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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CGEN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CGEN_3.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CGEN.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* 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 for sufficient/correct file permissions ... 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
* 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 is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 0x7fda93965638>
<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: 1 ERROR, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/CGEN.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CGEN
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CGEN’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Additive.c -o Additive.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c CML.c -o CML.o
CML.c:132:13: warning: unused function 'print_dVec' [-Wunused-function]
static void print_dVec(vec, n, name)
            ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ccl.c -o ccl.o
ccl.c:386:13: warning: function 'tree_print' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static void tree_print(tnode *node, int is_root)
            ^
1 warning generated.
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c csclust.f -o csclust.o
f951: Warning: Nonconforming tab character in column 1 of line 46 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 83 [-Wtabs]
f951: Warning: Nonconforming tab character in column 2 of line 190 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 203 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 205 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 207 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 270 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 271 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 275 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 276 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 277 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 278 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 282 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 283 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 286 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 287 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 288 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 289 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 290 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 291 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 292 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 293 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 294 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 295 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 296 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 306 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 307 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 309 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 310 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 311 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 312 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 313 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 314 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 315 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 316 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 317 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 319 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 320 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 321 [-Wtabs]
f951: Warning: Nonconforming tab character in column 1 of line 329 [-Wtabs]
csclust.f:222:3:

 650   RETURN
   1
Warning: Label 650 at (1) defined but not used [-Wunused-label]
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fsclust.c -o fsclust.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c hcl.c -o hcl.o
hcl.c:375:13: warning: function 'tree_print' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static void tree_print(tnode *node, int is_root)
            ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pmatch.c -o pmatch.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c score.c -o score.o
score.c:18:27: warning: unused variable 'ii' [-Wunused-variable]
  int  nr, nc, i, j, row, ii, nc2;
                          ^
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;
          ^
4 warnings generated.
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-CGEN/00new/CGEN/libs
** R
** data
** inst
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CGEN)