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BioC 3.5: CHECK report for recount on veracruz2

This page was generated on 2017-08-16 13:34:55 -0400 (Wed, 16 Aug 2017).

Package 1090/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
recount 1.2.3
Leonardo Collado-Torres
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/recount
Last Changed Rev: 131893 / Revision: 131943
Last Changed Date: 2017-08-10 17:28:30 -0400 (Thu, 10 Aug 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: recount
Version: 1.2.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings recount_1.2.3.tar.gz
StartedAt: 2017-08-16 07:15:14 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 07:28:18 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 784.4 seconds
RetCode: 0
Status:  OK 
CheckDir: recount.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings recount_1.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/recount.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘recount/DESCRIPTION’ ... OK
* this is package ‘recount’ version ‘1.2.3’
* 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 14.7Mb
  sub-directories of 1Mb or more:
    data  10.7Mb
    doc    3.8Mb
* 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 ... NOTE
add_predictions: no visible binding for global variable
  ‘PredictedPhenotypes’
Undefined global functions or variables:
  PredictedPhenotypes
* 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 135.909  5.320 156.043
coverage_matrix    3.907  0.476  11.984
snaptron_query     1.180  0.013   7.052
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/recount.Rcheck/00check.log’
for details.


recount.Rcheck/00install.out:

* 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)

recount.Rcheck/recount-Ex.timings:

nameusersystemelapsed
abstract_search0.5970.0070.635
add_predictions1.8140.0703.126
all_metadata0.5700.0401.577
browse_study0.6890.0200.723
coverage_matrix 3.907 0.47611.984
download_study0.4020.0281.288
expressed_regions2.5280.1763.888
find_geo0.5310.0101.613
geo_characteristics0.6250.0074.401
geo_info0.0790.0000.080
getRPKM1.1710.1821.562
reproduce_ranges135.909 5.320156.043
scale_counts0.1530.0160.170
snaptron_query1.1800.0137.052