##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:maPredictDSC.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings maPredictDSC_1.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/maPredictDSC.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 ‘maPredictDSC/DESCRIPTION’ ... OK
* this is package ‘maPredictDSC’ version ‘1.48.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.22/data/experiment/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.22/data/experiment/src/contrib/PACKAGES'
 INFO
Depends: includes the non-default packages:
  'MASS', 'affy', 'limma', 'gcrma', 'ROC', 'class', 'e1071', 'caret',
  'hgu133plus2.db', 'ROCR', 'AnnotationDbi', 'LungCancerACvsSCCGEO'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘maPredictDSC’ 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 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 ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘ROC’ ‘ROCR’ ‘affy’ ‘caret’ ‘class’ ‘e1071’ ‘gcrma’ ‘limma’
  Please remove these calls from your code.
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘LungCancerACvsSCCGEO’ ‘ROC’ ‘ROCR’ ‘affy’ ‘caret’ ‘class’ ‘e1071’
  ‘gcrma’ ‘hgu133plus2.db’ ‘limma’
  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
maPredictDSC: no visible global function definition for
  ‘installed.packages’
maPredictDSC: no visible global function definition for ‘ReadAffy’
maPredictDSC: no visible global function definition for ‘rma’
maPredictDSC: no visible global function definition for ‘mas5’
maPredictDSC: no visible global function definition for ‘gcrma’
maPredictDSC: no visible global function definition for ‘exprs’
maPredictDSC: no visible global function definition for ‘mas5calls’
maPredictDSC: no visible global function definition for ‘createFolds’
maPredictDSC : mff: no visible global function definition for
  ‘model.matrix’
maPredictDSC : mff: no visible global function definition for ‘formula’
maPredictDSC : mff: no visible global function definition for ‘lmFit’
maPredictDSC : mff: no visible global function definition for
  ‘makeContrasts’
maPredictDSC : mff: no visible global function definition for
  ‘contrasts.fit’
maPredictDSC : mff: no visible global function definition for ‘eBayes’
maPredictDSC : mff: no visible global function definition for
  ‘topTable’
maPredictDSC : mff: no visible global function definition for ‘pt’
maPredictDSC : mff : wf: no visible global function definition for
  ‘wilcox.test’
maPredictDSC : mff: no visible global function definition for ‘predict’
maPredictDSC : mff: no visible global function definition for ‘knn’
maPredictDSC : mff: no visible global function definition for ‘svm’
maPredictDSC : mff: no visible global function definition for
  ‘rocdemo.sca’
maPredictDSC : mff: no visible binding for global variable ‘dxrule.sca’
maPredictDSC : mff: no visible global function definition for ‘AUC’
maPredictDSC: no visible global function definition for ‘mclapply’
maPredictDSC: no visible global function definition for ‘sd’
maPredictDSC: no visible global function definition for ‘model.matrix’
maPredictDSC: no visible global function definition for ‘formula’
maPredictDSC: no visible global function definition for ‘lmFit’
maPredictDSC: no visible global function definition for ‘makeContrasts’
maPredictDSC: no visible global function definition for ‘contrasts.fit’
maPredictDSC: no visible global function definition for ‘eBayes’
maPredictDSC: no visible global function definition for ‘topTable’
maPredictDSC: no visible global function definition for ‘pt’
maPredictDSC : wf: no visible global function definition for
  ‘wilcox.test’
maPredictDSC: no visible global function definition for ‘predict’
maPredictDSC: no visible global function definition for ‘knn’
maPredictDSC: no visible global function definition for ‘svm’
perfDSC: no visible global function definition for ‘prediction’
perfDSC: no visible global function definition for ‘performance’
perfDSC: no visible global function definition for ‘na.omit’
perfDSC: no visible global function definition for ‘trapezint’
perfDSC: no visible global function definition for ‘rocdemo.sca’
perfDSC: no visible binding for global variable ‘dxrule.sca’
perfDSC: no visible global function definition for ‘AUC’
Undefined global functions or variables:
  AUC ReadAffy contrasts.fit createFolds dxrule.sca eBayes exprs
  formula gcrma installed.packages knn lmFit makeContrasts mas5
  mas5calls mclapply model.matrix na.omit performance predict
  prediction pt rma rocdemo.sca sd svm topTable trapezint wilcox.test
Consider adding
  importFrom("stats", "formula", "model.matrix", "na.omit", "predict",
             "pt", "sd", "wilcox.test")
  importFrom("utils", "installed.packages")
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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘maPredictDSC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predictDSC
> ### Title: Phenotype prediction using microarray data: approach of the best
> ###   overall team in the IMPROVER Diagnostic Signature Challenge
> ### Aliases: predictDSC
> ### Keywords: parametric methods
> 
> ### ** Examples
> 
> 
> library(maPredictDSC)
> library(LungCancerACvsSCCGEO)
> data(LungCancerACvsSCCGEO)
> anoLC
              files group
1  GSM137916.CEL.gz    AC
2  GSM258560.CEL.gz    AC
3  GSM258579.CEL.gz    AC
4  GSM258589.CEL.gz    AC
5  GSM258598.CEL.gz    AC
6  GSM353885.CEL.gz    AC
7  GSM467021.CEL.gz    AC
8  GSM152624.CEL.gz   SCC
9  GSM258580.CEL.gz   SCC
10 GSM277678.CEL.gz   SCC
11 GSM466956.CEL.gz   SCC
12 GSM466980.CEL.gz   SCC
13 GSM466989.CEL.gz   SCC
14 GSM467023.CEL.gz   SCC
15  GSM46976.CEL.gz   SCC
16     lung_100.CEL  Test
17     lung_107.CEL  Test
18     lung_111.CEL  Test
19      lung_15.CEL  Test
20     lung_150.CEL  Test
21      lung_29.CEL  Test
22      lung_30.CEL  Test
23      lung_35.CEL  Test
24      lung_40.CEL  Test
25      lung_41.CEL  Test
26      lung_50.CEL  Test
27      lung_51.CEL  Test
28      lung_59.CEL  Test
29      lung_62.CEL  Test
30       lung_8.CEL  Test
> gsLC
             SCC AC
lung_15.CEL    1  0
lung_29.CEL    0  1
lung_30.CEL    0  1
lung_59.CEL    0  1
lung_51.CEL    1  0
lung_100.CEL   1  0
lung_62.CEL    1  0
lung_8.CEL     1  0
lung_41.CEL    0  1
lung_40.CEL    1  0
lung_150.CEL   1  0
lung_111.CEL   1  0
lung_35.CEL    0  1
lung_107.CEL   1  0
lung_50.CEL    0  1
> table(anoLC$group)

