Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:08:06 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for GOexpress on machv2


To the developers/maintainers of the GOexpress package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GOexpress.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 798/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOexpress 1.28.0  (landing page)
Kevin Rue-Albrecht
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/GOexpress
git_branch: RELEASE_3_14
git_last_commit: 2ffb103
git_last_commit_date: 2021-10-26 12:15:58 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GOexpress
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GOexpress.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GOexpress_1.28.0.tar.gz
StartedAt: 2022-04-12 13:55:54 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 13:59:11 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 196.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GOexpress.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GOexpress.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GOexpress_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/GOexpress.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOexpress/DESCRIPTION’ ... OK
* this is package ‘GOexpress’ version ‘1.28.0’
* 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 for sufficient/correct file permissions ... 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
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
AlvMac_results.pVal 2.272  2.314   5.649
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/GOexpress.Rcheck/00check.log’
for details.



Installation output

GOexpress.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GOexpress
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* 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
** 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
* DONE (GOexpress)

Tests output


Example timings

GOexpress.Rcheck/GOexpress-Ex.timings

nameusersystemelapsed
AlvMac0.1740.0260.201
AlvMac_GOgenes0.5300.0130.543
AlvMac_allGO0.0370.0040.041
AlvMac_allgenes0.0180.0010.020
AlvMac_results0.2110.0160.229
AlvMac_results.pVal2.2722.3145.649
GO_analyse4.1540.1204.280
GOexpress-package0.0050.0070.011
cluster_GO0.1580.0030.161
expression_plot3.1010.0973.245
expression_plot_symbol1.0560.0101.068
expression_profiles1.0610.0091.073
expression_profiles_symbol1.6320.0131.646
heatmap_GO0.8780.0280.910
hist_scores0.3520.0120.365
list_genes0.1940.0050.200
microarray2dataset0.0140.0230.037
pValue_GO0.0000.0010.001
plot_design0.1680.0080.175
prefix2dataset0.0110.0050.015
quantiles_scores0.2350.0050.239
rerank0.3590.0050.365
subEset0.0550.0030.058
subset_scores0.2500.0090.260
table_genes0.1880.0080.197