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BioC 3.4: CHECK report for GOexpress on zin1

This page was generated on 2016-09-21 03:39:17 -0700 (Wed, 21 Sep 2016).

Package 524/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GOexpress
Version: 1.7.1
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.7.1.tar.gz
StartedAt: 2016-09-20 07:22:53 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 07:24:22 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 88.8 seconds
RetCode: 0
Status:  OK 
CheckDir: GOexpress.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.7.1.tar.gz
###
##############################################################################
##############################################################################


* 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.


GOexpress.Rcheck/00install.out:

* installing *source* package ‘GOexpress’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GOexpress)

GOexpress.Rcheck/GOexpress-Ex.timings:

nameusersystemelapsed
AlvMac0.1080.0000.110
AlvMac_GOgenes0.3200.0200.341
AlvMac_allGO0.0200.0080.026
AlvMac_allgenes0.0080.0000.006
AlvMac_results0.2560.0240.282
AlvMac_results.pVal3.2640.3763.640
GO_analyse2.9960.0363.030
GOexpress-package0.0040.0000.004
cluster_GO0.260.020.28
expression_plot0.7720.0320.804
expression_plot_symbol0.7640.0040.766
expression_profiles0.5640.0000.563
expression_profiles_symbol0.6280.0040.633
heatmap_GO0.6120.0000.613
hist_scores0.4080.0280.435
list_genes0.0960.0200.113
microarray2dataset0.0120.0080.019
overlap_GO0.8760.0680.953
pValue_GO0.0000.0000.001
plot_design0.1480.0120.160
prefix2dataset0.0080.0000.008
quantiles_scores0.1480.0000.149
rerank0.3760.0160.389
subEset0.0360.0000.035
subset_scores0.1680.0000.176
table_genes0.1120.0040.116