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BioC 3.1: CHECK report for GOexpress on zin2

This page was generated on 2015-10-09 09:26:25 -0700 (Fri, 09 Oct 2015).

Package 419/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOexpress 1.2.2
Kevin Rue-Albrecht
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/GOexpress
Last Changed Rev: 105314 / Revision: 109384
Last Changed Date: 2015-06-22 07:49:00 -0700 (Mon, 22 Jun 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  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: 1.2.2
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.2.2.tar.gz
StartedAt: 2015-10-09 01:56:03 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 01:58:20 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 137.6 seconds
RetCode: 0
Status:  OK 
CheckDir: GOexpress.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings GOexpress_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/GOexpress.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.2.2’
* 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 ... [10s/12s] 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’
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’
mart_from_ensembl: no visible binding for global variable
  ‘prefix2dataset’
microarray2dataset.build: no visible global function definition for
  ‘getCurlHandle’
prefix2dataset.build: no visible global function definition for
  ‘getCurlHandle’
sampleEnsemblGeneId: no visible global function definition for
  ‘getCurlHandle’
* 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 ... [17s/23s] 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-3.1-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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (GOexpress)

GOexpress.Rcheck/GOexpress-Ex.timings:

nameusersystemelapsed
AlvMac0.2080.0120.225
AlvMac_GOgenes0.3390.0000.344
AlvMac_allGO0.0250.0000.026
AlvMac_allgenes0.0070.0000.007
AlvMac_results0.2590.0040.267
AlvMac_results.pVal3.0820.3813.681
GO_analyse3.3900.0194.114
GOexpress-package0.0000.0040.004
cluster_GO0.2880.0070.392
expression_plot0.8250.0001.030
expression_plot_symbol0.9040.0041.021
expression_profiles0.5700.0010.825
expression_profiles_symbol0.6560.0000.849
heatmap_GO0.7830.0001.361
hist_scores0.2570.0000.514
list_genes0.1240.0030.218
microarray2dataset0.0080.0040.014
overlap_GO0.9440.0051.762
pValue_GO0.0010.0000.001
plot_design0.3420.0010.437
prefix2dataset0.0090.0000.021
quantiles_scores0.1380.0000.276
rerank0.2110.0000.394
subEset0.0330.0000.032
subset_scores0.1800.0000.272
table_genes0.1450.0000.196