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BioC 3.4: CHECK report for YAPSA on malbec1

This page was generated on 2017-04-15 16:14:03 -0400 (Sat, 15 Apr 2017).

Package 1293/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
YAPSA 1.0.0
Daniel Huebschmann
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/YAPSA
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  TIMEOUT  skipped  skipped 

Summary

Package: YAPSA
Version: 1.0.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings YAPSA_1.0.0.tar.gz
StartedAt: 2017-04-15 01:54:12 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 01:59:31 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 319.0 seconds
RetCode: 0
Status:  OK 
CheckDir: YAPSA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings YAPSA_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/YAPSA.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 ‘1.0.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘YAPSA’ 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 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: OK

YAPSA.Rcheck/00install.out:

* installing *source* package ‘YAPSA’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (YAPSA)

YAPSA.Rcheck/YAPSA-Ex.timings:

nameusersystemelapsed
LCD0.0080.0000.008
LCD_complex_cutoff000
add_annotation000
add_as_fist_to_list000
aggregate_exposures_by_category000
annotate_intermut_dist_PID0.020.000.02
annotate_intermut_dist_cohort0.0280.0000.025
annotation_exposures_barplot0.0000.0000.001
annotation_heatmap_exposures0.0000.0000.001
attribute_nucleotide_exchanges0.0000.0000.003
build_gene_list_for_pathway0.0000.0000.001
compare_SMCs0.0000.0000.001
compare_exposures0.0000.0000.001
compare_sets0.0040.0040.006
compare_to_catalogues0.0000.0000.001
complex_heatmap_exposures0.5920.0000.594
compute_comparison_stat_df000
cosineDist000
create_mutation_catalogue_from_VR1.9360.0321.969
create_mutation_catalogue_from_df0.7920.0320.823
cut_breaks_as_intervals0.160.000.16
exampleYAPSA0.0640.0080.076
exposures_barplot0.5600.0000.563
extract_names_from_gene_list000
find_affected_PIDs000
get_extreme_PIDs0.0320.0000.030
hclust_exposures0.0080.0000.010
makeVRangesFromDataFrame0.0800.0040.085
make_catalogue_strata_df000
make_comparison_matrix0.0840.0000.084
make_strata_df000
make_subgroups_df0.040.000.04
melt_exposures000
merge_exposures000
normalizeMotifs_otherRownames000
normalize_df_per_dim0.0120.0000.009
plotExchangeSpectra000
plot_SMC000
plot_exposures0.5320.0040.537
plot_strata000
repeat_df0.0000.0000.002
run_SMC4.3400.0924.441
run_annotate_vcf_pl000
run_comparison_catalogues000
run_comparison_general000
run_kmer_frequency_correction000
run_kmer_frequency_normalization000
run_plot_strata_general000
shapiro_if_possible0.0000.0000.001
split_exposures_by_subgroups000
stat_plot_subgroups000
stat_test_SMC000
stat_test_subgroups000
stderrmean0.0040.0000.001
sum_over_list_of_df0.0040.0000.004
test_exposureAffected000
test_gene_list_in_exposures000
transform_rownames_R_to_MATLAB0.0040.0000.001
translate_to_hg190.0040.0000.005
trellis_rainfall_plot2.4080.0002.417