage_BigWig | 0.214 | 0.000 | 0.214 | |
plot_differential_summary_scExp | 0.240 | 0.007 | 0.248 | |
plot_differential_volcano_scExp | 0.321 | 0.009 | 0.328 | |
plot_distribution_scExp | 0.478 | 0.000 | 0.478 | |
plot_gain_or_loss_barplots | 49.949 | 0.759 | 50.709 | |
plot_heatmap_scExp | 0.312 | 0.000 | 0.313 | |
plot_inter_correlation_scExp | 0.511 | 0.000 | 0.511 | |
plot_intra_correlation_scExp | 0.497 | 0.000 | 0.497 | |
plot_most_contributing_features | 0.411 | 0.004 | 0.416 | |
plot_pie_most_contributing_chr | 0.314 | 0.016 | 0.329 | |
plot_reduced_dim_scExp | 3.591 | 0.048 | 3.638 | |
plot_reduced_dim_scExp_CNA | 23.089 | 0.196 | 23.285 | |
plot_top_TF_scExp | 0.485 | 0.008 | 0.493 | |
plot_violin_feature_scExp | 2.244 | 0.052 | 2.296 | |
preprocess_CPM | 0.570 | 0.032 | 0.602 | |
preprocess_RPKM | 0.618 | 0.043 | 0.661 | |
preprocess_TFIDF | 0.590 | 0.036 | 0.626 | |
preprocess_TPM | 0.634 | 0.020 | 0.655 | |
preprocess_feature_size_only | 0.640 | 0.028 | 0.668 | |
preprocessing_filtering_and_reduction | 9.261 | 0.036 | 9.291 | |
read_sparse_matrix | 0.000 | 0.000 | 0.001 | |
rebin_matrix | 2.366 | 0.003 | 2.370 | |
reduce_dims_scExp | 1.621 | 0.017 | 1.637 | |
scExp | 1.313 | 0.011 | 1.325 | |
subsample_scExp | 0.798 | 0.004 | 0.802 | |
subset_bam_call_peaks | 0.001 | 0.000 | 0.000 | |
summary_DA | 0.254 | 0.001 | 0.254 | |
swapAltExp_sameColData | 0.308 | 0.011 | 0.320 | |
table_enriched_genes_scExp | 0.216 | 0.000 | 0.216 | |
wrapper_Signac_FeatureMatrix | 0 | 0 | 0 | |