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CHECK report for GOexpress on tokay1

This page was generated on 2020-04-15 12:23:40 -0400 (Wed, 15 Apr 2020).

Package 719/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOexpress 1.20.0
Kevin Rue-Albrecht
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/GOexpress
Branch: RELEASE_3_10
Last Commit: ed4991f
Last Changed Date: 2019-10-29 13:09:04 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GOexpress
Version: 1.20.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOexpress.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings GOexpress_1.20.0.tar.gz
StartedAt: 2020-04-15 03:36:08 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 03:38:53 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 165.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GOexpress.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOexpress.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings GOexpress_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/GOexpress.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '1.20.0'
* 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-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/GOexpress-package.Rd:100: file link 'Biobase' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/GOexpress-package.Rd:102: file link 'RColorBrewer' in package 'RColorBrewer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/GOexpress-package.Rd:103: file link 'VennDiagram' in package 'VennDiagram' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/GOexpress-package.Rd:109: file link 'bluered' in package 'gplots' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/GOexpress-package.Rd:110: file link 'greenred' in package 'gplots' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/expression_plot.Rd:140: file link 'Biobase' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/expression_plot_symbol.Rd:152: file link 'Biobase' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/expression_profiles.Rd:154: file link 'Biobase' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/expression_profiles_symbol.Rd:161: file link 'Biobase' in package 'Biobase' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/heatmap_GO.Rd:139: file link 'brewer.pal.info' in package 'RColorBrewer' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/subEset.Rd:46: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.10-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
* 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 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 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-3.10-bioc/meat/GOexpress.Rcheck/00check.log'
for details.

Installation output

GOexpress.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/GOexpress_1.20.0.tar.gz && rm -rf GOexpress.buildbin-libdir && mkdir GOexpress.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GOexpress.buildbin-libdir GOexpress_1.20.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL GOexpress_1.20.0.zip && rm GOexpress_1.20.0.tar.gz GOexpress_1.20.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 19 1952k   19  384k    0     0  1961k      0 --:--:-- --:--:-- --:--:-- 1989k
100 1952k  100 1952k    0     0  8689k      0 --:--:-- --:--:-- --:--:-- 8796k

install for i386

* installing *source* package 'GOexpress' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/GOexpress-package.Rd:100: file link 'Biobase' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/GOexpress-package.Rd:102: file link 'RColorBrewer' in package 'RColorBrewer' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/GOexpress-package.Rd:103: file link 'VennDiagram' in package 'VennDiagram' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/GOexpress-package.Rd:109: file link 'bluered' in package 'gplots' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/GOexpress-package.Rd:110: file link 'greenred' in package 'gplots' does not exist and so has been treated as a topic
    cluster_GO                              html  
    expression_plot                         html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/expression_plot.Rd:140: file link 'Biobase' in package 'Biobase' does not exist and so has been treated as a topic
    expression_plot_symbol                  html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/expression_plot_symbol.Rd:152: file link 'Biobase' in package 'Biobase' does not exist and so has been treated as a topic
    expression_profiles                     html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/expression_profiles.Rd:154: file link 'Biobase' in package 'Biobase' does not exist and so has been treated as a topic
    expression_profiles_symbol              html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/expression_profiles_symbol.Rd:161: file link 'Biobase' in package 'Biobase' does not exist and so has been treated as a topic
    heatmap_GO                              html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/heatmap_GO.Rd:139: file link 'brewer.pal.info' in package 'RColorBrewer' does not exist and so has been treated as a topic
    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-3.10-bioc/tmpdir/RtmpcLw4Lc/R.INSTALLb6056372431/GOexpress/man/subEset.Rd:46: file link 'ExpressionSet' in package 'Biobase' does not exist and so has been treated as a topic
    subset_scores                           html  
    table_genes                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'GOexpress' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GOexpress' as GOexpress_1.20.0.zip
* DONE (GOexpress)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'GOexpress' successfully unpacked and MD5 sums checked

Tests output

Example timings

GOexpress.Rcheck/examples_i386/GOexpress-Ex.timings

nameusersystemelapsed
AlvMac0.120.000.13
AlvMac_GOgenes0.160.030.19
AlvMac_allGO0.060.000.07
AlvMac_allgenes0.030.000.03
AlvMac_results0.20.00.2
AlvMac_results.pVal1.300.291.59
GO_analyse2.580.132.71
GOexpress-package0.000.020.01
cluster_GO0.150.010.17
expression_plot2.180.272.44
expression_plot_symbol0.840.010.86
expression_profiles0.670.030.70
expression_profiles_symbol0.860.020.88
heatmap_GO0.580.030.61
hist_scores0.610.060.67
list_genes0.080.030.11
microarray2dataset0.000.020.02
pValue_GO000
plot_design0.150.020.17
prefix2dataset0.020.010.03
quantiles_scores0.150.000.15
rerank0.250.030.29
subEset0.040.000.03
subset_scores0.280.020.29
table_genes0.110.030.14

GOexpress.Rcheck/examples_x64/GOexpress-Ex.timings

nameusersystemelapsed
AlvMac0.110.000.11
AlvMac_GOgenes0.10.00.1
AlvMac_allGO0.020.020.03
AlvMac_allgenes0.010.010.03
AlvMac_results0.160.030.19
AlvMac_results.pVal1.030.361.39
GO_analyse2.940.183.11
GOexpress-package0.010.000.02
cluster_GO0.180.010.19
expression_plot2.460.132.59
expression_plot_symbol0.860.060.92
expression_profiles0.830.010.84
expression_profiles_symbol0.970.000.97
heatmap_GO1.020.021.03
hist_scores0.280.020.30
list_genes0.520.000.51
microarray2dataset0.000.010.02
pValue_GO000
plot_design0.150.000.15
prefix2dataset0.020.000.02
quantiles_scores0.170.000.17
rerank0.240.030.27
subEset0.040.000.04
subset_scores0.300.020.32
table_genes0.140.010.15