Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:47 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 |
Package 2255/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ZygosityPredictor 1.5.0 (landing page) Marco Rheinnecker
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the ZygosityPredictor package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ZygosityPredictor.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: ZygosityPredictor |
Version: 1.5.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:ZygosityPredictor.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ZygosityPredictor_1.5.0.tar.gz |
StartedAt: 2024-08-27 10:24:51 -0000 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 10:30:24 -0000 (Tue, 27 Aug 2024) |
EllapsedTime: 333.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ZygosityPredictor.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:ZygosityPredictor.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings ZygosityPredictor_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ZygosityPredictor.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ZygosityPredictor/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ZygosityPredictor’ version ‘1.5.0’ * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ZygosityPredictor’ 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 code 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 loading without being on the library search path ... 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 ZP_ov: no visible binding for global variable ‘status’ ZP_ov: no visible binding for global variable ‘eval_by’ ZP_ov: no visible binding for global variable ‘nconst’ ZP_ov: no visible binding for global variable ‘gene’ add_snps_to_matrices: no visible binding for global variable ‘mut_id’ add_snps_to_matrices: no visible binding for global variable ‘block_final’ add_snps_to_matrices: no visible binding for global variable ‘gt_final’ add_snps_to_matrices: no visible binding for global variable ‘.’ add_snps_to_matrices : <anonymous>: no visible binding for global variable ‘block_final’ add_snps_to_matrices : <anonymous>: no visible binding for global variable ‘mut_id’ aggregate_likelihoods: no visible binding for global variable ‘.’ aggregate_likelihoods : <anonymous>: no visible binding for global variable ‘mut_id’ aggregate_likelihoods : <anonymous>: no visible binding for global variable ‘gt’ aggregate_likelihoods : <anonymous>: no visible binding for global variable ‘lklhd’ aggregate_phasing : <anonymous>: no visible binding for global variable ‘mut_id’ aggregate_phasing : <anonymous>: no visible binding for global variable ‘p_same’ aggregate_phasing : <anonymous>: no visible binding for global variable ‘p_diff’ aggregate_phasing : <anonymous>: no visible binding for global variable ‘ep’ aggregate_phasing: no visible binding for global variable ‘comb’ aggregate_phasing: no visible binding for global variable ‘nconst’ aggregate_phasing: no visible binding for global variable ‘const’ aggregate_phasing: no visible binding for global variable ‘phasing’ aggregate_phasing: no visible binding for global variable ‘via’ aggregate_phasing: no visible binding for global variable ‘conf’ aggregate_phasing: no visible binding for global variable ‘unplausible’ aggregate_phasing: no visible binding for global variable ‘subclonal’ aggregate_phasing: no visible binding for global variable ‘wt_cp’ aggregate_phasing: no visible binding for global variable ‘min_poss_wt_cp’ aggregate_phasing: no visible binding for global variable ‘max_poss_wt_cp’ aggregate_phasing: no visible binding for global variable ‘score’ append_loglist: no visible binding for global variable ‘.’ bind_incdel_to_final_eval: no visible binding for global variable ‘status’ calc_genotype_likelihood_per_mut : <anonymous>: no visible binding for global variable ‘mapq’ calc_genotype_likelihood_per_mut : <anonymous>: no visible binding for global variable ‘.’ calc_genotype_likelihood_per_mut : <anonymous>: no visible binding for global variable ‘qual’ calc_genotype_likelihood_per_mut : <anonymous>: no visible binding for global variable ‘processed_bq’ calc_genotype_likelihood_per_mut : <anonymous>: no visible binding for global variable ‘processed_mapq’ calc_genotype_likelihood_per_mut : <anonymous>: no visible binding for global variable ‘aggregated_qual’ cigar_element: no visible binding for global variable ‘.’ classify_combination: no visible binding for global variable ‘baseq1’ classify_combination: no visible binding for global variable ‘baseq2’ classify_combination: no visible binding for global variable ‘mapq1’ classify_combination: no visible binding for global variable ‘mapq2’ classify_combination: no visible binding for global variable ‘pb1’ classify_combination: no visible binding for global variable ‘mq1’ classify_combination: no visible binding for global variable ‘pb2’ classify_combination: no visible binding for global variable ‘mq2’ classify_combination: no visible binding for global variable ‘ppos1’ classify_combination: no visible binding for global variable ‘ppos2’ classify_combination: no visible binding for global variable ‘p_result’ classify_combination: no visible binding for global variable ‘prob_sum’ classify_combination: no visible binding for global variable ‘origin’ eval_lost_in_tumor: no visible binding for global variable ‘gene’ eval_lost_in_tumor: no visible binding for global variable ‘pre_info’ eval_lost_in_tumor: no visible binding for global variable ‘wt_cp’ eval_one_mut: no visible binding for global variable ‘gene’ eval_one_mut: no visible binding for global variable ‘n_mut’ eval_one_mut: no visible binding for global variable ‘vn_status’ eval_one_mut: no visible binding for global variable ‘conf’ eval_one_mut: no visible binding for global variable ‘pre_info’ eval_one_mut: no visible binding for global variable ‘wt_cp’ eval_one_mut: no visible binding for global variable ‘eval_by’ eval_one_mut_affects_all: no visible binding for global variable ‘vn_status’ eval_one_mut_affects_all: no visible binding for global variable ‘.’ eval_one_mut_affects_all: no visible binding for global variable ‘mut_id’ eval_one_mut_affects_all: no visible binding for global variable ‘gene’ eval_one_mut_affects_all: no visible binding for global variable ‘n_mut’ eval_one_mut_affects_all: no visible binding for global variable ‘conf’ eval_one_mut_affects_all: no visible binding for global variable ‘eval_by’ eval_one_mut_affects_all: no visible binding for global variable ‘wt_cp’ eval_phasing_new: no visible binding for global variable ‘score’ eval_phasing_new: no visible binding for global variable ‘wt_cp’ eval_phasing_new: no visible binding for global variable ‘.’ eval_phasing_new: no visible binding for global variable ‘p_comb’ eval_phasing_new: no visible binding for global variable ‘comb’ eval_phasing_new: no visible binding for global variable ‘gene’ eval_phasing_new: no visible binding for global variable ‘phasing’ eval_rare_case: no visible binding for global variable ‘.’ find_unplaus_issues: no visible binding for global variable ‘unplausible’ find_unplaus_issues: no visible binding for global variable ‘comb’ find_unplaus_issues: no visible binding for global variable ‘.’ gene_ov: no visible binding for global variable ‘gene’ gene_ov: no visible binding for global variable ‘vn_status’ gene_ov: no visible binding for global variable ‘pre_info’ gene_ov: no visible binding for global variable ‘purity’ gene_ov: no visible binding for global variable ‘nconst’ gene_ov: no visible binding for global variable ‘conf’ gene_ov: no visible binding for global variable ‘xsq_diff’ gene_ov: no visible binding for global variable ‘xsq_same’ gene_ov: no visible binding for global variable ‘v_same’ gene_ov: no visible binding for global variable ‘v_diff’ gene_ov: no visible binding for global variable ‘phasing’ get_next_path: no visible binding for global variable ‘.’ get_xy_index: no visible binding for global variable ‘.’ loadVcf: no visible binding for global variable ‘.’ load_snps: no visible binding for global variable ‘.’ load_snps: no visible binding for global variable ‘QUAL’ load_snps: no visible binding for global variable ‘gt’ load_snps: no visible binding for global variable ‘mut_id’ make_mut_template: no visible global function definition for ‘expand_grid’ make_mut_template: no visible binding for global variable ‘.’ merge_sCNAs: no visible binding for global variable ‘all_imb’ merge_sCNAs: no visible binding for global variable ‘gt_cna’ merge_sCNAs: no visible binding for global variable ‘seg_id’ parse_cigar: no visible binding for global variable ‘.’ perform_copy_number_phasing : <anonymous>: no visible binding for global variable ‘seg_id’ perform_copy_number_phasing : <anonymous>: no visible binding for global variable ‘mut_id2’ perform_copy_number_phasing : <anonymous>: no visible binding for global variable ‘mut_id1’ perform_copy_number_phasing : <anonymous>: no visible binding for global variable ‘llr’ perform_indirect_phasing: no visible binding for global variable ‘af’ perform_indirect_phasing: no visible binding for global variable ‘tcn’ perform_indirect_phasing: no visible binding for global variable ‘chr’ perform_indirect_phasing: no visible binding for global variable ‘pos’ perform_indirect_phasing: no visible binding for global variable ‘ref’ perform_indirect_phasing: no visible binding for global variable ‘alt’ perform_indirect_phasing: no visible binding for global variable ‘mut_id’ perform_indirect_phasing: no visible binding for global variable ‘REF’ perform_indirect_phasing: no visible binding for global variable ‘ALT’ perform_indirect_phasing: no visible binding for global variable ‘gt_final’ phase: no visible binding for global variable ‘comb’ phase: no visible binding for global variable ‘ncomb’ phase_combination: no visible binding for global variable ‘purity’ phase_combination: no visible binding for global variable ‘printLog’ predict_zygosity: no visible binding for global variable ‘n_mut’ predict_zygosity: no visible binding for global variable ‘conf’ predict_zygosity: no visible binding for global variable ‘eval_by’ predict_zygosity: no visible binding for global variable ‘wt_cp_range’ predict_zygosity: no visible binding for global variable ‘phasing’ predict_zygosity: no visible binding for global variable ‘eval_time_s’ predict_zygosity_genewise: no visible binding for global variable ‘vn_status’ prepare_germline_variants: no visible binding for global variable ‘all_imb’ prepare_germline_variants: no visible binding for global variable ‘gt_cna’ prepare_germline_variants: no visible binding for global variable ‘seg_id’ prepare_germline_variants: no visible binding for global variable ‘vn_status’ prioritize_combination: no visible binding for global variable ‘.’ prioritize_combination : <anonymous>: no visible binding for global variable ‘.’ prioritize_combination: no visible binding for global variable ‘m’ prioritize_combination: no visible binding for global variable ‘n’ prioritize_combination: no visible binding for global variable ‘n1’ prioritize_combination: no visible binding for global variable ‘n2’ remove_duplicated_variants: no visible binding for global variable ‘chr’ remove_duplicated_variants: no visible binding for global variable ‘pos’ remove_duplicated_variants: no visible binding for global variable ‘n’ remove_duplicated_variants : <anonymous>: no visible binding for global variable ‘chr’ remove_duplicated_variants : <anonymous>: no visible binding for global variable ‘pos’ remove_duplicated_variants : <anonymous>: no visible binding for global variable ‘.’ remove_duplicated_variants : <anonymous>: no visible binding for global variable ‘mut_id’ vm: no visible binding for global variable ‘.’ Undefined global functions or variables: . ALT QUAL REF af aggregated_qual all_imb alt baseq1 baseq2 block_final chr comb conf const ep eval_by eval_time_s expand_grid gene gt gt_cna gt_final lklhd llr m mapq mapq1 mapq2 max_poss_wt_cp min_poss_wt_cp mq1 mq2 mut_id mut_id1 mut_id2 n n1 n2 n_mut ncomb nconst origin p_comb p_diff p_result p_same pb1 pb2 phasing pos ppos1 ppos2 pre_info printLog prob_sum processed_bq processed_mapq purity qual ref score seg_id status subclonal tcn unplausible v_diff v_same via vn_status wt_cp wt_cp_range xsq_diff xsq_same * checking Rd files ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/home/biocbuild/bbs-3.20-bioc/meat/ZygosityPredictor.Rcheck/00check.log’ for details.
ZygosityPredictor.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL ZygosityPredictor ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘ZygosityPredictor’ ... ** using staged installation ** 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 (ZygosityPredictor)
ZygosityPredictor.Rcheck/ZygosityPredictor-Ex.timings
name | user | system | elapsed | |
ZP_ov | 1.294 | 0.064 | 1.361 | |
aff_germ_copies | 0.040 | 0.004 | 0.044 | |
aff_som_copies | 0.041 | 0.000 | 0.041 | |
gene_ov | 1.877 | 0.048 | 1.928 | |
predict_per_variant | 0.786 | 0.072 | 0.860 | |
predict_zygosity | 0.885 | 0.076 | 0.963 | |