BioC 3.5: CHECK report for recount on oaxaca

Package: recount

Version: 1.1.22

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings recount_1.1.22.tar.gz

StartedAt: 2017-03-04 07:54:48 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 08:11:45 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 1017.6 seconds

RetCode: 0

Status:  OK

CheckDir: recount.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings recount_1.1.22.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/recount.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recount/DESCRIPTION’ ... OK
* this is package ‘recount’ version ‘1.1.22’
* 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 ‘recount’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 14.0Mb
  sub-directories of 1Mb or more:
    data  10.2Mb
    doc    3.6Mb
* 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 ... NOTE
  Note: found 347 marked UTF-8 strings
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... 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
reproduce_ranges    130.028  7.034 213.972
coverage_matrix       4.274  0.247  13.361
snaptron_query        1.536  0.033   7.497
geo_characteristics   0.648  0.012   6.142
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/recount.Rcheck/00check.log’
for details.

* installing *source* package ‘recount’ ...
** 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 (recount)

name	user	system	elapsed
abstract_search	0.492	0.008	0.500
all_metadata	0.678	0.035	1.983
browse_study	0.637	0.006	0.645
coverage_matrix	4.274	0.247	13.361
download_study	1.139	0.082	3.432
expressed_regions	1.516	0.136	3.773
find_geo	0.613	0.030	2.050
geo_characteristics	0.648	0.012	6.142
geo_info	0.123	0.001	0.124
reproduce_ranges	130.028	7.034	213.972
scale_counts	0.225	0.023	0.248
snaptron_query	1.536	0.033	7.497