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BioC 3.5: CHECK report for YAPSA on veracruz2

This page was generated on 2017-10-18 14:34:56 -0400 (Wed, 18 Oct 2017).

Package 1378/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
YAPSA 1.2.0
Daniel Huebschmann
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/YAPSA
Branch: RELEASE_3_5
Last Commit: 320809b
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
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
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: YAPSA
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings YAPSA_1.2.0.tar.gz
StartedAt: 2017-10-18 10:13:36 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 10:20:03 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 386.8 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_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/YAPSA.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.2.0’
* 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 4.916  0.151   5.148
* 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
LCD0.1110.0040.117
LCD_complex_cutoff0.0000.0000.001
add_annotation0.0010.0010.000
add_as_fist_to_list000
aggregate_exposures_by_category0.0000.0000.001
annotate_intermut_dist_PID0.2480.0350.285
annotate_intermut_dist_cohort0.0690.0010.070
annotation_exposures_barplot0.0000.0000.001
annotation_heatmap_exposures0.0000.0000.001
attribute_nucleotide_exchanges0.0040.0010.003
build_gene_list_for_pathway0.0000.0000.001
compare_SMCs0.0010.0000.001
compare_exposures000
compare_sets0.0190.0010.020
compare_to_catalogues0.0000.0000.001
complex_heatmap_exposures2.1270.0172.168
compute_comparison_stat_df0.0010.0000.000
cosineDist0.0010.0000.001
create_mutation_catalogue_from_VR3.3180.2854.445
create_mutation_catalogue_from_df0.8740.0530.948
cut_breaks_as_intervals1.3250.0141.359
exampleYAPSA0.070.010.08
exposures_barplot1.3560.0491.430
extract_names_from_gene_list000
find_affected_PIDs0.0000.0000.001
get_extreme_PIDs0.0280.0020.029
hclust_exposures0.0080.0010.009
makeVRangesFromDataFrame0.0710.0050.079
make_catalogue_strata_df0.0010.0000.001
make_comparison_matrix0.1170.0090.131
make_strata_df0.0010.0000.000
make_subgroups_df0.0370.0060.043
melt_exposures0.0010.0000.001
merge_exposures000
normalizeMotifs_otherRownames0.0000.0000.001
normalize_df_per_dim0.0110.0010.012
plotExchangeSpectra000
plot_SMC000
plot_exposures1.4750.0181.515
plot_strata000
repeat_df0.0030.0000.003
run_SMC4.9160.1515.148
run_annotate_vcf_pl000
run_comparison_catalogues0.0000.0000.001
run_comparison_general000
run_kmer_frequency_correction0.0010.0010.001
run_kmer_frequency_normalization0.0010.0000.000
run_plot_strata_general0.0010.0000.000
shapiro_if_possible0.0010.0000.002
split_exposures_by_subgroups000
stat_plot_subgroups0.0000.0000.001
stat_test_SMC0.0010.0000.000
stat_test_subgroups0.0010.0000.001
stderrmean0.0000.0000.001
sum_over_list_of_df0.0030.0010.003
test_exposureAffected000
test_gene_list_in_exposures0.0010.0000.001
transform_rownames_R_to_MATLAB0.0010.0000.000
translate_to_hg190.0040.0010.005
trellis_rainfall_plot2.5710.0222.631