Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-08 01:15:35 -0000 (Wed, 08 Feb 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4164 |
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 YAPSA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/YAPSA.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 2158/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
YAPSA 1.25.0 (landing page) Daniel Huebschmann
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
Package: YAPSA |
Version: 1.25.0 |
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:YAPSA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings YAPSA_1.25.0.tar.gz |
StartedAt: 2023-02-07 19:08:11 -0000 (Tue, 07 Feb 2023) |
EndedAt: 2023-02-07 19:22:44 -0000 (Tue, 07 Feb 2023) |
EllapsedTime: 873.3 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: YAPSA.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:YAPSA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings YAPSA_1.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/YAPSA.Rcheck’ * using R Under development (unstable) (2023-01-14 r83615) * using platform: aarch64-unknown-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.1 LTS * using session charset: UTF-8 * checking for file ‘YAPSA/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘YAPSA’ version ‘1.25.0’ * 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 ‘YAPSA’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘GenomicRanges::subtract’ by ‘magrittr::subtract’ when loading ‘YAPSA’ See ‘/home/biocbuild/bbs-3.17-bioc/meat/YAPSA.Rcheck/00install.out’ for details. * 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 ... WARNING Loading required package: GenomicRanges Loading required package: methods Loading required package: stats4 Loading required package: BiocGenerics Loading required package: utils Loading required package: graphics Attaching package: ‘graphics’ The following object is masked from ‘package:stats4’: plot Loading required package: stats Attaching package: ‘stats’ The following objects are masked from ‘package:stats4’: AIC, BIC, coef, confint, logLik, nobs, profile, update, vcov Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: ggplot2 Loading required package: grid Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Killed It looks like this package (or one of its dependent packages) has an unstated dependence on a standard package. All dependencies must be declared in DESCRIPTION. See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. * 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 ... NOTE Killed See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE read_list: no visible global function definition for 'detectCores' read_list: no visible global function definition for 'makeCluster' read_list: no visible global function definition for 'mclapply' read_list: no visible global function definition for 'stopCluster' Undefined global functions or variables: detectCores makeCluster mclapply stopCluster * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... WARNING Killed Killed * 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 installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘YAPSA-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: build_gene_list_for_pathway > ### Title: Build a gene list for a given pathway name > ### Aliases: build_gene_list_for_pathway > > ### ** Examples > > species <- "hsa" > gene_lists_meta_df <- data.frame( + name=c("BER","NHEJ","MMR"), + explanation=c("base excision repair", + "non homologous end joining", + "mismatch repair")) > number_of_pathways <- dim(gene_lists_meta_df)[1] > gene_lists_list <- list() > for (i in seq_len(number_of_pathways)) { + temp_list <- + build_gene_list_for_pathway(gene_lists_meta_df$explanation[i], + species) + gene_lists_list <- c(gene_lists_list,list(temp_list)) + } Killed * 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 ... ‘YAPSA.Rmd’ using ‘UTF-8’... OK ‘vignette_confidenceIntervals.Rmd’ using ‘UTF-8’... OK ‘vignette_exomes.Rmd’ using ‘UTF-8’... OK ‘vignette_signature_specific_cutoffs.Rmd’ using ‘UTF-8’... OK ‘vignette_stratifiedAnalysis.Rmd’ using ‘UTF-8’... OK ‘vignettes_Indel.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 3 WARNINGs, 2 NOTEs See ‘/home/biocbuild/bbs-3.17-bioc/meat/YAPSA.Rcheck/00check.log’ for details.
YAPSA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL YAPSA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘YAPSA’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Warning: replacing previous import ‘GenomicRanges::subtract’ by ‘magrittr::subtract’ when loading ‘YAPSA’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Warning: replacing previous import ‘GenomicRanges::subtract’ by ‘magrittr::subtract’ when loading ‘YAPSA’ ** testing if installed package can be loaded from final location Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by ‘Rmpfr’ Warning: replacing previous import ‘GenomicRanges::subtract’ by ‘magrittr::subtract’ when loading ‘YAPSA’ ** testing if installed package keeps a record of temporary installation path * DONE (YAPSA)
YAPSA.Rcheck/tests/testthat.Rout
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > Sys.setenv(R_TESTS=" ") > library(testthat) > library(YAPSA) Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: ggplot2 Loading required package: grid Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Found more than one class "atomicVector" in cache; using the first, from namespace 'Matrix' Also defined by 'Rmpfr' Warning message: replacing previous import 'GenomicRanges::subtract' by 'magrittr::subtract' when loading 'YAPSA' > > test_check("YAPSA") YAPSA:::shapiro_if_possible::error: Non-numeric inputYAPSA:::makeVRangesFromDataFrame::warning:strand information missing, set to "+". YAPSA:::makeVRangesFromDataFrame::in_PID.field found. Retrieving PID information. YAPSA:::makeVRangesFromDataFrame::in_subgroup.field found. Retrieving subgroup information. [ FAIL 0 | WARN 1 | SKIP 0 | PASS 62 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 62 ] > > proc.time() user system elapsed 23.028 0.901 24.747
YAPSA.Rcheck/YAPSA-Ex.timings
name | user | system | elapsed | |
GenomeOfNl_raw | 0.011 | 0.000 | 0.012 | |
LCD | 0.048 | 0.000 | 0.051 | |
LCD_complex_cutoff | 0 | 0 | 0 | |
MutCat_indel_df | 0.005 | 0.001 | 0.006 | |
SMC | 0.000 | 0.001 | 0.000 | |
SMC_perPID | 0.000 | 0.000 | 0.001 | |
add_annotation | 0 | 0 | 0 | |
add_as_fist_to_list | 0.000 | 0.001 | 0.000 | |
aggregate_exposures_by_category | 0 | 0 | 0 | |
annotate_intermut_dist_PID | 0.024 | 0.000 | 0.024 | |
annotate_intermut_dist_cohort | 0.03 | 0.00 | 0.03 | |
annotation_exposures_barplot | 0 | 0 | 0 | |
annotation_exposures_list_barplot | 0 | 0 | 0 | |
annotation_heatmap_exposures | 0 | 0 | 0 | |
attribute_nucleotide_exchanges | 0.003 | 0.001 | 0.004 | |
attribute_sequence_contex_indel | 0.751 | 0.032 | 0.785 | |
attribution_of_indels | 0.662 | 0.072 | 0.736 | |