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This page was generated on 2024-06-11 15:40 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4394
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 865/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOexpress 1.39.0  (landing page)
Kevin Rue-Albrecht
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/GOexpress
git_branch: devel
git_last_commit: a8aa379
git_last_commit_date: 2024-04-30 10:38:52 -0400 (Tue, 30 Apr 2024)
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 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 1.39.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GOexpress.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GOexpress_1.39.0.tar.gz
StartedAt: 2024-06-10 03:26:49 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 03:31:06 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 257.1 seconds
RetCode: 0
Status:   OK  
CheckDir: GOexpress.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GOexpress.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GOexpress_1.39.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GOexpress.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '1.39.0'
* 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 code 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 ... NOTE
checkRd: (-1) AlvMac_GOgenes.Rd:22-23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AlvMac_GOgenes.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AlvMac_allGO.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AlvMac_allGO.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AlvMac_allGO.Rd:25-27: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AlvMac_allgenes.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AlvMac_allgenes.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) AlvMac_allgenes.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) hist_scores.Rd:11: Lost braces; missing escapes or markup?
    11 | variable of the {GO_analyse()} function.
       |                 ^
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/GOexpress.Rcheck/00check.log'
for details.


Installation output

GOexpress.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GOexpress
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-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
AlvMac0.110.000.10
AlvMac_GOgenes0.440.010.45
AlvMac_allGO0.010.020.03
AlvMac_allgenes0.020.000.02
AlvMac_results0.090.020.11
AlvMac_results.pVal2.041.013.04
GO_analyse3.000.113.11
GOexpress-package0.000.020.02
cluster_GO0.140.000.14
expression_plot2.390.422.81
expression_plot_symbol1.000.111.11
expression_profiles0.610.020.62
expression_profiles_symbol0.710.010.73
heatmap_GO0.410.040.44
hist_scores0.330.010.35
list_genes0.070.050.11
microarray2dataset0.010.010.03
pValue_GO000
plot_design0.190.010.20
prefix2dataset000
quantiles_scores0.110.010.13
rerank0.170.030.20
subEset0.060.000.06
subset_scores0.220.030.25
table_genes0.130.000.13