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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:a4.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings a4_1.47.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/a4.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘a4/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4’ version ‘1.47.0’
* 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 ‘a4’ can be installed ... OK
* 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 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘a4Base’ ‘a4Classif’ ‘a4Core’ ‘a4Preproc’ ‘a4Reporting’
  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 ... OK
* checking for missing documentation entries ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘a4vignette.Rnw’... failed
 WARNING
Errors in running code in vignettes:
when running code in ‘a4vignette.Rnw’
  ...
+     nNoEffectCols = 5, withinClassSd = 0.2)

> ALL <- addGeneInfo(ALL)
Loading required package: hgu95av2.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘hgu95av2.db’

  When sourcing ‘a4vignette.R’:
Error: error in evaluating the argument 'envir' in selecting a method for function 'mget': object 'hgu95av2ENTREZID' not found
Execution halted

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘a4vignette.Rnw’ using Sweave
Loading required package: a4Base
Loading required package: a4Preproc
Loading required package: a4Core

a4Base version 1.47.0

Loading required package: a4Classif

a4Classif version 1.47.0

Loading required package: a4Reporting

a4 version 1.47.0

Loading required package: ALL
Loading required package: Biobase
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce,
    anyDuplicated, aperm, append,
    as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated,
    eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply,
    match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind,
    rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material;
    view with 'browseVignettes()'. To cite
    Bioconductor, see 'citation("Biobase")',
    and for packages 'citation("pkgname")'.

Loading required package: nlcv
Loading required package: MLInterfaces
Loading required package: Rcpp
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: XML
Loading required package: cluster
Loading required package: xtable

Attaching package: ‘xtable’

The following object is masked from ‘package:a4Reporting’:

    xtable


nlcv version 0.3.5

Loading required package: hgu95av2.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘hgu95av2.db’

Error: processing vignette 'a4vignette.Rnw' failed with diagnostics:
 chunk 4 (label = prepareALL) 
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'envir' in selecting a method for function 'mget': object 'hgu95av2ENTREZID' not found

--- failed re-building ‘a4vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘a4vignette.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/a4.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL a4
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘a4’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘a4’ 
*** 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 (a4)