BioC 3.5: CHECK report for ChIPXpress on veracruz2
This page was generated on 2017-10-18 14:30:35 -0400 (Wed, 18 Oct 2017).
ChIPXpress 1.18.0 George Wu
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | URL: https://git.bioconductor.org/packages/ChIPXpress | Branch: RELEASE_3_5 | Last Commit: 70f8527 | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | ...NOT SUPPORTED...NOT SUPPORTED...NOT SUPPORTED... |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ OK ] | OK | |
Summary
Package: ChIPXpress |
Version: 1.18.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ChIPXpress_1.18.0.tar.gz |
StartedAt: 2017-10-18 01:40:16 -0400 (Wed, 18 Oct 2017) |
EndedAt: 2017-10-18 01:49:16 -0400 (Wed, 18 Oct 2017) |
EllapsedTime: 540.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ChIPXpress.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 --no-vignettes --timings ChIPXpress_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ChIPXpress.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ChIPXpress/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ChIPXpress’ version ‘1.18.0’
* 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:
.BBSoptions
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 ‘ChIPXpress’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘ChIPXpressData’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ChIPXpress: no visible global function definition for ‘quantile’
ChIPXpress : <anonymous>: no visible global function definition for
‘cor’
cleanDatabase: no visible binding for global variable ‘var’
Undefined global functions or variables:
cor quantile var
Consider adding
importFrom("stats", "cor", "quantile", "var")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... 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
ChIPXpress 4.496 0.795 5.466
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.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/ChIPXpress.Rcheck/00check.log’
for details.
ChIPXpress.Rcheck/00install.out:
* installing *source* package ‘ChIPXpress’ ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (ChIPXpress)
ChIPXpress.Rcheck/ChIPXpress-Ex.timings:
name | user | system | elapsed
|
ChIPXpress | 4.496 | 0.795 | 5.466 |
|
Oct4ESC_ChIPgenes | 0.041 | 0.006 | 0.047 |
|
buildDatabase | 0.003 | 0.000 | 0.003 |
|
cleanDatabase | 0.001 | 0.000 | 0.002 |
|