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BioC 3.5: CHECK report for YAPSA on oaxaca

This page was generated on 2017-03-04 16:53:08 -0500 (Sat, 04 Mar 2017).

Package 1336/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
YAPSA 1.1.0
Daniel Huebschmann
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/YAPSA
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: YAPSA
Version: 1.1.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings YAPSA_1.1.0.tar.gz
StartedAt: 2017-03-04 10:31:30 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 10:40:09 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 519.2 seconds
RetCode: 0
Status:  OK 
CheckDir: YAPSA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings YAPSA_1.1.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/YAPSA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.1.0’
* 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
Examples with CPU or elapsed time > 5s
                                   user system elapsed
run_SMC                           6.784  0.157   6.943
create_mutation_catalogue_from_VR 5.081  0.098   5.182
* 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
LCD0.1880.0050.206
LCD_complex_cutoff0.0000.0000.001
add_annotation0.0000.0010.001
add_as_fist_to_list000
aggregate_exposures_by_category000
annotate_intermut_dist_PID0.3620.0400.402
annotate_intermut_dist_cohort0.1060.0030.109
annotation_exposures_barplot0.0000.0000.001
annotation_heatmap_exposures0.0010.0010.000
attribute_nucleotide_exchanges0.0030.0000.004
build_gene_list_for_pathway0.0010.0000.000
compare_SMCs0.0000.0000.001
compare_exposures0.0010.0000.000
compare_sets0.0090.0000.010
compare_to_catalogues0.0010.0000.000
complex_heatmap_exposures3.5880.0133.602
compute_comparison_stat_df0.0000.0000.001
cosineDist0.0010.0010.000
create_mutation_catalogue_from_VR5.0810.0985.182
create_mutation_catalogue_from_df1.2150.0721.287
cut_breaks_as_intervals1.9020.0091.951
exampleYAPSA0.1090.0120.120
exposures_barplot2.0620.0702.135
extract_names_from_gene_list000
find_affected_PIDs0.0000.0000.001
get_extreme_PIDs0.0420.0020.044
hclust_exposures0.0110.0010.013
makeVRangesFromDataFrame0.0990.0060.104
make_catalogue_strata_df0.0000.0000.001
make_comparison_matrix0.1290.0070.136
make_strata_df0.0010.0000.000
make_subgroups_df0.0640.0080.071
melt_exposures0.0010.0000.001
merge_exposures0.0010.0000.000
normalizeMotifs_otherRownames0.0010.0000.000
normalize_df_per_dim0.0180.0010.018
plotExchangeSpectra0.0010.0000.001
plot_SMC0.0010.0000.001
plot_exposures2.2920.0112.304
plot_strata0.0010.0010.001
repeat_df0.0050.0000.004
run_SMC6.7840.1576.943
run_annotate_vcf_pl0.0010.0000.001
run_comparison_catalogues0.0010.0000.000
run_comparison_general0.0000.0000.001
run_kmer_frequency_correction0.0010.0000.000
run_kmer_frequency_normalization000
run_plot_strata_general0.0010.0000.000
shapiro_if_possible0.0010.0000.001
split_exposures_by_subgroups0.0000.0000.001
stat_plot_subgroups0.0010.0000.000
stat_test_SMC0.0010.0000.000
stat_test_subgroups0.0000.0000.001
stderrmean0.0010.0000.001
sum_over_list_of_df0.0040.0000.004
test_exposureAffected0.0000.0000.001
test_gene_list_in_exposures0.0000.0000.001
transform_rownames_R_to_MATLAB000
translate_to_hg190.0080.0000.009
trellis_rainfall_plot4.0710.0264.118