Back to Multiple platform build/check report for BioC 3.6
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

CHECK report for GOexpress on tokay1

This page was generated on 2018-04-12 13:24:58 -0400 (Thu, 12 Apr 2018).

Package 595/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOexpress 1.12.0
Kevin Rue-Albrecht
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GOexpress
Branch: RELEASE_3_6
Last Commit: 33e70a3
Last Changed Date: 2017-10-30 12:40:37 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GOexpress
Version: 1.12.0
Command: rm -rf GOexpress.buildbin-libdir GOexpress.Rcheck && mkdir GOexpress.buildbin-libdir GOexpress.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOexpress.buildbin-libdir GOexpress_1.12.0.tar.gz >GOexpress.Rcheck\00install.out 2>&1 && cp GOexpress.Rcheck\00install.out GOexpress-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GOexpress.buildbin-libdir --install="check:GOexpress-install.out" --force-multiarch --no-vignettes --timings GOexpress_1.12.0.tar.gz
StartedAt: 2018-04-12 00:27:14 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:30:11 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 176.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GOexpress.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GOexpress.buildbin-libdir GOexpress.Rcheck && mkdir GOexpress.buildbin-libdir GOexpress.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GOexpress.buildbin-libdir GOexpress_1.12.0.tar.gz >GOexpress.Rcheck\00install.out 2>&1 && cp GOexpress.Rcheck\00install.out GOexpress-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GOexpress.buildbin-libdir --install="check:GOexpress-install.out" --force-multiarch --no-vignettes --timings GOexpress_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GOexpress.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.12.0'
* 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 whether package 'GOexpress' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/GOexpress-package.Rd:100: missing file link 'Biobase'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/GOexpress-package.Rd:102: missing file link 'RColorBrewer'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/GOexpress-package.Rd:103: missing file link 'VennDiagram'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/GOexpress-package.Rd:109: missing file link 'bluered'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/GOexpress-package.Rd:110: missing file link 'greenred'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/expression_plot.Rd:140: missing file link 'Biobase'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/expression_plot_symbol.Rd:152: missing file link 'Biobase'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/expression_profiles.Rd:154: missing file link 'Biobase'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/expression_profiles_symbol.Rd:161: missing file link 'Biobase'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/heatmap_GO.Rd:139: missing file link 'brewer.pal.info'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/subEset.Rd:46: missing file link 'ExpressionSet'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GOexpress.Rcheck/00install.out' for details.
* 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'
mart_from_ensembl: no visible binding for global variable
  'prefix2dataset'
Undefined global functions or variables:
  microarray2dataset prefix2dataset
* 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' ... OK
** running examples for arch 'x64' ... 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 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GOexpress.Rcheck/00check.log'
for details.

Installation output

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
  converting help for package 'GOexpress'
    finding HTML links ... done
    AlvMac                                  html  
    AlvMac_GOgenes                          html  
    AlvMac_allGO                            html  
    AlvMac_allgenes                         html  
    AlvMac_results                          html  
    AlvMac_results.pVal                     html  
    GO_analyse                              html  
    GOexpress-package                       html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/GOexpress-package.Rd:100: missing file link 'Biobase'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/GOexpress-package.Rd:102: missing file link 'RColorBrewer'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/GOexpress-package.Rd:103: missing file link 'VennDiagram'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/GOexpress-package.Rd:109: missing file link 'bluered'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/GOexpress-package.Rd:110: missing file link 'greenred'
    cluster_GO                              html  
    expression_plot                         html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/expression_plot.Rd:140: missing file link 'Biobase'
    expression_plot_symbol                  html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/expression_plot_symbol.Rd:152: missing file link 'Biobase'
    expression_profiles                     html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/expression_profiles.Rd:154: missing file link 'Biobase'
    expression_profiles_symbol              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/expression_profiles_symbol.Rd:161: missing file link 'Biobase'
    heatmap_GO                              html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/heatmap_GO.Rd:139: missing file link 'brewer.pal.info'
    hist_scores                             html  
    list_genes                              html  
    microarray2dataset                      html  
    pValue_GO                               html  
    plot_design                             html  
    prefix2dataset                          html  
    quantiles_scores                        html  
    rerank                                  html  
    subEset                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpKI8NxX/R.INSTALLf2812ca2f5f/GOexpress/man/subEset.Rd:46: missing file link 'ExpressionSet'
    subset_scores                           html  
    table_genes                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GOexpress' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOexpress' as GOexpress_1.12.0.zip
* DONE (GOexpress)
In R CMD INSTALL
In R CMD INSTALL

Tests output

Example timings

GOexpress.Rcheck/examples_i386/GOexpress-Ex.timings

nameusersystemelapsed
AlvMac0.110.000.11
AlvMac_GOgenes0.390.000.39
AlvMac_allGO0.030.000.03
AlvMac_allgenes0.040.010.04
AlvMac_results0.360.000.36
AlvMac_results.pVal1.870.362.24
GO_analyse3.030.113.14
GOexpress-package0.000.020.01
cluster_GO0.350.010.36
expression_plot3.140.103.24
expression_plot_symbol0.890.010.90
expression_profiles1.000.021.02
expression_profiles_symbol1.220.001.22
heatmap_GO1.430.031.47
hist_scores0.580.030.61
list_genes0.130.000.12
microarray2dataset0.000.020.02
pValue_GO000
plot_design0.150.010.17
prefix2dataset0.020.000.01
quantiles_scores0.470.020.49
rerank0.220.060.28
subEset0.040.000.05
subset_scores0.310.000.31
table_genes0.210.020.22

GOexpress.Rcheck/examples_x64/GOexpress-Ex.timings

nameusersystemelapsed
AlvMac0.140.000.14
AlvMac_GOgenes0.520.000.51
AlvMac_allGO0.040.000.05
AlvMac_allgenes0.030.000.03
AlvMac_results0.390.020.40
AlvMac_results.pVal1.720.372.10
GO_analyse3.110.143.25
GOexpress-package0.000.020.01
cluster_GO0.380.020.39
expression_plot3.370.013.39
expression_plot_symbol0.960.020.97
expression_profiles0.730.000.74
expression_profiles_symbol0.830.000.82
heatmap_GO1.450.011.47
hist_scores0.490.070.55
list_genes0.100.000.11
microarray2dataset0.000.010.02
pValue_GO000
plot_design0.150.030.17
prefix2dataset0.010.020.03
quantiles_scores0.220.010.23
rerank0.230.050.28
subEset0.070.000.07
subset_scores0.230.020.25
table_genes0.110.010.12