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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:farms.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings farms_1.51.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/farms.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 ‘farms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘farms’ version ‘1.51.0’
* checking package namespace information ... NOTE
  Namespace with empty importFrom: ‘methods’
* 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 ‘farms’ 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.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘affy’ ‘MASS’ ‘methods’ ‘Biobase’
A package should be listed in only one of these fields.
* 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
'library' or 'require' calls to packages already attached by Depends:
  ‘affy’ ‘methods’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Biobase’ ‘utils’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘MASS’
  All declared Imports should be used.
Package in Depends field not imported from: ‘MASS’
  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
File ‘farms/R/zzz.R’:
  .onLoad calls:
    require("methods", quietly = TRUE)
    packageStartupMessage(" _                             ", "\n",     "| |                            ", "\n", "| |  __,   ,_    _  _  _    ,  ",     "\n", "|/  /  |  /  |  / |/ |/ |  / \\_", "\n", "|__/\\_/|_/   |_/  |  |  |_/ \\/ ",     "\n", "|\\                             ", "\n", "|/   ",     "\n")
    require(utils)
    require(Biobase, quietly = TRUE)
    require(affy, quietly = TRUE)
    packageStartupMessage("Citation: S. Hochreiter et al.,", "\n",     "A new summarization method for affymetrix probe level data,",     "\n", "Bioinformatics, 22, 8, 943-949, 2006", "\n", "\n",     "Citation: W. Talloen et al.,", "\n", "I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data,",     "\n", "Bioinformatics, 23, 21, 2897-2902, 2007", "\n", "BibTex: enter 'toBibtex(citation(\"farms\"))'",     "\n\n", "Homepage: http://www.bioinf.jku.at/software/farms/farms.html",     "\n\n", "FARMS Package Version ", version, "\n")
    packageStartupMessage("\n", "Changes in FARMS:", "\n", "For all changes previous to 1.3.0, see the farms vignette.",     "\n", "Version 1.3.0: Added I/NI-calls for filtering", "\n",     "               Adjusted Hyperparameters for alternative CDFs,",     "\n", "               probes set standardized, weighted mean",     "\n", "               Works now with R >= 2.8 and Bioconductor 2.3,",     "\n", "               Changed termination criterion, initialization values,",     "\n", "               factors and loadings scaled, added argument robust",     "\n", "               Update for R-2.11", "\n", "               Updated I/NI-Call for Laplace-FARMS version,",     "\n", "               Maximum likelihood correlation structure given",     "\n", "               non-negative constraints", "\n", "Version 1.4.0: Default centering changed to median",     "\n", "Version 1.8.x: Suppression of spurious correlation (Laplace-FARMS)",     "\n")

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

plot,INI_Calls-missing: no visible global function definition for
  ‘truehist’
Undefined global functions or variables:
  truehist
* 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 ...
  ‘farms.Rnw’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘farms.Rnw’
  ...

The downloaded source packages are in
	‘/tmp/Rtmp6sukKN/downloaded_packages’

  When sourcing ‘farms.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 ‘farms.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: MASS
 _                             
| |                            
| |  __,   ,_    _  _  _    ,  
|/  /  |  /  |  / |/ |/ |  / \_
|__/\_/|_/   |_/  |  |  |_/ \/ 
|\                             
|/   

Citation: S. Hochreiter et al.,
A new summarization method for affymetrix probe level data,
Bioinformatics, 22, 8, 943-949, 2006

Citation: W. Talloen et al.,
I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data,
Bioinformatics, 23, 21, 2897-2902, 2007
BibTex: enter 'toBibtex(citation("farms"))'

Homepage: http://www.bioinf.jku.at/software/farms/farms.html

FARMS Package Version 1.51.0


Changes in FARMS:
For all changes previous to 1.3.0, see the farms vignette.
Version 1.3.0: Added I/NI-calls for filtering
               Adjusted Hyperparameters for alternative CDFs,
               probes set standardized, weighted mean
               Works now with R >= 2.8 and Bioconductor 2.3,
               Changed termination criterion, initialization values,
               factors and loadings scaled, added argument robust
               Update for R-2.11
               Updated I/NI-Call for Laplace-FARMS version,
               Maximum likelihood correlation structure given
               non-negative constraints
Version 1.4.0: Default centering changed to median
Version 1.8.x: Suppression of spurious correlation (Laplace-FARMS)

also installing the dependencies ‘RSQLite’, ‘AnnotationDbi’

trying URL 'https://cloud.r-project.org/src/contrib/RSQLite_2.3.1.tar.gz'
Content type 'application/x-gzip' length 4149793 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/AnnotationDbi_1.61.2.tar.gz'
Content type 'application/x-gzip' length 4359482 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

trying URL 'https://bioconductor.org/packages/3.17/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/RtmpV8LILx/RLIBS_12b8d73a5a678d/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/RtmpV8LILx/RLIBS_12b8d73a5a678d/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/RtmpV8LILx/RLIBS_12b8d73a5a678d/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/RtmpByVDap/downloaded_packages’

Error: processing vignette 'farms.Rnw' failed with diagnostics:
 chunk 3 
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 ‘farms.Rnw’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/farms.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL farms
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘farms’ ...
** using staged installation
** R
** data
** inst
** 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 (farms)