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This page was generated on 2025-09-04 15:01 -0400 (Thu, 04 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
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 208/432HostnameOS / ArchINSTALLBUILDCHECK
KEGGdzPathwaysGEO 1.46.0  (landing page)
Gaurav Bhatti
Snapshot Date: 2025-09-04 07:30 -0400 (Thu, 04 Sep 2025)
git_url: https://git.bioconductor.org/packages/KEGGdzPathwaysGEO
git_branch: RELEASE_3_21
git_last_commit: 3b4f21a
git_last_commit_date: 2025-04-15 09:19:44 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published


CHECK results for KEGGdzPathwaysGEO on nebbiolo1

To the developers/maintainers of the KEGGdzPathwaysGEO 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: KEGGdzPathwaysGEO
Version: 1.46.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:KEGGdzPathwaysGEO.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings KEGGdzPathwaysGEO_1.46.0.tar.gz
StartedAt: 2025-09-04 13:08:06 -0400 (Thu, 04 Sep 2025)
EndedAt: 2025-09-04 13:12:54 -0400 (Thu, 04 Sep 2025)
EllapsedTime: 288.4 seconds
RetCode: 0
Status:   OK  
CheckDir: KEGGdzPathwaysGEO.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:KEGGdzPathwaysGEO.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings KEGGdzPathwaysGEO_1.46.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/KEGGdzPathwaysGEO.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘KEGGdzPathwaysGEO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGdzPathwaysGEO’ version ‘1.46.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘KEGGdzPathwaysGEO’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 301.0Mb
  sub-directories of 1Mb or more:
    data  300.8Mb
* checking package 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 ... NOTE
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘BiocGenerics’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-data-experiment/meat/KEGGdzPathwaysGEO.Rcheck/00check.log’
for details.


Installation output

KEGGdzPathwaysGEO.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘KEGGdzPathwaysGEO’ ...
** this is package ‘KEGGdzPathwaysGEO’ version ‘1.46.0’
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (KEGGdzPathwaysGEO)

Tests output


Example timings

KEGGdzPathwaysGEO.Rcheck/KEGGdzPathwaysGEO-Ex.timings

nameusersystemelapsed
GSE12970.0520.0070.058
GSE147620.1130.0100.123
GSE154710.2650.0230.289
GSE165150.1460.0140.161
GSE188420.3040.0480.353
GSE191880.5690.0710.642
GSE197280.1110.0070.118
GSE201530.0960.0030.100
GSE202910.0630.0050.068
GSE213540.1030.0030.107
GSE34670.1040.0030.108
GSE35850.0360.0000.037
GSE36780.0910.0040.095
GSE41070.1160.0060.123
GSE5281_EC0.1110.0060.117
GSE5281_HIP0.1260.0040.130
GSE5281_VCX0.1410.0090.150
GSE6956AA0.0340.0000.035
GSE6956C0.0790.0050.084
GSE7810.0410.0010.043
GSE86710.2430.0170.260
GSE87620.1190.0040.124
GSE93480.3010.0160.318
GSE94760.0990.0070.107
KEGGdzPathwaysGEO-package0.2870.0180.306