Back to Multiple platform build/check report for BioC 3.12
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for CGEN on tokay1

This page was generated on 2020-08-13 11:35:44 -0400 (Thu, 13 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CGEN PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 255/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGEN 3.25.1
William Wheeler
Snapshot Date: 2020-08-12 14:52:00 -0400 (Wed, 12 Aug 2020)
URL: https://git.bioconductor.org/packages/CGEN
Branch: master
Last Commit: adf5934
Last Changed Date: 2020-06-01 09:59:32 -0400 (Mon, 01 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  ERROR 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  ERROR  OK 

Summary

Package: CGEN
Version: 3.25.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CGEN.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CGEN_3.25.1.tar.gz
StartedAt: 2020-08-13 00:41:29 -0400 (Thu, 13 Aug 2020)
EndedAt: 2020-08-13 00:43:38 -0400 (Thu, 13 Aug 2020)
EllapsedTime: 129.2 seconds
RetCode: 1
Status:  ERROR  
CheckDir: CGEN.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CGEN.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings CGEN_3.25.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CGEN.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CGEN/DESCRIPTION' ... OK
* this is package 'CGEN' version '3.25.1'
* 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 'CGEN' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'CGEN' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/CGEN.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
  GPL-2 + file LICENSE
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GC.adj.pvalues: no visible global function definition for 'pnorm'
GC.adj.pvalues: no visible global function definition for 'pchisq'
GxE.setup.1: no visible global function definition for 'glm'
GxE.setup.1: no visible global function definition for 'binomial'
GxE.setup.1_2: no visible global function definition for 'rbinom'
GxE.setup.2: no visible global function definition for 'glm'
GxE.setup.2: no visible global function definition for 'binomial'
GxE.setup.3: no visible global function definition for 'glm'
GxE.setup.3: no visible global function definition for 'binomial'
GxE.setup.3a: no visible global function definition for 'glm'
GxE.setup.3a: no visible global function definition for 'binomial'
GxE.setup.3a: no visible global function definition for 'fitted'
GxE.setup.4: no visible global function definition for 'rbinom'
Manhattan.plot: no visible global function definition for
  'split.screen'
Manhattan.plot: no visible global function definition for 'screen'
Manhattan.plot: no visible global function definition for
  'close.screen'
Modified_Wald_Test: no visible global function definition for 'var'
Modified_Wald_Test: no visible global function definition for 'pchisq'
OR.plot.main: no visible global function definition for 'polygon'
OR.plot.main: no visible global function definition for 'lines'
OR.plot.main: no visible global function definition for 'axis'
OR.plot.main: no visible global function definition for 'box'
QQ.plot: no visible global function definition for 'split.screen'
QQ.plot: no visible global function definition for 'screen'
QQ.plot: no visible global function definition for 'axis'
QQ.plot: no visible global function definition for 'box'
QQ.plot: no visible global function definition for 'abline'
QQ.plot: no visible global function definition for 'qchisq'
QQ.plot: no visible global function definition for 'text'
QQ.plot: no visible global function definition for 'points'
QQ.plot: no visible global function definition for 'close.screen'
QQ.plot2: no visible global function definition for 'qchisq'
QQ.plot2: no visible global function definition for 'axis'
QQ.plot2: no visible global function definition for 'box'
QQ.plot2: no visible global function definition for 'title'
QQ.plot2: no visible global function definition for 'abline'
QQ.plot_old0: no visible global function definition for 'axis'
QQ.plot_old0: no visible global function definition for 'box'
QQ.plot_old0: no visible global function definition for 'title'
QQ.plot_old0: no visible global function definition for 'abline'
QQ.plot_old0: no visible global function definition for 'points'
RERI.AP.S: no visible global function definition for 'glm'
RERI.AP.S: no visible binding for global variable 'binomial'
RERI.AP.S.small: no visible global function definition for 'qnorm'
RERI.AP.S.small: no visible global function definition for 'vcov'
RERI.AP.S.small: no visible global function definition for 'pnorm'
RERI.AP.S_retro: no visible global function definition for 'qnorm'
RERI.AP.S_retro: no visible global function definition for 'pnorm'
addLineSegments: no visible global function definition for 'segments'
additiveTest.small: no visible global function definition for 'glm'
additiveTest.small: no visible global function definition for
  'binomial'
additiveTest.small: no visible global function definition for 'vcov'
additiveTest.small: no visible global function definition for 'pchisq'
additiveTest.small: no visible global function definition for 'optim'
applyFormulas: no visible global function definition for 'model.matrix'
callGLM: no visible global function definition for 'glm'
ccmatch: no visible global function definition for 'as.dist'
chrm.plot.main: no visible global function definition for 'axis'
chrm.plot.main: no visible global function definition for 'box'
chrm.plot.main: no visible global function definition for 'points'
chrm.plot.main: no visible global function definition for 'abline'
convertParams3: no visible global function definition for 'qnorm'
convertParams3: no visible global function definition for 'pnorm'
create.formula: no visible global function definition for 'as.formula'
crossTab: no visible binding for global variable 'data'
dsgnMat: no visible global function definition for 'as.formula'
dsgnMat: no visible global function definition for 'model.matrix'
gene.plot: no visible global function definition for 'split.screen'
gene.plot: no visible global function definition for 'screen'
gene.plot.main: no visible global function definition for 'axis'
gene.plot.main: no visible global function definition for 'box'
gene.plot.main: no visible global function definition for 'points'
gene.plot.main: no visible global function definition for 'abline'
gene.plot.main: no visible global function definition for 'mtext'
getCI: no visible global function definition for 'qnorm'
getColors: no visible global function definition for 'colors'
getColors: no visible global function definition for 'pie'
getDesignMatrix: no visible global function definition for
  'model.matrix'
getMAF.control: no visible global function definition for 'read.table'
getMatchedSets: no visible global function definition for 'as.dist'
getMatchedSets: no visible global function definition for 'dist'
getOR.CI: no visible global function definition for 'qnorm'
getPermutation: no visible global function definition for 'rbinom'
getSummary: no visible global function definition for 'pnorm'
getSummary.main: no visible global function definition for 'pnorm'
glu.LD.snps: no visible global function definition for 'read.table'
glu.create_ped: no visible global function definition for 'write.table'
glu.ldMatrix: no visible global function definition for 'read.table'
glu.nBins: no visible global function definition for 'read.table'
glu.r2: no visible global function definition for 'read.table'
her2.log: no visible global function definition for 'dnorm'
her2.log: no visible global function definition for 'qnorm'
heterTest: no visible global function definition for 'glm'
impute.R2.file: no visible global function definition for 'cor'
inflationFactor: no visible global function definition for 'qchisq'
inflationFactor: no visible global function definition for 'median'
