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BioC 3.2: CHECK report for GOexpress on windows1.bioconductor.org

This page was generated on 2015-10-27 17:31:35 -0400 (Tue, 27 Oct 2015).

Package 446/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOexpress 1.4.1
Kevin Rue-Albrecht
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/GOexpress
Last Changed Rev: 109765 / Revision: 109947
Last Changed Date: 2015-10-19 20:11:55 -0400 (Mon, 19 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GOexpress
Version: 1.4.1
Command: rm -rf GOexpress.buildbin-libdir GOexpress.Rcheck && mkdir GOexpress.buildbin-libdir GOexpress.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOexpress.buildbin-libdir GOexpress_1.4.1.tar.gz >GOexpress.Rcheck\00install.out 2>&1 && cp GOexpress.Rcheck\00install.out GOexpress-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GOexpress.buildbin-libdir --install="check:GOexpress-install.out" --force-multiarch --no-vignettes --timings GOexpress_1.4.1.tar.gz
StartedAt: 2015-10-27 02:18:34 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 02:20:58 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 143.6 seconds
RetCode: 0
Status:  OK  
CheckDir: GOexpress.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GOexpress.buildbin-libdir GOexpress.Rcheck && mkdir GOexpress.buildbin-libdir GOexpress.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOexpress.buildbin-libdir GOexpress_1.4.1.tar.gz >GOexpress.Rcheck\00install.out 2>&1 && cp GOexpress.Rcheck\00install.out GOexpress-install.out  && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=GOexpress.buildbin-libdir --install="check:GOexpress-install.out" --force-multiarch --no-vignettes --timings GOexpress_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/GOexpress.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GOexpress/DESCRIPTION' ... OK
* this is package 'GOexpress' version '1.4.1'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [16s] OK
** running examples for arch 'x64' ... [18s] 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
  'C:/biocbld/bbs-3.2-bioc/meat/GOexpress.Rcheck/00check.log'
for details.


GOexpress.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'GOexpress' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOexpress' as GOexpress_1.4.1.zip
* DONE (GOexpress)

GOexpress.Rcheck/examples_i386/GOexpress-Ex.timings:

nameusersystemelapsed
AlvMac0.080.030.11
AlvMac_GOgenes0.280.000.28
AlvMac_allGO0.020.000.02
AlvMac_allgenes0.010.000.01
AlvMac_results0.250.000.25
AlvMac_results.pVal1.570.391.96
GO_analyse3.320.183.50
GOexpress-package0.000.010.01
cluster_GO0.240.020.25
expression_plot0.700.030.74
expression_plot_symbol0.800.000.79
expression_profiles0.610.030.65
expression_profiles_symbol0.70.00.7
heatmap_GO0.640.010.65
hist_scores0.530.050.58
list_genes0.110.020.12
microarray2dataset0.000.010.01
overlap_GO0.750.331.10
pValue_GO000
plot_design0.320.030.34
prefix2dataset000
quantiles_scores0.120.010.14
rerank0.210.020.24
subEset0.040.000.03
subset_scores0.290.000.30
table_genes0.140.000.14

GOexpress.Rcheck/examples_x64/GOexpress-Ex.timings:

nameusersystemelapsed
AlvMac0.110.000.11
AlvMac_GOgenes0.400.000.39
AlvMac_allGO0.030.000.03
AlvMac_allgenes000
AlvMac_results0.290.000.30
AlvMac_results.pVal1.740.392.12
GO_analyse4.360.124.49
GOexpress-package000
cluster_GO0.140.000.14
expression_plot0.820.020.83
expression_plot_symbol0.990.031.01
expression_profiles0.680.000.69
expression_profiles_symbol0.660.020.67
heatmap_GO0.580.030.61
hist_scores0.230.040.28
list_genes0.130.000.13
microarray2dataset0.010.000.01
overlap_GO0.770.411.17
pValue_GO000
plot_design0.150.020.18
prefix2dataset000
quantiles_scores0.160.000.16
rerank0.20.00.2
subEset0.050.000.05
subset_scores0.340.000.34
table_genes0.160.000.16