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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:LMGene.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings LMGene_2.44.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/LMGene.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LMGene/DESCRIPTION’ ... OK
* this is package ‘LMGene’ version ‘2.44.0’
* 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 ‘LMGene’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'LMGene' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.11-bioc/meat/LMGene.Rcheck/00install.out’ for details.
* 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.
* 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘multtest’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘affy’ ‘multtest’ ‘survival’
  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
GetLMObj: no visible global function definition for ‘exprs’
GetLMObj: no visible global function definition for ‘varLabels’
GetLMObj: no visible global function definition for ‘as.formula’
GetLMObj: no visible global function definition for ‘lm’
GetLMObj: no visible global function definition for ‘pData’
LMGene: no visible global function definition for ‘exprs’
arrayGlogSDStability: no visible global function definition for ‘exprs’
arrayGlogSDStability: no visible global function definition for ‘pData’
arrayGlogSDStability: no visible binding for global variable ‘sd’
arrayGlogSDStability : pooled.sd: no visible global function definition
  for ‘var’
arrayGlogSDStability: no visible global function definition for ‘lm’
arrayGlogSDStability: no visible global function definition for ‘coef’
fitFDist: no visible global function definition for ‘median’
fitScaledF : like: no visible global function definition for ‘df’
fitScaledF: no visible global function definition for ‘optim’
genediff: no visible global function definition for ‘exprs’
genediff: no visible global function definition for ‘varLabels’
genediff : owaov: no visible global function definition for
  ‘as.formula’
genediff : owaov: no visible global function definition for ‘anova’
genediff : owaov: no visible global function definition for ‘lm’
genediff : owaov: no visible global function definition for ‘pData’
genediff: no visible global function definition for ‘median’
genediff: no visible global function definition for ‘var’
genediff: no visible global function definition for ‘pf’
lnorm : lcol: no visible global function definition for ‘lowess’
lnormeS: no visible global function definition for ‘exprs’
lnormeS: no visible global function definition for ‘exprs<-’
msecalc: no visible global function definition for ‘exprs’
msecalcmult: no visible global function definition for ‘exprs’
neweS: no visible global function definition for ‘new’
neweS: no visible global function definition for ‘pData<-’
neweS: no visible global function definition for ‘varLabels<-’
plotMeanSD: no visible global function definition for ‘exprs’
plotMeanSD : msd.row: no visible binding for global variable ‘var’
plotMeanSD: no visible global function definition for ‘lines’
plotMeanSD: no visible global function definition for ‘lowess’
psmeans: no visible global function definition for ‘exprs’
psmeans: no visible global function definition for ‘pData’
pvadjust: no visible global function definition for ‘mt.rawp2adjp’
rowaov: no visible global function definition for ‘exprs’
rowaov: no visible global function definition for ‘varLabels’
rowaov: no visible global function definition for ‘pData’
rowaov: no visible global function definition for ‘as.formula’
rowaov: no visible global function definition for ‘lm’
rowaov: no visible global function definition for ‘anova’
tranest: no visible global function definition for ‘exprs’
tranest: no visible global function definition for ‘new’
tranest: no visible global function definition for ‘phenoData’
tranest2: no visible global function definition for ‘exprs’
tranest2: no visible global function definition for ‘median’
tranest2: no visible global function definition for ‘quantile’
tranest2: no visible global function definition for ‘nlm’
tranest2: no visible global function definition for ‘optim’
tranestAffyProbeLevel: no visible global function definition for
  ‘featureNames’
tranestAffyProbeLevel: no visible global function definition for ‘pm’
tranestAffyProbeLevel: no visible global function definition for
  ‘exprs<-’
tranestAffyProbeLevel: no visible global function definition for
  ‘exprs’
tranestmult: no visible global function definition for ‘exprs’
tranestmult: no visible global function definition for ‘median’
tranestmult: no visible global function definition for ‘nlm’
tranestmult: no visible global function definition for ‘optim’
transeS: no visible global function definition for ‘exprs’
transeS: no visible global function definition for ‘exprs<-’
Undefined global functions or variables:
  anova as.formula coef df exprs exprs<- featureNames lines lm lowess
  median mt.rawp2adjp new nlm optim pData pData<- pf phenoData pm
  quantile sd var varLabels varLabels<-
Consider adding
  importFrom("graphics", "lines")
  importFrom("methods", "new")
  importFrom("stats", "anova", "as.formula", "coef", "df", "lm",
             "lowess", "median", "nlm", "optim", "pf", "quantile", "sd",
             "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 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 ... ERROR
Running examples in ‘LMGene-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lnorm
> ### Title: Lowess normalization function
> ### Aliases: lnorm
> ### Keywords: smooth
> 
> ### ** Examples
> 
> library(Biobase)
> library(LMGene)
> 
> #data
> data(sample.mat)
> data(vlist)
> 
> raw.eS <- neweS(sample.mat, vlist)
> 
> # glog transform data
> trans.eS <- transeS(raw.eS, lambda = 727, alpha = 56)
> 
> # normalize
> normed.exprs <- lnorm(exprs(trans.eS))
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
LMGene
 --- call from context --- 
lnorm(exprs(trans.eS))
 --- call from argument --- 
if (class(mat1) == "ExpressionSet") {
    stop("'mat1' may not be of class 'ExpressionSet'.  use function 'lnormeS' instead")
}
 --- R stacktrace ---
where 1: lnorm(exprs(trans.eS))

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (mat1, span = 0.1) 
{
    if (class(mat1) == "ExpressionSet") {
        stop("'mat1' may not be of class 'ExpressionSet'.  use function 'lnormeS' instead")
    }
    mat2 <- as.matrix(mat1)
    p <- dim(mat2)[1]
    n <- dim(mat2)[2]
    rmeans <- apply(mat2, 1, mean)
    rranks <- rank(rmeans, ties.method = "first")
    matsort <- mat2[order(rranks), ]
    r0 <- 1:p
    lcol <- function(x) {
        lx <- lowess(r0, x, f = span)$y
    }
    lmeans <- apply(matsort, 2, lcol)
    lgrand <- apply(lmeans, 1, mean)
    lgrand <- matrix(rep(lgrand, n), byrow = FALSE, ncol = n)
    matnorm0 <- matsort - lmeans + lgrand
    matnorm1 <- matnorm0[rranks, ]
    return(matnorm1)
}
<bytecode: 0x5592bfe0af30>
<environment: namespace:LMGene>
 --- function search by body ---
Function lnorm in namespace LMGene has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/LMGene.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL LMGene
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘LMGene’ ...
** 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
Warning: Package 'LMGene' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'LMGene' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (LMGene)