info.small_probit: no visible global function definition for 'dnorm'
likelihoodRatio.main: no visible global function definition for
  'pchisq'
logistic.dsgnMat: no visible global function definition for
  'model.matrix'
myMatrixPlot: no visible global function definition for 'layout'
myMatrixPlot: no visible global function definition for 'rgb'
myMatrixPlot: no visible global function definition for 'par'
myMatrixPlot: no visible global function definition for 'image'
myMatrixPlot: no visible global function definition for 'axis'
myPlot_OR_E: no visible global function definition for 'lines'
myPlot_genScoreCompare: no visible global function definition for
  'qqplot'
myPlot_genScoreCompare: no visible global function definition for
  'abline'
myPlot_genScoreCompare: no visible global function definition for
  'legend'
myStrat.inter.OR.CI4: no visible global function definition for 'glm'
myStrat.inter.OR.CI4: no visible global function definition for
  'binomial'
myStrat.inter.OR.CI4: no visible global function definition for 'vcov'
myrmvnorm: no visible global function definition for 'rnorm'
nnmatch: no visible global function definition for 'cutree'
partialDeriv.P.betas: no visible global function definition for 'dnorm'
postEps.small: no visible global function definition for 'dnorm'
postEps.small: no visible global function definition for 'pnorm'
printEffects: no visible global function definition for 'ftable'
probit.retro: no visible global function definition for 'pnorm'
pvalue.normal: no visible global function definition for 'pnorm'
readTable: no visible global function definition for 'read.table'
riskAdd_LT: no visible global function definition for 'pnorm'
riskAdd_LT2: no visible global function definition for 'pnorm'
riskAdd_LT3: no visible global function definition for 'pnorm'
riskAdd_LT_general: no visible global function definition for 'pnorm'
save.plot: no visible global function definition for 'savePlot'
scan.UML_CML: no visible global function definition for 'rbinom'
scan.UML_CML: no visible global function definition for 'addmargins'
scan.lin_log: no visible global function definition for 'lm'
scan.lin_log: no visible global function definition for 'glm'
scan.lin_log: no visible global function definition for 'binomial'
score.logReg: no visible global function definition for 'pchisq'
score.wald: no visible global function definition for 'glm'
score.wald: no visible global function definition for 'binomial'
score.wald: no visible global function definition for 'fitted'
scoreTest.general9: no visible global function definition for 'glm'
scoreTest.general9: no visible global function definition for
  'binomial'
scoreTest.general9: no visible global function definition for 'pchisq'
scoreTest.general9: no visible global function definition for 'qnorm'
scoreTest.general9: no visible global function definition for 'pnorm'
scoreTest.general9: no visible global function definition for 'coef'
scoreTest.general9: no visible global function definition for 'vcov'
scoreTest.small.logit5.max: no visible global function definition for
  'pchisq'
scoreTest.small.logit5.max: no visible global function definition for
  'cov2cor'
scoreTest.small.logit5.max.indep6: no visible global function
  definition for 'pchisq'
scoreTest.small.logit5.max.indep6: no visible global function
  definition for 'cov2cor'
set.plot: no visible global function definition for 'bitmap'
setDevice: no visible global function definition for 'postscript'
setDevice: no visible global function definition for 'pdf'
setDevice: no visible global function definition for 'jpeg'
setDevice: no visible global function definition for 'graphics.off'
setDevice: no visible global function definition for 'savePlot'
setup.lin_log: no visible global function definition for 'lm'
setup.lin_log: no visible global function definition for 'glm'
setup.lin_log: no visible global function definition for 'binomial'
snp.ccl.main: no visible global function definition for 'aggregate'
snp.ccl.main: no visible global function definition for 'as.formula'
snp.ccl.main: no visible global function definition for 'runif'
snp.effects.plot: no visible global function definition for
  'split.screen'
snp.effects.plot: no visible global function definition for 'screen'
snp.effects.plot: no visible global function definition for
  'close.screen'
snp.hcl.main: no visible global function definition for 'glm'
snp.hcl.main: no visible global function definition for 'as.formula'
snp.hcl.main: no visible global function definition for 'binomial'
snp.main : getInit: no visible global function definition for
  'as.formula'
snp.main : getInit: no visible global function definition for 'glm'
snp.main : getInit: no visible global function definition for
  'binomial'
snp.main : callOptim: no visible global function definition for 'optim'
snp.scan.logistic : outputRow: no visible global function definition
  for 'pnorm'
snp.scan.logistic: no visible global function definition for 'binomial'
snpPlot3: no visible global function definition for 'par'
snpPlot3: no visible global function definition for 'lines'
snpPlot3: no visible global function definition for 'axis'
snpPlot3: no visible global function definition for 'abline'
snpPlot3: no visible global function definition for 'points'
standardize.z: no visible global function definition for 'var'
unadjustedGLM.counts: no visible global function definition for 'glm'
unadjustedGLM.counts: no visible binding for global variable 'binomial'
unadjustedGLM.counts: no visible global function definition for
  'write.table'
wald.test: no visible global function definition for 'pchisq'
wald.test: no visible global function definition for 'pf'
wald.weight.indep: no visible global function definition for 'pnorm'
wald.weight.indep: no visible global function definition for 'glm'
wald.weight.indep: no visible global function definition for 'binomial'
waldTest.main: no visible global function definition for 'pnorm'
waldTest.main: no visible global function definition for 'pchisq'
writeTable: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline addmargins aggregate as.dist as.formula axis binomial bitmap
  box close.screen coef colors cor cov2cor cutree data dist dnorm
  fitted ftable glm graphics.off image jpeg layout legend lines lm
  median model.matrix mtext optim par pchisq pdf pf pie pnorm points
  polygon postscript qchisq qnorm qqplot rbinom read.table rgb rnorm
  runif savePlot screen segments split.screen text title var vcov
  write.table
Consider adding
  importFrom("grDevices", "bitmap", "colors", "graphics.off", "jpeg",
             "pdf", "postscript", "rgb", "savePlot")
  importFrom("graphics", "abline", "axis", "box", "close.screen",
             "image", "layout", "legend", "lines", "mtext", "par", "pie",
             "points", "polygon", "screen", "segments", "split.screen",
             "text", "title")
  importFrom("stats", "addmargins", "aggregate", "as.dist", "as.formula",
             "binomial", "coef", "cor", "cov2cor", "cutree", "dist",
             "dnorm", "fitted", "ftable", "glm", "lm", "median",
             "model.matrix", "optim", "pchisq", "pf", "pnorm", "qchisq",
             "qnorm", "qqplot", "rbinom", "rnorm", "runif", "var",
             "vcov")
  importFrom("utils", "data", "read.table", "write.table")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/CGEN/libs/i386/CGEN.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/CGEN/libs/x64/CGEN.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'CGEN-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: additive.test
> ### Title: A test for gene-environment interaction under an additive risk
> ###   model for case-control data
> ### Aliases: additive.test
> ### Keywords: models
> 
> ### ** Examples
> 
>  # Use the ovarian cancer data
>  data(Xdata, package="CGEN")
> 
>  table(Xdata[, "gynSurgery.history"])

