Daniel Huebschmann
| Snapshot Date: 2018-07-24 16:45:59 -0400 (Tue, 24 Jul 2018) |
| URL: https://git.bioconductor.org/packages/YAPSA |
| Branch: RELEASE_3_7 |
| Last Commit: 2455d27 |
| Last Changed Date: 2018-04-30 10:35:43 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-07-25 10:22:29 -0400 (Wed, 25 Jul 2018).
| Package 1555/1560 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| YAPSA 1.6.0 Daniel Huebschmann
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: YAPSA |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:YAPSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings YAPSA_1.6.0.tar.gz |
| StartedAt: 2018-07-25 05:21:31 -0400 (Wed, 25 Jul 2018) |
| EndedAt: 2018-07-25 05:30:21 -0400 (Wed, 25 Jul 2018) |
| EllapsedTime: 530.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: YAPSA.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:YAPSA.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings YAPSA_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/YAPSA.Rcheck'
* using R version 3.5.1 RC (2018-06-24 r74929)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'YAPSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'YAPSA' version '1.6.0'
* 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:
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/create_mutation_catalogue_from_VR.Rd:49: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/create_mutation_catalogue_from_VR.Rd:51: file link 'motifMatrix' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/create_mutation_catalogue_from_VR.Rd:18: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/create_mutation_catalogue_from_VR.Rd:22: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/create_mutation_catalogue_from_VR.Rd:86: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/create_mutation_catalogue_from_VR.Rd:88: file link 'motifMatrix' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/create_mutation_catalogue_from_df.Rd:39: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/create_mutation_catalogue_from_df.Rd:43: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/normalizeMotifs_otherRownames.Rd:20: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/normalizeMotifs_otherRownames.Rd:22: file link 'SomaticSignatures' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/normalizeMotifs_otherRownames.Rd:10: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/normalizeMotifs_otherRownames.Rd:15: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/run_kmer_frequency_correction.Rd:40: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/run_kmer_frequency_correction.Rd:51: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/run_kmer_frequency_correction.Rd:52: file link 'kmerFrequency' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/run_kmer_frequency_correction.Rd:62: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/run_kmer_frequency_normalization.Rd:29: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/run_kmer_frequency_normalization.Rd:40: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/run_kmer_frequency_normalization.Rd:41: file link 'kmerFrequency' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/run_kmer_frequency_normalization.Rd:51: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/translate_to_hg19.Rd:31: file link 'BSgenome.Hsapiens.UCSC.hg19' in package 'BSgenome.Hsapiens.UCSC.hg19' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.7-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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
run_SMC 5.29 0.18 5.46
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
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
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/YAPSA.Rcheck/00check.log'
for details.
YAPSA.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/YAPSA_1.6.0.tar.gz && rm -rf YAPSA.buildbin-libdir && mkdir YAPSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=YAPSA.buildbin-libdir YAPSA_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL YAPSA_1.6.0.zip && rm YAPSA_1.6.0.tar.gz YAPSA_1.6.0.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
100 1077k 100 1077k 0 0 15.4M 0 --:--:-- --:--:-- --:--:-- 17.2M
install for i386
* installing *source* package 'YAPSA' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'YAPSA'
finding HTML links ... done
LCD html
LCD_complex_cutoff html
YAPSA html
add_annotation html
add_as_fist_to_list html
aggregate_exposures_by_category html
annotate_intermut_dist_PID html
annotate_intermut_dist_cohort html
annotation_exposures_barplot html
annotation_heatmap_exposures html
attribute_nucleotide_exchanges html
build_gene_list_for_pathway html
compare_SMCs html
compare_exposures html
compare_sets html
compare_to_catalogues html
complex_heatmap_exposures html
compute_comparison_stat_df html
cosineDist html
create_mutation_catalogue_from_VR html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/create_mutation_catalogue_from_VR.Rd:49: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/create_mutation_catalogue_from_VR.Rd:51: file link 'motifMatrix' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/create_mutation_catalogue_from_VR.Rd:18: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/create_mutation_catalogue_from_VR.Rd:22: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/create_mutation_catalogue_from_VR.Rd:86: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/create_mutation_catalogue_from_VR.Rd:88: file link 'motifMatrix' in package 'SomaticSignatures' does not exist and so has been treated as a topic
create_mutation_catalogue_from_df html
finding level-2 HTML links ... done
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/create_mutation_catalogue_from_df.Rd:39: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/create_mutation_catalogue_from_df.Rd:43: file link 'mutationContext' in package 'SomaticSignatures' does not exist and so has been treated as a topic
cut_breaks_as_intervals html
cutoffs html
exampleYAPSA html
exchange_colour_vector html
exposures_barplot html
extract_names_from_gene_list html
find_affected_PIDs html
get_extreme_PIDs html
hclust_exposures html
makeVRangesFromDataFrame html
make_catalogue_strata_df html
make_comparison_matrix html
make_strata_df html
make_subgroups_df html
melt_exposures html
merge_exposures html
normalizeMotifs_otherRownames html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/normalizeMotifs_otherRownames.Rd:20: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/normalizeMotifs_otherRownames.Rd:22: file link 'SomaticSignatures' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/normalizeMotifs_otherRownames.Rd:10: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/normalizeMotifs_otherRownames.Rd:15: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
normalize_df_per_dim html
plotExchangeSpectra html
plot_SMC html
plot_exposures html
plot_strata html
repeat_df html
run_SMC html
run_annotate_vcf_pl html
run_comparison_catalogues html
run_comparison_general html
run_kmer_frequency_correction html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/run_kmer_frequency_correction.Rd:40: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/run_kmer_frequency_correction.Rd:51: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/run_kmer_frequency_correction.Rd:52: file link 'kmerFrequency' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/run_kmer_frequency_correction.Rd:62: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
run_kmer_frequency_normalization html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/run_kmer_frequency_normalization.Rd:29: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/run_kmer_frequency_normalization.Rd:40: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/run_kmer_frequency_normalization.Rd:41: file link 'kmerFrequency' in package 'SomaticSignatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/run_kmer_frequency_normalization.Rd:51: file link 'normalizeMotifs' in package 'SomaticSignatures' does not exist and so has been treated as a topic
run_plot_strata_general html
shapiro_if_possible html
sigs html
split_exposures_by_subgroups html
stat_plot_subgroups html
stat_test_SMC html
stat_test_subgroups html
stderrmean html
sum_over_list_of_df html
targetCapture_cor_factors html
test_exposureAffected html
test_gene_list_in_exposures html
transform_rownames_R_to_MATLAB html
translate_to_hg19 html
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpaKL65h/R.INSTALL1c6c71ba45e7/YAPSA/man/translate_to_hg19.Rd:31: file link 'BSgenome.Hsapiens.UCSC.hg19' in package 'BSgenome.Hsapiens.UCSC.hg19' does not exist and so has been treated as a topic
trellis_rainfall_plot html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'YAPSA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'YAPSA' as YAPSA_1.6.0.zip
* DONE (YAPSA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'YAPSA' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
YAPSA.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 RC (2018-06-24 r74929) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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(YAPSA)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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
>
> 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.
== testthat results ===========================================================
OK: 63 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
13.42 1.37 14.95
|
YAPSA.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 RC (2018-06-24 r74929) -- "Feather Spray"
Copyright (C) 2018 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.
> library(testthat)
> library(YAPSA)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
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
>
> 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.
== testthat results ===========================================================
OK: 63 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
14.34 0.70 15.20
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YAPSA.Rcheck/examples_i386/YAPSA-Ex.timings
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YAPSA.Rcheck/examples_x64/YAPSA-Ex.timings
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