| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:33 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 2200/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| YAPSA 1.25.0 (landing page) Daniel Huebschmann
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | ||||||||||
| 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/site-library --timings YAPSA_1.25.0.tar.gz |
| StartedAt: 2023-04-12 00:28:02 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 00:39:29 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 687.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: YAPSA.Rcheck |
| Warnings: NA |
##############################################################################
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###
### 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/site-library --timings YAPSA_1.25.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/YAPSA.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-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 22.04.2 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 ... 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
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 ... 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 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: get_extreme_PIDs
> ### Title: Return those PIDs which have an extreme pattern for signature
> ### exposure
> ### Aliases: get_extreme_PIDs
>
> ### ** Examples
>
> data(lymphoma_cohort_LCD_results)
> get_extreme_PIDs(lymphoma_Nature2013_COSMIC_cutoff_exposures_df,0.05)
Error in xtfrm.data.frame(x) : cannot xtfrm data frames
Calls: get_extreme_PIDs ... lapply -> FUN -> as.vector -> xtfrm -> xtfrm.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 ...
‘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, 1 WARNING, 1 NOTE
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/site-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 version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 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.
> 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
16.083 0.824 16.901
YAPSA.Rcheck/YAPSA-Ex.timings
| name | user | system | elapsed | |
| GenomeOfNl_raw | 0.008 | 0.000 | 0.009 | |
| LCD | 0.008 | 0.000 | 0.007 | |
| LCD_complex_cutoff | 0 | 0 | 0 | |
| MutCat_indel_df | 0.004 | 0.000 | 0.004 | |
| SMC | 0 | 0 | 0 | |
| SMC_perPID | 0 | 0 | 0 | |
| add_annotation | 0 | 0 | 0 | |
| add_as_fist_to_list | 0 | 0 | 0 | |
| aggregate_exposures_by_category | 0 | 0 | 0 | |
| annotate_intermut_dist_PID | 0.015 | 0.006 | 0.019 | |
| annotate_intermut_dist_cohort | 0.019 | 0.003 | 0.023 | |
| annotation_exposures_barplot | 0 | 0 | 0 | |
| annotation_exposures_list_barplot | 0 | 0 | 0 | |
| annotation_heatmap_exposures | 0.001 | 0.000 | 0.000 | |
| attribute_nucleotide_exchanges | 0.003 | 0.000 | 0.003 | |
| attribute_sequence_contex_indel | 0.528 | 0.032 | 0.561 | |
| attribution_of_indels | 0.458 | 0.092 | 0.550 | |
| build_gene_list_for_pathway | 6.520 | 0.683 | 26.858 | |
| classify_indels | 0.001 | 0.000 | 0.000 | |
| compare_SMCs | 0 | 0 | 0 | |
| compare_exposures | 0 | 0 | 0 | |
| compare_expousre_sets | 0.002 | 0.002 | 0.004 | |
| compare_sets | 0.004 | 0.000 | 0.004 | |
| compare_to_catalogues | 0.001 | 0.000 | 0.001 | |
| complex_heatmap_exposures | 0.870 | 0.068 | 0.938 | |
| computeLogLik | 0 | 0 | 0 | |
| compute_comparison_stat_df | 0 | 0 | 0 | |
| confIntExp | 1.203 | 0.396 | 1.607 | |
| confidence_indel_calulation | 0.001 | 0.000 | 0.002 | |
| confidence_indel_only_calulation | 20.597 | 0.523 | 21.120 | |
| correct_rounded | 0.000 | 0.001 | 0.000 | |
| cosineDist | 0.000 | 0.000 | 0.001 | |
| cosineMatchDist | 0.000 | 0.002 | 0.003 | |
| create_indel_mut_cat_from_df | 0.387 | 0.028 | 0.415 | |
| create_indel_mutation_catalogue_from_df | 12.307 | 0.840 | 13.147 | |
| create_mutation_catalogue_from_VR | 1.135 | 0.208 | 1.343 | |
| create_mutation_catalogue_from_df | 0.820 | 0.148 | 0.968 | |
| cut_breaks_as_intervals | 0.136 | 0.005 | 0.141 | |
| deriveSigInd_df | 0 | 0 | 0 | |
| disambiguateVector | 0.000 | 0.000 | 0.001 | |
| enrichSigs | 0 | 0 | 0 | |
| exampleYAPSA | 0.086 | 0.001 | 0.087 | |
| exome_mutCatRaw_df | 0.008 | 0.004 | 0.011 | |
| exposures_barplot | 2.621 | 0.028 | 2.649 | |
| extract_names_from_gene_list | 0.001 | 0.000 | 0.000 | |
| find_affected_PIDs | 0 | 0 | 0 | |
| getSequenceContext | 0.118 | 0.008 | 0.125 | |