   0    2 
1396  183 
> 
>  # Recode the exposure variable so that it is 0-1
>  temp <- Xdata[, "gynSurgery.history"] == 2
>  Xdata[temp, "gynSurgery.history"] <- 1 
> 
>  # Standard likelihood (indep = FALSE by default)
>  out1 <- additive.test(Xdata, "case.control", "BRCA.status", "gynSurgery.history", 
+                main.vars=c("n.children","oral.years"), op=list(genetic.model=1))
Warning in additive.test(Xdata, "case.control", "BRCA.status", "gynSurgery.history",  :
  SNP only has 2 levels. Changing genetic.model.
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
CGEN
 --- call from context --- 
waldTest.main(estcov$estimates, estcov$cov, parmNames)
 --- call from argument --- 
if (class(temp) == "try-error") {
    return(list(test = NA, df = np, pvalue = NA))
}
 --- R stacktrace ---
where 1: waldTest.main(estcov$estimates, estcov$cov, parmNames)
where 2: getWaldTest(FULL, bNames[-1])
where 3: additiveTest.small(y, x1, x2, covs, method, optim.method, control, 
    indep, x.st, strDat, use.C.code = use.C.code, genetic.model = genetic.model, 
    snp.orig = snp.orig)
where 4: additiveTest(Y, snp, exv, design.X0, method, indep = op$indep, 
    X.st = strataVec, control = list(maxit = op$maxit, reltol = op$reltol), 
    optim.method = op$optim.method, use.C.code = op$use.C.code, 
    genetic.model = op$genetic.model)
where 5: additive.test(Xdata, "case.control", "BRCA.status", "gynSurgery.history", 
    main.vars = c("n.children", "oral.years"), op = list(genetic.model = 1))

