Package: celaref

Version: 1.0.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:celaref.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings celaref_1.0.1.tar.gz

StartedAt: 2019-04-15 22:49:25 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 22:52:52 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 207.1 seconds

RetCode: 0

Status:  OK

CheckDir: celaref.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:celaref.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings celaref_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/celaref.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘celaref/DESCRIPTION’ ... OK
* this is package ‘celaref’ version ‘1.0.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘celaref’ 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                                         user system elapsed
contrast_each_group_to_the_rest_for_norm_ma_with_limma 35.289 10.119   0.762
contrast_each_group_to_the_rest                         0.067  0.019  16.958
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/celaref.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL celaref
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘celaref’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (celaref)

name	user	system	elapsed
contrast_each_group_to_the_rest	0.067	0.019	16.958
contrast_each_group_to_the_rest_for_norm_ma_with_limma	35.289	10.119	0.762
convert_se_gene_ids	0.090	0.009	0.099
get_rankstat_table	0.058	0.006	0.065
get_the_up_genes_for_all_possible_groups	0.004	0.001	0.005
get_the_up_genes_for_group	0.001	0.000	0.001
load_dataset_10Xdata	0.155	0.011	0.169
load_se_from_tables	0.261	0.011	0.276
make_ranking_violin_plot	2.794	0.163	2.974
make_ref_similarity_names	2.447	0.047	2.511
trim_small_groups_and_low_expression_genes	0.080	0.003	0.084