DEGreport 1.12.0
Lorena Pantano
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/DEGreport | | Branch: RELEASE_3_5 | | Last Commit: a01dc72 | | 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 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings DEGreport_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/DEGreport.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-pc-linux-gnu (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 ‘1.12.0’
* 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:
.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’
degPlotWide: no visible global function definition for ‘colData’
degPlotWide : <anonymous>: no visible global function definition for
‘plotCounts’
degPlotWide: no visible binding for global variable ‘gene’
degPlotWide: no visible binding for global variable ‘count’
degPlotWide: 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 gene 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
degPlotWide 9.028 0.128 9.208
degResults 8.084 0.020 8.145
* 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
‘/home/biocbuild/bbs-3.5-bioc/meat/DEGreport.Rcheck/00check.log’
for details.