BioC 3.5: CHECK report for CountClust on oaxaca

Package: CountClust

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CountClust_1.3.0.tar.gz

StartedAt: 2016-10-25 23:25:44 -0700 (Tue, 25 Oct 2016)

EndedAt: 2016-10-25 23:27:43 -0700 (Tue, 25 Oct 2016)

EllapsedTime: 118.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: CountClust.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CountClust_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/CountClust.Rcheck’
* using R Under development (unstable) (2016-10-21 r71549)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CountClust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CountClust’ version ‘1.3.0’
* package encoding: UTF-8
* 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 ‘CountClust’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 17.9Mb
  sub-directories of 1Mb or more:
    data  17.5Mb
* 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 ... WARNING
Codoc mismatches from documentation object 'StructureGGplot':
StructureGGplot
  Code: function(omega, annotation = NULL, palette =
                 RColorBrewer::brewer.pal(8, "Accent"), figure_title =
                 "", yaxis_label = "Tissue type", order_sample = TRUE,
                 sample_order_decreasing = TRUE, split_line =
                 list(split_lwd = 1, split_col = "white"), plot_labels
                 = TRUE, axis_tick = list(axis_ticks_length = 0.1,
                 axis_ticks_lwd_y = 0.1, axis_ticks_lwd_x = 0.1,
                 axis_label_size = 3, axis_label_face = "bold"))
  Docs: function(omega, annotation, palette =
                 RColorBrewer::brewer.pal(8, "Accent"), figure_title =
                 "", yaxis_label = "Tissue type", order_sample = TRUE,
                 sample_order_decreasing = TRUE, split_line =
                 list(split_lwd = 1, split_col = "white"), axis_tick =
                 list(axis_ticks_length = 0.1, axis_ticks_lwd_y = 0.1,
                 axis_ticks_lwd_x = 0.1, axis_label_size = 3,
                 axis_label_face = "bold"))
  Argument names in code not in docs:
    plot_labels
  Mismatches in argument names:
    Position: 9 Code: plot_labels Docs: axis_tick
  Mismatches in argument default values:
    Name: 'annotation' Code: NULL Docs: 

* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/CountClust.Rcheck/00check.log’
for details.

* installing *source* package ‘CountClust’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CountClust)

name	user	system	elapsed
BatchCorrectedCounts	1.059	0.027	1.102
ExtractTopFeatures	3.689	0.127	3.820
FitGoM	0.754	0.114	0.896
RemoveSparseFeatures	0.002	0.000	0.002
StructureGGplot	1.095	0.130	1.227
Structure_omega	0.001	0.000	0.001
cg_topics	0.338	0.053	0.393
compare_omega	0.009	0.000	0.009
handleNA	0.002	0.000	0.003
nullmodel_GoM	2.844	0.509	3.383