Back to Multiple platform build/check report for BioC 3.12
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for AGDEX on malbec1

This page was generated on 2020-08-09 11:19:05 -0400 (Sun, 09 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE AGDEX PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 36/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AGDEX 1.37.0
Cuilan lani Gao
Snapshot Date: 2020-08-08 14:51:01 -0400 (Sat, 08 Aug 2020)
URL: https://git.bioconductor.org/packages/AGDEX
Branch: master
Last Commit: b3b3d17
Last Changed Date: 2020-04-27 14:27:03 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: AGDEX
Version: 1.37.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:AGDEX.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings AGDEX_1.37.0.tar.gz
StartedAt: 2020-08-08 23:38:08 -0400 (Sat, 08 Aug 2020)
EndedAt: 2020-08-08 23:39:38 -0400 (Sat, 08 Aug 2020)
EllapsedTime: 89.7 seconds
RetCode: 0
Status:  OK 
CheckDir: AGDEX.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:AGDEX.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings AGDEX_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/AGDEX.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AGDEX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AGDEX’ version ‘1.37.0’
* 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 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 ... 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 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/AGDEX.Rcheck/00check.log’
for details.



Installation output

AGDEX.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL AGDEX
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/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
agdex0.9240.0040.941
agdex.scatterplot0.0480.0000.049
get.gset.result.details0.0480.0000.047
gset.data000
human.data0.0160.0000.015
make.dex.set.object0.0400.0040.044
map.data0.0040.0000.001
mouse.data0.0280.0000.027
read.agdex.gset.details000
read.agdex.result000
write.agdex.gset.details0.0440.0000.042
write.agdex.result0.0080.0000.008