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CHECK report for GOexpress on tokay1

This page was generated on 2019-04-13 11:24:20 -0400 (Sat, 13 Apr 2019).

Package 659/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOexpress 1.16.1
Kevin Rue-Albrecht
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/GOexpress
Branch: RELEASE_3_8
Last Commit: a9b01a7
Last Changed Date: 2019-01-04 13:05:38 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 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: 1.16.1
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOexpress.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GOexpress_1.16.1.tar.gz
StartedAt: 2019-04-13 02:45:44 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 02:49:17 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 212.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GOexpress.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GOexpress.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings GOexpress_1.16.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/GOexpress.Rcheck'
* using R version 3.5.3 (2019-03-11)
* 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 '1.16.1'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-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-3.8-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/3.8/bioc/src/contrib/GOexpress_1.16.1.tar.gz && rm -rf GOexpress.buildbin-libdir && mkdir GOexpress.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GOexpress.buildbin-libdir GOexpress_1.16.1.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL GOexpress_1.16.1.zip && rm GOexpress_1.16.1.tar.gz GOexpress_1.16.1.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
100 1952k  100 1952k    0     0  22.6M      0 --:--:-- --:--:-- --:--:-- 23.5M

install for i386

* installing *source* package 'GOexpress' ...
** 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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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-3.8-bioc/tmpdir/RtmpeC46od/R.INSTALL91c2f92ce6/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
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_1.16.1.zip
* DONE (GOexpress)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'GOexpress' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Example timings

GOexpress.Rcheck/examples_i386/GOexpress-Ex.timings

nameusersystemelapsed
AlvMac0.160.020.17
AlvMac_GOgenes0.150.010.17
AlvMac_allGO0.060.000.06
AlvMac_allgenes0.060.000.06
AlvMac_results0.30.00.3
AlvMac_results.pVal1.440.281.72
GO_analyse3.230.243.47
GOexpress-package0.000.010.01
cluster_GO0.220.030.25
expression_plot1.250.031.28
expression_plot_symbol1.330.001.33
expression_profiles1.250.021.26
expression_profiles_symbol1.30.01.3
heatmap_GO0.600.040.64
hist_scores0.780.050.83
list_genes0.150.000.15
microarray2dataset0.000.020.02
pValue_GO000
plot_design0.170.040.22
prefix2dataset0.020.000.01
quantiles_scores0.160.020.17
rerank0.610.000.61
subEset0.040.010.07
subset_scores0.270.020.28
table_genes0.140.000.14

GOexpress.Rcheck/examples_x64/GOexpress-Ex.timings

nameusersystemelapsed
AlvMac0.140.000.15
AlvMac_GOgenes0.110.010.12
AlvMac_allGO0.060.000.06
AlvMac_allgenes0.040.000.05
AlvMac_results0.270.020.28
AlvMac_results.pVal1.590.402.00
GO_analyse3.960.244.18
GOexpress-package0.010.010.04
cluster_GO0.240.020.25
expression_plot1.760.061.82
expression_plot_symbol1.600.031.63
expression_profiles1.120.001.12
expression_profiles_symbol1.810.031.85
heatmap_GO0.880.020.89
hist_scores0.260.060.33
list_genes0.490.000.48
microarray2dataset0.010.000.02
pValue_GO000
plot_design0.160.000.15
prefix2dataset0.020.000.02
quantiles_scores0.150.020.17
rerank0.210.060.27
subEset0.040.000.04
subset_scores0.250.020.27
table_genes0.480.000.49