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This page was generated on 2023-10-20 09:38:03 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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 857/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOexpress 1.34.0  (landing page)
Kevin Rue-Albrecht
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/GOexpress
git_branch: RELEASE_3_17
git_last_commit: 3db4c6e
git_last_commit_date: 2023-04-25 10:34:39 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for GOexpress on kjohnson2


To the developers/maintainers of the GOexpress package:
- 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: 1.34.0
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_1.34.0.tar.gz
StartedAt: 2023-10-17 22:52:39 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 22:56:33 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 234.9 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_1.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GOexpress.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GOexpress/DESCRIPTION’ ... OK
* this is package ‘GOexpress’ version ‘1.34.0’
* 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
* 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-3.17-bioc-mac-arm64/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/4.3-arm64/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
AlvMac0.1810.0160.306
AlvMac_GOgenes0.4130.0080.639
AlvMac_allGO0.0240.0030.041
AlvMac_allgenes0.0070.0020.013
AlvMac_results0.1600.0110.261
AlvMac_results.pVal1.9341.1774.771
GO_analyse2.7800.0794.438
GOexpress-package0.0040.0050.009
cluster_GO0.4710.0110.731
expression_plot2.4870.1253.973
expression_plot_symbol1.1980.0221.857
expression_profiles0.8500.0141.327
expression_profiles_symbol1.4790.0202.306
heatmap_GO0.5260.0210.822
hist_scores0.2880.0100.458
list_genes0.1330.0040.194
microarray2dataset0.0100.0110.031
pValue_GO000
plot_design0.6060.0160.951
prefix2dataset0.0080.0050.022
quantiles_scores0.1460.0030.228
rerank0.2500.0120.398
subEset0.0510.0020.083
subset_scores0.2120.0170.348
table_genes0.1190.0050.188