  AC  SCC Test 
   7    8   15 
> 
> #run a series of methods combinations
> modlist=predictDSC(ano=anoLC,celfile.path=system.file("extdata/lungcancer",package="LungCancerACvsSCCGEO"),
+ annotation="hgu133plus2.db",
+ preprocs=c("rma"),filters=c("mttest","wilcox"),FCT=1.0,classifiers=c("LDA","kNN"),
+ CVP=2,NF=4, NR=1)
Loading required package: parallel
trying URL 'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/hgu133plus2cdf_2.18.0.tar.gz'
Warning in download.file(urls, destfiles, "libcurl", mode = "wb", ...) :
  URL 'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/hgu133plus2cdf_2.18.0.tar.gz': status was 'SSL connect error'
Error in download.file(urls, destfiles, "libcurl", mode = "wb", ...) : 
  cannot open URL 'https://bioconductor.org/packages/3.22/data/annotation/src/contrib/hgu133plus2cdf_2.18.0.tar.gz'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘hgu133plus2cdf’ failed
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain HG-U133_Plus_2
Library - package hgu133plus2cdf not installed
Library - package hgu133plus2cdf not installed
Calls: predictDSC ... .local -> indexProbes -> indexProbes -> .local -> getCdfInfo
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘maPredictDSC.Rnw’ using Sweave
Loading required package: MASS
Loading required package: affy
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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: limma

Attaching package: ‘limma’

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

    plotMA

Loading required package: gcrma
Loading required package: ROC
Loading required package: class
Loading required package: e1071

Attaching package: ‘e1071’

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

    interpolate

Loading required package: caret
Loading required package: ggplot2

Attaching package: ‘ggplot2’

The following object is masked from ‘package:e1071’:

    element

Loading required package: lattice

Attaching package: ‘caret’

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

    train

Loading required package: hgu133plus2.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

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

    findMatches

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

    I, expand.grid, unname


Attaching package: ‘AnnotationDbi’

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

    select

Loading required package: org.Hs.eg.db


Loading required package: ROCR
Loading required package: LungCancerACvsSCCGEO
Loading required package: parallel
Warning in download.file(..., destfile = tmp_config, quiet = TRUE) :
  URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'
Warning in download.file(..., destfile = tmp_config, quiet = TRUE) :
  URL 'https://bioconductor.org/config.yaml': status was 'SSL connect error'

Error: processing vignette 'maPredictDSC.Rnw' failed with diagnostics:
 chunk 2 
Error : Bioconductor version cannot be validated; no internet connection?  See
  #troubleshooting section in vignette

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

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

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/maPredictDSC.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL maPredictDSC
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘maPredictDSC’ ...
** this is package ‘maPredictDSC’ version ‘1.48.0’
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (maPredictDSC)