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (parms, cov, parmNames) 
{
    df <- length(parmNames)
    nrcov <- nrow(cov)
    vnames <- names(parms)
    if (is.numeric(parmNames)) {
        temp <- parmNames %in% 1:nrcov
        vpos <- parmNames[temp]
        np <- length(vpos)
        if (!np) 
            return(list(test = NA, df = 0, pvalue = NA))
        parms <- parms[vpos]
        cov <- cov[vpos, vpos]
    }
    else {
        vnames <- vnames[vnames %in% parmNames]
        parms <- parms[vnames]
        temp <- !is.na(parms)
        parms <- parms[temp]
        vnames <- vnames[temp]
        np <- length(parms)
        if (!np) 
            return(list(test = NA, df = 0, pvalue = NA))
        cov <- cov[vnames, vnames]
    }
    if (np == 1) {
        test <- parms/sqrt(cov)
        pvalue <- 2 * pnorm(abs(test), lower.tail = FALSE)
        return(list(test = test, df = np, pvalue = pvalue))
    }
    temp <- try(solve(cov), silent = TRUE)
    if (class(temp) == "try-error") {
        return(list(test = NA, df = np, pvalue = NA))
    }
    dim(parms) <- c(np, 1)
    test <- t(parms) %*% temp %*% parms
    dim(test) <- NULL
    if (test >= 0) {
        pvalue <- pchisq(test, df = np, lower.tail = FALSE)
    }
    else {
        pvalue <- NA
    }
    list(test = test, df = np, pvalue = pvalue)
}
<bytecode: 0x0d0ab6f0>
<environment: namespace:CGEN>
 --- function search by body ---
Function waldTest.main in namespace CGEN has this body.
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: the condition has length > 1

