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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CGEN.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings CGEN_3.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/CGEN.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 'CGEN/DESCRIPTION' ... OK
* this is package 'CGEN' version '3.24.0'
* 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 'CGEN' can be installed ... OK
* 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-3.11-bioc/R/library/CGEN/libs/i386/CGEN.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.11-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: 0x08f5d358>
<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: 0x000000000fae4150>
<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, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/CGEN.Rcheck/00check.log'
for details.