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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:sscore.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings sscore_1.74.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/sscore.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘sscore/DESCRIPTION’ ... OK
* this is package ‘sscore’ version ‘1.74.0’
* 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 ‘sscore’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'sscore' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.18-bioc/meat/sscore.Rcheck/00install.out’ for details.
* 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
Package in Depends field not imported from: ‘affyio’
  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
OneStepBiweightAlgorithm: no visible global function definition for
  ‘median’
SScore: no visible global function definition for ‘read.celfile’
SScore: no visible global function definition for ‘new’
SScore: no visible global function definition for ‘annotation’
SScoreBatch: no visible global function definition for ‘read.celfile’
SScoreBatch: no visible global function definition for ‘new’
SScoreBatch: no visible global function definition for ‘annotation’
computeAffxSFandSDT: no visible binding for global variable ‘var’
computeAffxSFandSDT: no visible global function definition for ‘x11’
computeAffxSFandSDT: no visible global function definition for ‘par’
computeSFandSDT: no visible binding for global variable ‘var’
computeSFandSDT: no visible global function definition for ‘x11’
computeSFandSDT: no visible global function definition for ‘par’
Undefined global functions or variables:
  annotation median new par read.celfile var x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par")
  importFrom("methods", "new")
  importFrom("stats", "median", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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 ...
  ‘sscore.Rnw’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘sscore.Rnw’
  ...

The downloaded source packages are in
	‘/tmp/RtmpRkbbFJ/downloaded_packages’

  When sourcing ‘sscore.R’:
Error: Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95Av2
Library - package hgu95av2cdf not installed
Library - package hgu95av2cdf not installed
Execution halted

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

Loading required package: Biobase
Welcome to Bioconductor

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

Loading required package: affyio
Warning: Package 'sscore' is deprecated and will be removed from Bioconductor
  version 3.19
also installing the dependencies ‘RSQLite’, ‘AnnotationDbi’

trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.3.6.tar.gz'
Content type 'application/x-gzip' length 4249332 bytes (4.1 MB)
==================================================
downloaded 4.1 MB

trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/AnnotationDbi_1.64.1.tar.gz'
Content type 'application/x-gzip' length 4359564 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/hgu95av2cdf_2.18.0.tar.gz'
Content type 'application/x-gzip' length 1331391 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

ERROR: dependencies ‘plogr’, ‘cpp11’ are not available for package ‘RSQLite’
* removing ‘/tmp/RtmpN5fNZj/RLIBS_2d7224673d2037/RSQLite’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘RSQLite’ had non-zero exit status
ERROR: dependency ‘RSQLite’ is not available for package ‘AnnotationDbi’
* removing ‘/tmp/RtmpN5fNZj/RLIBS_2d7224673d2037/AnnotationDbi’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘AnnotationDbi’ had non-zero exit status
ERROR: dependency ‘AnnotationDbi’ is not available for package ‘hgu95av2cdf’
* removing ‘/tmp/RtmpN5fNZj/RLIBS_2d7224673d2037/hgu95av2cdf’
Warning in install.packages(cdfname, lib = lib, repos = repositories(),  :
  installation of package ‘hgu95av2cdf’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/Rtmp3YRZ4f/downloaded_packages’

Error: processing vignette 'sscore.Rnw' failed with diagnostics:
 chunk 2 
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG_U95Av2
Library - package hgu95av2cdf not installed
Library - package hgu95av2cdf not installed

--- failed re-building ‘sscore.Rnw’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/sscore.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL sscore
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘sscore’ ...
** using staged installation
** R
** 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
Warning: Package 'sscore' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package can be loaded from final location
Warning: Package 'sscore' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (sscore)