** running examples for arch 'x64' ... ERROR
Running examples in 'CGEN-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: additive.test
> ### Title: A test for gene-environment interaction under an additive risk
> ###   model for case-control data
> ### Aliases: additive.test
> ### Keywords: models
> 
> ### ** Examples
> 
>  # Use the ovarian cancer data
>  data(Xdata, package="CGEN")
> 
>  table(Xdata[, "gynSurgery.history"])

   0    2 
1396  183 
> 
>  # Recode the exposure variable so that it is 0-1
>  temp <- Xdata[, "gynSurgery.history"] == 2
>  Xdata[temp, "gynSurgery.history"] <- 1 
> 
>  # Standard likelihood (indep = FALSE by default)
>  out1 <- additive.test(Xdata, "case.control", "BRCA.status", "gynSurgery.history", 
+                main.vars=c("n.children","oral.years"), op=list(genetic.model=1))
Warning in additive.test(Xdata, "case.control", "BRCA.status", "gynSurgery.history",  :
  SNP only has 2 levels. Changing genetic.model.
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
CGEN
 --- call from context --- 
waldTest.main(estcov$estimates, estcov$cov, parmNames)
 --- call from argument --- 
if (class(temp) == "try-error") {
    return(list(test = NA, df = np, pvalue = NA))
}
 --- R stacktrace ---
where 1: waldTest.main(estcov$estimates, estcov$cov, parmNames)
where 2: getWaldTest(FULL, bNames[-1])
where 3: additiveTest.small(y, x1, x2, covs, method, optim.method, control, 
    indep, x.st, strDat, use.C.code = use.C.code, genetic.model = genetic.model, 
    snp.orig = snp.orig)
where 4: additiveTest(Y, snp, exv, design.X0, method, indep = op$indep, 
    X.st = strataVec, control = list(maxit = op$maxit, reltol = op$reltol), 
    optim.method = op$optim.method, use.C.code = op$use.C.code, 
    genetic.model = op$genetic.model)
where 5: additive.test(Xdata, "case.control", "BRCA.status", "gynSurgery.history", 
    main.vars = c("n.children", "oral.years"), op = list(genetic.model = 1))

