Daniel Huebschmann
| Snapshot Date: 2022-08-05 14:00:05 -0400 (Fri, 05 Aug 2022) |
| git_url: https://git.bioconductor.org/packages/YAPSA |
| git_branch: master |
| git_last_commit: 68d5478 |
| git_last_commit_date: 2022-04-26 11:35:04 -0400 (Tue, 26 Apr 2022) |
| Back to Multiple platform build/check report for BioC 3.16 |
|
This page was generated on 2022-08-06 11:07:07 -0400 (Sat, 06 Aug 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4371 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4155 |
| lconway | macOS 12.2.1 Monterey | x86_64 | 4.2.1 Patched (2022-07-09 r82577) -- "Funny-Looking Kid" | 4155 |
| 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 2132/2137 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| YAPSA 1.23.0 (landing page) Daniel Huebschmann
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | NA | |||||||||
| lconway | macOS 12.2.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: YAPSA |
| Version: 1.23.0 |
| Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:YAPSA.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings YAPSA_1.23.0.tar.gz |
| StartedAt: 2022-08-06 07:07:41 -0400 (Sat, 06 Aug 2022) |
| EndedAt: 2022-08-06 07:15:30 -0400 (Sat, 06 Aug 2022) |
| EllapsedTime: 469.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: YAPSA.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:YAPSA.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings YAPSA_1.23.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/YAPSA.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'YAPSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'YAPSA' version '1.23.0'
* 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 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 'F:/biocbuild/bbs-3.16-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 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
confidence_indel_only_calulation 20.69 0.71 21.41
create_indel_mutation_catalogue_from_df 14.45 1.13 15.57
build_gene_list_for_pathway 3.81 0.14 18.47
* 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 WARNING, 1 NOTE
See
'F:/biocbuild/bbs-3.16-bioc/meat/YAPSA.Rcheck/00check.log'
for details.
YAPSA.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.16/bioc/src/contrib/YAPSA_1.23.0.tar.gz && rm -rf YAPSA.buildbin-libdir && mkdir YAPSA.buildbin-libdir && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=YAPSA.buildbin-libdir YAPSA_1.23.0.tar.gz && F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL YAPSA_1.23.0.zip && rm YAPSA_1.23.0.tar.gz YAPSA_1.23.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
11 1293k 11 150k 0 0 1794k 0 --:--:-- --:--:-- --:--:-- 1792k
100 1293k 100 1293k 0 0 2706k 0 --:--:-- --:--:-- --:--:-- 2705k
only one architecture so ignoring '--merge-multiarch'
* 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'
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'
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'
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
* MD5 sums
packaged installation of 'YAPSA' as YAPSA_1.23.0.zip
* DONE (YAPSA)
* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
package 'YAPSA' successfully unpacked and MD5 sums checked
YAPSA.Rcheck/tests/testthat.Rout
R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 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.
> 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, 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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
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'
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 0 | SKIP 0 | PASS 62 ]
>
> proc.time()
user system elapsed
17.25 1.21 18.42
YAPSA.Rcheck/YAPSA-Ex.timings
