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This page was generated on 2024-03-27 11:36:43 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
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

Package 878/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOexpress 1.36.0  (landing page)
Kevin Rue-Albrecht
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/GOexpress
git_branch: RELEASE_3_18
git_last_commit: 453c83c
git_last_commit_date: 2023-10-24 10:38:33 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for GOexpress on palomino4


To the developers/maintainers of the GOexpress package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GOexpress
Version: 1.36.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GOexpress.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings GOexpress_1.36.0.tar.gz
StartedAt: 2024-03-26 01:27:58 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 01:30:26 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 148.3 seconds
RetCode: 0
Status:   OK  
CheckDir: GOexpress.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GOexpress.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings GOexpress_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/GOexpress.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GOexpress/DESCRIPTION' ... OK
* this is package 'GOexpress' version '1.36.0'
* 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 ... 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
* 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
  'F:/biocbuild/bbs-3.18-bioc/meat/GOexpress.Rcheck/00check.log'
for details.



Installation output

GOexpress.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL GOexpress
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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
AlvMac0.480.000.49
AlvMac_GOgenes0.130.000.12
AlvMac_allGO0.050.000.05
AlvMac_allgenes0.010.000.02
AlvMac_results0.170.000.17
AlvMac_results.pVal3.321.004.31
GO_analyse3.750.143.89
GOexpress-package0.010.000.02
cluster_GO0.130.010.14
expression_plot3.000.133.12
expression_plot_symbol1.090.031.13
expression_profiles0.620.030.65
expression_profiles_symbol0.520.000.52
heatmap_GO0.410.020.42
hist_scores0.760.030.80
list_genes0.080.000.08
microarray2dataset0.000.010.01
pValue_GO000
plot_design0.110.030.14
prefix2dataset000
quantiles_scores0.090.020.11
rerank0.160.010.18
subEset0.030.000.03
subset_scores0.160.020.17
table_genes0.110.000.11