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (parms, cov, parmNames) 
{
    df <- length(parmNames)
    nrcov <- nrow(cov)
    vnames <- names(parms)
    if (is.numeric(parmNames)) {
        temp <- parmNames %in% 1:nrcov
        vpos <- parmNames[temp]
        np <- length(vpos)
        if (!np) 
            return(list(test = NA, df = 0, pvalue = NA))
        parms <- parms[vpos]
        cov <- cov[vpos, vpos]
    }
    else {
        vnames <- vnames[vnames %in% parmNames]
        parms <- parms[vnames]
        temp <- !is.na(parms)
        parms <- parms[temp]
        vnames <- vnames[temp]
        np <- length(parms)
        if (!np) 
            return(list(test = NA, df = 0, pvalue = NA))
        cov <- cov[vnames, vnames]
    }
    if (np == 1) {
        test <- parms/sqrt(cov)
        pvalue <- 2 * pnorm(abs(test), lower.tail = FALSE)
        return(list(test = test, df = np, pvalue = pvalue))
    }
    temp <- try(solve(cov), silent = TRUE)
    if (class(temp) == "try-error") {
        return(list(test = NA, df = np, pvalue = NA))
    }
    dim(parms) <- c(np, 1)
    test <- t(parms) %*% temp %*% parms
    dim(test) <- NULL
    if (test >= 0) {
        pvalue <- pchisq(test, df = np, lower.tail = FALSE)
    }
    else {
        pvalue <- NA
    }
    list(test = test, df = np, pvalue = pvalue)
}
<bytecode: 0x0000000013c45128>
<environment: namespace:CGEN>
 --- function search by body ---
Function waldTest.main in namespace CGEN 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-3.12-bioc/meat/CGEN.Rcheck/00check.log'
for details.


Installation output

CGEN.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/CGEN_3.25.1.tar.gz && rm -rf CGEN.buildbin-libdir && mkdir CGEN.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CGEN.buildbin-libdir CGEN_3.25.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CGEN_3.25.1.zip && rm CGEN_3.25.1.tar.gz CGEN_3.25.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 79  641k   79  512k    0     0  3823k      0 --:--:-- --:--:-- --:--:-- 3908k
100  641k  100  641k    0     0  4751k      0 --:--:-- --:--:-- --:--:-- 4860k

