BioC 3.5: CHECK report for biomformat on toluca2
This page was generated on 2017-04-23 14:40:47 -0400 (Sun, 23 Apr 2017).
biomformat 1.3.0 Paul J. McMurdie
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/biomformat | Last Changed Rev: 122712 / Revision: 129046 | Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK |  |
toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |  |
Summary
Package: biomformat |
Version: 1.3.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biomformat_1.3.0.tar.gz |
StartedAt: 2017-04-23 01:00:44 -0400 (Sun, 23 Apr 2017) |
EndedAt: 2017-04-23 01:01:52 -0400 (Sun, 23 Apr 2017) |
EllapsedTime: 67.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: biomformat.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 biomformat_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/biomformat.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biomformat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biomformat’ version ‘1.3.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biomformat’ 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 ... NOTE
make_biom: no visible global function definition for ‘packageVersion’
namedList: no visible global function definition for ‘setNames’
Undefined global functions or variables:
packageVersion setNames
Consider adding
importFrom("stats", "setNames")
importFrom("utils", "packageVersion")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat-biomformat.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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/biomformat.Rcheck/00check.log’
for details.
biomformat.Rcheck/00install.out:
* installing *source* package ‘biomformat’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘biomformat’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘biomformat’
Creating a generic function for ‘rownames’ from package ‘base’ in package ‘biomformat’
Creating a generic function for ‘colnames’ from package ‘base’ in package ‘biomformat’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (biomformat)
biomformat.Rcheck/biomformat-Ex.timings:
name | user | system | elapsed
|
biom-class | 0.312 | 0.018 | 0.379 |
|
biom-methods | 0.163 | 0.002 | 0.171 |
|
biom_data-methods | 0.254 | 0.003 | 0.264 |
|
biom_shape-methods | 0.005 | 0.000 | 0.005 |
|
colnames-methods | 0.006 | 0.001 | 0.006 |
|
header-methods | 0.005 | 0.000 | 0.005 |
|
make_biom | 0.162 | 0.002 | 0.165 |
|
matrix_element_type-methods | 0.005 | 0.000 | 0.005 |
|
ncol-methods | 0.005 | 0.000 | 0.005 |
|
nrow-methods | 0.005 | 0.001 | 0.005 |
|
observation_metadata-methods | 0.049 | 0.002 | 0.052 |
|
read_biom | 0.009 | 0.001 | 0.011 |
|
read_hdf5_biom | 0.322 | 0.003 | 0.332 |
|
rownames-methods | 0.005 | 0.000 | 0.006 |
|
sample_metadata-methods | 0.044 | 0.002 | 0.048 |
|
show-methods | 0.005 | 0.000 | 0.006 |
|
write_biom | 0.015 | 0.000 | 0.016 |
|