Multiple platform build/check report for BioC 3.11 - CHECK report for LMGene on tokay2

Package: LMGene

Version: 2.44.0

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LMGene.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings LMGene_2.44.0.tar.gz

StartedAt: 2020-10-17 05:32:22 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 05:33:48 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 86.2 seconds

RetCode: 1

Status: ERROR

CheckDir: LMGene.Rcheck

Warnings: NA

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:LMGene.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings LMGene_2.44.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/LMGene.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'LMGene' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'LMGene' is deprecated and will be removed from Bioconductor
See 'C:/Users/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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... 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: 0x0a699db0>
<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

** running examples for arch 'x64' ... 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: 0x0000000010016a90>
<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: 2 ERRORs, 1 WARNING, 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/LMGene.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/LMGene_2.44.0.tar.gz && rm -rf LMGene.buildbin-libdir && mkdir LMGene.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=LMGene.buildbin-libdir LMGene_2.44.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL LMGene_2.44.0.zip && rm LMGene_2.44.0.tar.gz LMGene_2.44.0.zip
###
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100 98001  100 98001    0     0  1708k      0 --:--:-- --:--:-- --:--:-- 1953k

install for i386

* installing *source* package 'LMGene' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'LMGene'
    finding HTML links ... done
    LMGene                                  html  
    genediff                                html  
    glog                                    html  
    lnorm                                   html  
    lnormeS                                 html  
    neweS                                   html  
    norm                                    html  
    plotMeanSD                              html  
    psmeans                                 html  
    pvadjust                                html  
    rowaov                                  html  
    sample.eS                               html  
    sample.ind                              html  
    sample.mat                              html  
    tranest                                 html  
    tranestAffyProbeLevel                   html  
    transeS                                 html  
    vlist                                   html  
** 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

install for x64

* installing *source* package 'LMGene' ...
** testing if installed package can be loaded
Warning: Package 'LMGene' is deprecated and will be removed from Bioconductor
  version 3.12
* MD5 sums
packaged installation of 'LMGene' as LMGene_2.44.0.zip
* DONE (LMGene)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'LMGene' successfully unpacked and MD5 sums checked

CHECK report for LMGene on tokay2

Summary

Command output

Installation output

Tests output

Example timings