| name | user | system | elapsed | |
| GenomeOfNl_raw | 0.01 | 0.00 | 0.01 | |
| LCD | 0.02 | 0.00 | 0.02 | |
| LCD_complex_cutoff | 0 | 0 | 0 | |
| MutCat_indel_df | 0.01 | 0.00 | 0.02 | |
| 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 | 0.02 | 0.00 | 0.02 | |
| 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 | 0 | 0 | |
| attribute_sequence_contex_indel | 1.72 | 0.02 | 1.73 | |
| attribution_of_indels | 0.48 | 0.04 | 0.53 | |
| build_gene_list_for_pathway | 3.81 | 0.14 | 18.47 | |
| classify_indels | 0 | 0 | 0 | |
| compare_SMCs | 0 | 0 | 0 | |
| compare_exposures | 0 | 0 | 0 | |
| compare_expousre_sets | 0 | 0 | 0 | |
| compare_sets | 0 | 0 | 0 | |
| compare_to_catalogues | 0 | 0 | 0 | |
| complex_heatmap_exposures | 0.91 | 0.00 | 0.90 | |
| computeLogLik | 0 | 0 | 0 | |
| compute_comparison_stat_df | 0 | 0 | 0 | |
| confIntExp | 1.36 | 0.28 | 1.64 | |
| confidence_indel_calulation | 0.00 | 0.02 | 0.02 | |
| confidence_indel_only_calulation | 20.69 | 0.71 | 21.41 | |
| correct_rounded | 0 | 0 | 0 | |
| cosineDist | 0 | 0 | 0 | |
| cosineMatchDist | 0 | 0 | 0 | |
| create_indel_mut_cat_from_df | 0.48 | 0.02 | 0.50 | |
| create_indel_mutation_catalogue_from_df | 14.45 | 1.13 | 15.57 | |
| create_mutation_catalogue_from_VR | 1.27 | 0.15 | 1.43 | |
| create_mutation_catalogue_from_df | 0.78 | 0.30 | 1.07 | |
| cut_breaks_as_intervals | 0.11 | 0.01 | 0.13 | |
| deriveSigInd_df | 0 | 0 | 0 | |
| disambiguateVector | 0 | 0 | 0 | |
| enrichSigs | 0 | 0 | 0 | |
| exampleYAPSA | 0.08 | 0.00 | 0.08 | |
| exome_mutCatRaw_df | 0.01 | 0.00 | 0.01 | |
| exposures_barplot | 2.43 | 0.02 | 2.44 | |
| extract_names_from_gene_list | 0 | 0 | 0 | |
| find_affected_PIDs | 0 | 0 | 0 | |
| getSequenceContext | 0.12 | 0.03 | 0.16 | |
| get_extreme_PIDs | 0.01 | 0.02 | 0.03 | |
| hclust_exposures | 0.02 | 0.00 | 0.02 | |
| logLikelihood | 0.86 | 0.22 | 1.08 | |
| lymphomaNature2013_mutCat_df | 0 | 0 | 0 | |
| makeVRangesFromDataFrame | 0.12 | 0.00 | 0.12 | |
| make_catalogue_strata_df | 0 | 0 | 0 | |
| make_comparison_matrix | 0.08 | 0.01 | 0.10 | |
| make_strata_df | 0 | 0 | 0 | |
| make_subgroups_df | 0.02 | 0.02 | 0.03 | |
| melt_exposures | 0 | 0 | 0 | |
| merge_exposures | 0 | 0 | 0 | |
| normalizeMotifs_otherRownames | 0 | 0 | 0 | |
| normalize_df_per_dim | 0 | 0 | 0 | |
| plotExchangeSpectra | 0 | 0 | 0 | |
| plotExchangeSpectra_indel | 1.05 | 0.03 | 1.08 | |
| plotExposuresConfidence | 0 | 0 | 0 | |
| plotExposuresConfidence_indel | 0 | 0 | 0 | |
| plot_SMC | 0 | 0 | 0 | |
| plot_exposures | 0.47 | 0.00 | 0.47 | |
| plot_strata | 0 | 0 | 0 | |
| read_entry | 0 | 0 | 0 | |
| relateSigs | 0 | 0 | 0 | |
| repeat_df | 0 | 0 | 0 | |
| round_precision | 0 | 0 | 0 | |
| run_SMC | 4.32 | 0.62 | 4.93 | |
| run_annotate_vcf_pl | 0 | 0 | 0 | |
| run_comparison_catalogues | 0 | 0 | 0 | |
| run_comparison_general | 0 | 0 | 0 | |
| run_kmer_frequency_correction | 0 | 0 | 0 | |
| run_kmer_frequency_normalization | 0 | 0 | 0 | |
| run_plot_strata_general | 0 | 0 | 0 | |
| shapiro_if_possible | 0 | 0 | 0 | |
| split_exposures_by_subgroups | 0 | 0 | 0 | |
| stat_plot_subgroups | 0 | 0 | 0 | |
| stat_test_SMC | 0 | 0 | 0 | |
| stat_test_subgroups | 0 | 0 | 0 | |
| stderrmean | 0 | 0 | 0 | |
| sum_over_list_of_df | 0 | 0 | 0 | |
| temp_trellis_rainfall_plot | 2.06 | 0.01 | 2.09 | |
| testSigs | 0 | 0 | 0 | |
| test_exposureAffected | 0 | 0 | 0 | |
| test_gene_list_in_exposures | 0 | 0 | 0 | |
| transform_rownames_R_to_MATLAB | 0 | 0 | 0 | |
| translate_to_hg19 | 0.00 | 0.02 | 0.02 | |
| trellis_rainfall_plot | 2.11 | 0.06 | 2.17 | |
| trellis_rainfall_plot_old | 2.04 | 0.05 | 2.09 | |
| variateExp | 2.49 | 0.25 | 2.74 | |
| variateExpSingle | 0.86 | 0.25 | 1.11 | |