BioC 3.5: CHECK report for DEGreport on oaxaca

Package: DEGreport

Version: 1.11.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DEGreport_1.11.4.tar.gz

StartedAt: 2017-03-04 01:41:23 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 01:43:18 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 115.2 seconds

RetCode: 0

Status:  OK

CheckDir: DEGreport.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 DEGreport_1.11.4.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/DEGreport.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 ‘DEGreport/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DEGreport’ version ‘1.11.4’
* 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:
  .travis.yml
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 ‘DEGreport’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.convertIDs: no visible global function definition for ‘keys’
.mds: no visible binding for global variable ‘one’
.mds: no visible binding for global variable ‘two’
.mds: no visible binding for global variable ‘label’
.plot_base: no visible binding for global variable ‘value’
.plot_base: no visible binding for global variable ‘variable’
.plot_cluster: no visible binding for global variable ‘x’
.plot_cluster: no visible binding for global variable ‘value’
.plot_cluster: no visible binding for global variable ‘group’
.run_cluster_profiler: no visible global function definition for
  ‘enrichGO’
.run_cluster_profiler: no visible global function definition for
  ‘simplify’
.table_w_fc: no visible global function definition for ‘colData’
.table_w_fc : <anonymous>: no visible global function definition for
  ‘results’
.table_w_fc : <anonymous>: no visible binding for global variable
  ‘log2FoldChange’
.table_w_fc: no visible binding for global variable ‘comp’
.table_w_fc: no visible binding for global variable ‘log2FoldChange’
degBI: no visible global function definition for ‘bplapply’
degBI: no visible global function definition for ‘MulticoreParam’
degBIcmd: no visible global function definition for ‘jags.model’
degBIcmd: no visible global function definition for ‘coda.samples’
degCheckFactors: no visible binding for global variable ‘value’
degPlot: no visible global function definition for ‘colData’
degPlot : <anonymous>: no visible global function definition for
  ‘plotCounts’
degPlot : <anonymous>: no visible binding for global variable ‘count’
degPlot : <anonymous>: no visible binding for global variable
  ‘treatment’
degResults: no visible global function definition for ‘assay’
degResults: no visible global function definition for ‘rlog’
degResults: no visible global function definition for ‘results’
degResults: no visible global function definition for ‘colData’
degResults: no visible global function definition for ‘rowMax’
degVolcano: no visible binding for global variable ‘logFC’
degVolcano: no visible binding for global variable ‘V1’
degVolcano: no visible binding for global variable ‘V2’
degVolcano: no visible binding for global variable ‘adj.P.Val’
degVolcano: no visible binding for global variable ‘x’
degVolcano: no visible binding for global variable ‘y’
degVolcano: no visible binding for global variable ‘name’
Undefined global functions or variables:
  MulticoreParam V1 V2 adj.P.Val assay bplapply coda.samples colData
  comp count enrichGO group jags.model keys label log2FoldChange logFC
  name one plotCounts results rlog rowMax simplify treatment two value
  variable x y
* 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
degResults 14.982   0.23  15.248
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/DEGreport.Rcheck/00check.log’
for details.

* installing *source* package ‘DEGreport’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DEGreport)

name	user	system	elapsed
degCheckFactors	2.565	0.023	2.588
degMB	1.035	0.012	1.061
degMV	0.954	0.004	0.960
degMean	0.261	0.011	0.273
degObj	0.004	0.001	0.004
degPR	0.680	0.003	0.683
degPatterns	1.267	0.010	1.278
degRank	0.004	0.001	0.004
degResults	14.982	0.230	15.248
degVB	0.424	0.015	0.442
degVar	0.415	0.002	0.417
degVolcano	0.429	0.003	0.446