install for i386

* installing *source* package 'CGEN' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Additive.c -o Additive.o
Additive.c: In function 'compute_g':
Additive.c:233:19: warning: 'et22' may be used uninitialized in this function [-Wmaybe-uninitialized]
       x    = et12 + et22 - 1;
              ~~~~~^~~~~~
Additive.c:235:25: warning: 't22' may be used uninitialized in this function [-Wmaybe-uninitialized]
       *g22 = logx - t12 - t22;
              ~~~~~~~~~~~^~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CML.c -o CML.o
CML.c:132:13: warning: 'print_dVec' defined but not used [-Wunused-function]
 static void print_dVec(vec, n, name)
             ^~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ccl.c -o ccl.o
ccl.c:386:13: warning: 'tree_print' defined but not used [-Wunused-function]
 static void tree_print(tnode *node, int is_root)
             ^~~~~~~~~~
"C:/rtools40/mingw32/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign -c csclust.f -o csclust.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fsclust.c -o fsclust.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hcl.c -o hcl.o
hcl.c:375:13: warning: 'tree_print' defined but not used [-Wunused-function]
 static void tree_print(tnode *node, int is_root)
             ^~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pmatch.c -o pmatch.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c score.c -o score.o
score.c: In function 'infoSmallStandard':
score.c:18:27: warning: unused variable 'ii' [-Wunused-variable]
   int  nr, nc, i, j, row, ii, nc2;
                           ^~
score.c: In function 'getScoreEB':
score.c:183:21: warning: unused variable 'p6' [-Wunused-variable]
   double *p4, *p5, *p6;
                     ^~
score.c:183:16: warning: unused variable 'p5' [-Wunused-variable]
   double *p4, *p5, *p6;
                ^~
score.c:183:11: warning: unused variable 'p4' [-Wunused-variable]
   double *p4, *p5, *p6;
           ^~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o CGEN.dll tmp.def Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/CGEN.buildbin-libdir/00LOCK-CGEN/00new/CGEN/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CGEN'
    finding HTML links ... done
    CGEN                                    html  
    GxE.scan                                html  
    GxE.scan.combine                        html  
    GxE.scan.partition                      html  
    LocusMapData                            html  
    QQ.plot                                 html  
    Xdata                                   html  
    additive.test                           html  
    chromosome.plot                         html  
    getMatchedSets                          html  
    getSummary                              html  
    getWaldTest                             html  
    locusMap.list                           html  
    pheno.list                              html  
    printEffects                            html  
    snp.effects                             html  
    snp.effects.plot                        html  
    snp.list                                html  
    snp.logistic                            html  
    snp.matched                             html  
    snp.score                               html  
    subject.list                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'CGEN' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'CGEN' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CGEN' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Additive.c -o Additive.o
Additive.c: In function 'compute_g':
Additive.c:233:19: warning: 'et22' may be used uninitialized in this function [-Wmaybe-uninitialized]
       x    = et12 + et22 - 1;
              ~~~~~^~~~~~
Additive.c:235:25: warning: 't22' may be used uninitialized in this function [-Wmaybe-uninitialized]
       *g22 = logx - t12 - t22;
              ~~~~~~~~~~~^~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c CML.c -o CML.o
CML.c:132:13: warning: 'print_dVec' defined but not used [-Wunused-function]
 static void print_dVec(vec, n, name)
             ^~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c ccl.c -o ccl.o
ccl.c:386:13: warning: 'tree_print' defined but not used [-Wunused-function]
 static void tree_print(tnode *node, int is_root)
             ^~~~~~~~~~
"C:/rtools40/mingw64/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign -c csclust.f -o csclust.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fsclust.c -o fsclust.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hcl.c -o hcl.o
hcl.c:375:13: warning: 'tree_print' defined but not used [-Wunused-function]
 static void tree_print(tnode *node, int is_root)
             ^~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pmatch.c -o pmatch.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c score.c -o score.o
score.c: In function 'infoSmallStandard':
score.c:18:27: warning: unused variable 'ii' [-Wunused-variable]
   int  nr, nc, i, j, row, ii, nc2;
                           ^~
score.c: In function 'getScoreEB':
score.c:183:21: warning: unused variable 'p6' [-Wunused-variable]
   double *p4, *p5, *p6;
                     ^~
score.c:183:16: warning: unused variable 'p5' [-Wunused-variable]
   double *p4, *p5, *p6;
                ^~
score.c:183:11: warning: unused variable 'p4' [-Wunused-variable]
   double *p4, *p5, *p6;
           ^~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o CGEN.dll tmp.def Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/CGEN.buildbin-libdir/CGEN/libs/x64
** testing if installed package can be loaded
Warning: Package 'CGEN' is deprecated and will be removed from Bioconductor
  version 3.13
* MD5 sums
packaged installation of 'CGEN' as CGEN_3.25.1.zip
* DONE (CGEN)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CGEN' successfully unpacked and MD5 sums checked

Tests output


Example timings

CGEN.Rcheck/examples_i386/CGEN-Ex.timings

nameusersystemelapsed
GxE.scan0.010.000.01
GxE.scan.combine000
GxE.scan.partition000
LocusMapData0.040.000.04
QQ.plot0.040.000.04
Xdata0.000.020.02

CGEN.Rcheck/examples_x64/CGEN-Ex.timings

nameusersystemelapsed
GxE.scan000
GxE.scan.combine000
GxE.scan.partition000
LocusMapData0.010.010.04
QQ.plot0.030.000.03
Xdata000