Movatterモバイル変換

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:AGDEX.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings AGDEX_1.58.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/AGDEX.Rcheck’* using R version 4.5.2 (2025-10-31)* 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 ‘AGDEX/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘AGDEX’ version ‘1.58.0’* 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 ... NOTEMalformed Description field: should contain one or more complete sentences.Non-standard license specification:  GPL Version 2 or laterStandardizable: TRUEStandardized 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 ... NOTEPackages 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 ... NOTEagdex: 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.tableConsider 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* DONEStatus: 3 NOTEsSee  ‘/home/biocbuild/bbs-3.22-bioc/meat/AGDEX.Rcheck/00check.log’for details.

################################################################################################################################################################## Running command:######   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL AGDEX###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘AGDEX’ ...** this is package ‘AGDEX’ version ‘1.58.0’** 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)