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CHECK report for celaref on merida1

This page was generated on 2019-04-16 12:11:44 -0400 (Tue, 16 Apr 2019).

Package 213/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
celaref 1.0.1
Sarah Williams
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/celaref
Branch: RELEASE_3_8
Last Commit: 5e4a446
Last Changed Date: 2019-01-04 13:24:34 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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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.



Installation output

celaref.Rcheck/00install.out

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### Running command:
###
###   /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)

Tests output


Example timings

celaref.Rcheck/celaref-Ex.timings

nameusersystemelapsed
contrast_each_group_to_the_rest 0.067 0.01916.958
contrast_each_group_to_the_rest_for_norm_ma_with_limma35.28910.119 0.762
convert_se_gene_ids0.0900.0090.099
get_rankstat_table0.0580.0060.065
get_the_up_genes_for_all_possible_groups0.0040.0010.005
get_the_up_genes_for_group0.0010.0000.001
load_dataset_10Xdata0.1550.0110.169
load_se_from_tables0.2610.0110.276
make_ranking_violin_plot2.7940.1632.974
make_ref_similarity_names2.4470.0472.511
trim_small_groups_and_low_expression_genes0.0800.0030.084