GOexpress 1.7.1
Kevin Rue-Albrecht
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GOexpress | | Last Changed Rev: 118842 / Revision: 121152 | | Last Changed Date: 2016-06-22 02:18:20 -0700 (Wed, 22 Jun 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.7.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GOexpress.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOexpress/DESCRIPTION’ ... OK
* this is package ‘GOexpress’ version ‘1.7.1’
* 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 ‘GOexpress’ 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
GO_analyse: no visible binding for global variable ‘microarray2dataset’
GO_analyse: no visible binding for global variable ‘prefix2dataset’
GO_analyse : <anonymous>: no visible global function definition for
‘oneway.test’
GO_analyse: no visible global function definition for ‘aggregate’
cluster_GO: no visible global function definition for ‘dist’
cluster_GO: no visible global function definition for ‘hclust’
cluster_GO: no visible global function definition for ‘par’
cluster_GO: no visible global function definition for ‘plot’
expression_plot: no visible binding for global variable ‘X’
expression_plot: no visible binding for global variable ‘Expression’
expression_plot: no visible binding for global variable ‘Factor’
expression_profiles: no visible binding for global variable ‘X’
expression_profiles: no visible binding for global variable
‘Expression’
expression_profiles: no visible binding for global variable ‘Profile’
expression_profiles: no visible binding for global variable ‘LineType’
expression_profiles: no visible binding for global variable ‘Colour’
heatmap_GO: no visible global function definition for ‘par’
hist_scores: no visible global function definition for ‘hist’
mart_from_ensembl: no visible binding for global variable
‘prefix2dataset’
microarray2dataset.build: no visible global function definition for
‘getCurlHandle’
pValue_GO: no visible global function definition for ‘aggregate’
plot_design: no visible global function definition for ‘plot.design’
prefix2dataset.build: no visible global function definition for
‘getCurlHandle’
quantiles_scores: no visible global function definition for ‘quantile’
sampleEnsemblGeneId: no visible global function definition for
‘getCurlHandle’
Undefined global functions or variables:
Colour Expression Factor LineType Profile X aggregate dist
getCurlHandle hclust hist microarray2dataset oneway.test par plot
plot.design prefix2dataset quantile
Consider adding
importFrom("graphics", "hist", "par", "plot", "plot.design")
importFrom("stats", "aggregate", "dist", "hclust", "oneway.test",
"quantile")
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
* 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
‘/home/biocbuild/bbs-3.4-bioc/meat/GOexpress.Rcheck/00check.log’
for details.