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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 876/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOexpress 1.41.0  (landing page)
Kevin Rue-Albrecht
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/GOexpress
git_branch: devel
git_last_commit: 015022e
git_last_commit_date: 2024-10-29 09:54:48 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for GOexpress on nebbiolo1

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: 1.41.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GOexpress.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GOexpress_1.41.0.tar.gz
StartedAt: 2024-12-23 22:33:22 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 22:35:36 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 134.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GOexpress.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GOexpress.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GOexpress_1.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GOexpress.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘GOexpress/DESCRIPTION’ ... OK
* this is package ‘GOexpress’ version ‘1.41.0’
* 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 ... WARNING
Found the following significant warnings:
  Note: possible error in 'getBM(attributes = microarray.header, ': unused argument (curl = curlHandle) 
  Note: possible error in 'getBM(attributes = "ensembl_gene_id", ': unused argument (curl = curl) 
See ‘/home/biocbuild/bbs-3.21-bioc/meat/GOexpress.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* 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 loading without being on the library search path ... 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’
microarray2dataset.build: possible error in getBM(attributes =
  microarray.header, mart = mart.loop, curl = curlHandle): unused
  argument (curl = curlHandle)
sampleEnsemblGeneId: possible error in getBM(attributes =
  "ensembl_gene_id", mart = mart.loop, curl = curl): unused argument
  (curl = curl)
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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/GOexpress.Rcheck/00check.log’
for details.


Installation output

GOexpress.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL GOexpress
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘GOexpress’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'getBM(attributes = microarray.header, ': unused argument (curl = curlHandle) 
Note: possible error in 'getBM(attributes = "ensembl_gene_id", ': unused argument (curl = curl) 
** 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
AlvMac0.0830.0120.095
AlvMac_GOgenes0.5080.0100.518
AlvMac_allGO0.0150.0020.017
AlvMac_allgenes0.0050.0000.006
AlvMac_results0.0950.0140.110
AlvMac_results.pVal1.1521.4632.616
GO_analyse1.8610.0781.939
GOexpress-package0.0010.0020.003
cluster_GO0.1040.0080.113
expression_plot2.1160.0982.214
expression_plot_symbol0.7480.0140.762
expression_profiles0.4570.0020.459
expression_profiles_symbol0.9260.0550.981
heatmap_GO0.3910.0110.404
hist_scores0.1880.0200.207
list_genes0.0830.0080.091
microarray2dataset0.0050.0090.013
pValue_GO0.0010.0000.001
plot_design0.1100.0070.118
prefix2dataset0.0040.0030.008
quantiles_scores0.1220.0080.130
rerank0.1480.0170.165
subEset0.0340.0000.034
subset_scores0.1490.0000.150
table_genes0.0990.0010.102