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This page was generated on 2024-12-24 11:39 -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 33/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AGDEX 1.55.0  (landing page)
Cuilan lani Gao
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/AGDEX
git_branch: devel
git_last_commit: 8b30309
git_last_commit_date: 2024-10-29 09:38:37 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for AGDEX on nebbiolo1

To the developers/maintainers of the AGDEX package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AGDEX.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: AGDEX
Version: 1.55.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:AGDEX.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings AGDEX_1.55.0.tar.gz
StartedAt: 2024-12-23 19:38:40 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 19:39:48 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 68.1 seconds
RetCode: 0
Status:   OK  
CheckDir: AGDEX.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:AGDEX.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings AGDEX_1.55.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/AGDEX.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 ‘AGDEX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AGDEX’ version ‘1.55.0’
* 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 ‘AGDEX’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
  GPL Version 2 or later
Standardizable: TRUE
Standardized license specification:
  GPL (>= 2)
* 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
Packages in Depends field not imported from:
  ‘Biobase’ ‘GSEABase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
agdex: no visible global function definition for ‘exprs’
agdex: no visible global function definition for ‘qnorm’
agdex: no visible global function definition for ‘pnorm’
agdex: no visible global function definition for ‘sampleNames’
agdex: no visible global function definition for ‘pData’
agdex.scatterplot: no visible global function definition for ‘points’
agdex.scatterplot: no visible global function definition for ‘lines’
agdex.scatterplot: no visible global function definition for ‘prcomp’
agdex.scatterplot: no visible global function definition for ‘abline’
gsc.to.index.list: no visible global function definition for ‘geneIds’
prep.dex.set: no visible global function definition for ‘exprs’
prep.dex.set: no visible global function definition for ‘pData’
read.agdex.gset.details: no visible global function definition for
  ‘read.table’
read.agdex.gset.list: no visible global function definition for
  ‘read.table’
read.agdex.result: no visible global function definition for
  ‘read.table’
read.enrich.gset.list: no visible global function definition for
  ‘read.table’
read.gset.collection: no visible global function definition for
  ‘read.table’
read.gset.collection: no visible global function definition for
  ‘GeneSet’
read.gset.collection: no visible global function definition for
  ‘geneIds<-’
read.gset.collection: no visible global function definition for
  ‘GeneSetCollection’
write.agdex.gset.details: no visible global function definition for
  ‘write.table’
write.agdex.result: no visible global function definition for
  ‘write.table’
write.gset.list.result: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  GeneSet GeneSetCollection abline exprs geneIds geneIds<- lines pData
  pnorm points prcomp qnorm read.table sampleNames write.table
Consider adding
  importFrom("graphics", "abline", "lines", "points")
  importFrom("stats", "pnorm", "prcomp", "qnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* 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 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/AGDEX.Rcheck/00check.log’
for details.


Installation output

AGDEX.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘AGDEX’ ...
** using staged installation
** R
** data
** 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 (AGDEX)

Tests output


Example timings

AGDEX.Rcheck/AGDEX-Ex.timings

nameusersystemelapsed
agdex0.8590.0250.885
agdex.scatterplot0.0320.0010.033
get.gset.result.details0.0270.0020.030
gset.data0.0000.0010.001
human.data0.0110.0000.011
make.dex.set.object0.0280.0040.031
map.data000
mouse.data0.0180.0010.019
read.agdex.gset.details000
read.agdex.result0.0000.0000.001
write.agdex.gset.details0.0220.0050.027
write.agdex.result0.0030.0020.005