BioC 3.5: CHECK report for YAPSA on malbec2

Package: YAPSA

Version: 1.2.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings YAPSA_1.2.0.tar.gz

StartedAt: 2017-08-16 02:57:22 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 03:02:45 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 323.4 seconds

RetCode: 0

Status:  OK

CheckDir: YAPSA.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings YAPSA_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/YAPSA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.2.0’
* 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 5.432   0.08   5.517
* 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

* installing *source* package ‘YAPSA’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (YAPSA)

name	user	system	elapsed
LCD	0.096	0.004	0.098
LCD_complex_cutoff	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	0.204	0.008	0.212
annotate_intermut_dist_cohort	0.068	0.004	0.072
annotation_exposures_barplot	0	0	0
annotation_heatmap_exposures	0.004	0.000	0.000
attribute_nucleotide_exchanges	0.000	0.000	0.003
build_gene_list_for_pathway	0.000	0.000	0.001
compare_SMCs	0.000	0.000	0.001
compare_exposures	0.000	0.000	0.001
compare_sets	0.004	0.000	0.005
compare_to_catalogues	0.000	0.000	0.001
complex_heatmap_exposures	2.000	0.000	2.004
compute_comparison_stat_df	0	0	0
cosineDist	0	0	0
create_mutation_catalogue_from_VR	2.920	0.024	2.944
create_mutation_catalogue_from_df	0.752	0.020	0.773
cut_breaks_as_intervals	0.696	0.000	0.697
exampleYAPSA	0.072	0.000	0.072
exposures_barplot	1.204	0.000	1.204
extract_names_from_gene_list	0.004	0.000	0.000
find_affected_PIDs	0	0	0
get_extreme_PIDs	0.024	0.000	0.026
hclust_exposures	0.004	0.000	0.007
makeVRangesFromDataFrame	0.068	0.000	0.071
make_catalogue_strata_df	0	0	0
make_comparison_matrix	0.108	0.000	0.110
make_strata_df	0	0	0
make_subgroups_df	0.036	0.000	0.037
melt_exposures	0	0	0
merge_exposures	0	0	0
normalizeMotifs_otherRownames	0	0	0
normalize_df_per_dim	0.008	0.000	0.009
plotExchangeSpectra	0	0	0
plot_SMC	0	0	0
plot_exposures	1.352	0.004	1.359
plot_strata	0.000	0.000	0.001
repeat_df	0.000	0.000	0.003
run_SMC	5.432	0.080	5.517
run_annotate_vcf_pl	0.004	0.000	0.001
run_comparison_catalogues	0.000	0.000	0.001
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	0.000	0.000	0.001
split_exposures_by_subgroups	0	0	0
stat_plot_subgroups	0.004	0.000	0.000
stat_test_SMC	0	0	0
stat_test_subgroups	0.000	0.000	0.001
stderrmean	0.000	0.000	0.001
sum_over_list_of_df	0.004	0.000	0.002
test_exposureAffected	0	0	0
test_gene_list_in_exposures	0	0	0
transform_rownames_R_to_MATLAB	0	0	0
translate_to_hg19	0.004	0.000	0.004
trellis_rainfall_plot	2.220	0.008	2.246