Package: CGEN

Version: 3.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CGEN_3.14.0.tar.gz

StartedAt: 2018-04-12 01:26:21 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:28:27 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 126.6 seconds

RetCode: 0

Status:  OK

CheckDir: CGEN.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CGEN_3.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/CGEN.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CGEN/DESCRIPTION’ ... OK
* this is package ‘CGEN’ version ‘3.14.0’
* 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 loading without being on the library search path ... 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 ‘plot’
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 ‘plot’
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 ‘plot’
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 ‘plot’
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 ‘plot’
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 ‘plot’
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 ‘plot’
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’
myPlot_genScoreCompare: no visible global function definition for
  ‘plot’
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’
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’
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 ‘plot’
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 plot pnorm
  points polygon postscript qchisq qnorm qqplot rbinom read.table rgb
  rnorm runif screen segments split.screen text title var vcov
  write.table
Consider adding
  importFrom("grDevices", "bitmap", "colors", "graphics.off", "jpeg",
             "pdf", "postscript", "rgb")
  importFrom("graphics", "abline", "axis", "box", "close.screen",
             "image", "layout", "legend", "lines", "mtext", "par", "pie",
             "plot", "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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
getMatchedSets 10.708  0.263  11.146
snp.matched    10.400  0.029  10.584
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/CGEN.Rcheck/00check.log’
for details.

* installing *source* package ‘CGEN’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Additive.c -o Additive.o
clang -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 -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   -fPIC  -g -O2  -c csclust.f -o csclust.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c fsclust.c -o fsclust.o
clang -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 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pmatch.c -o pmatch.o
clang -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:183:16: warning: unused variable 'p5' [-Wunused-variable]
  double *p4, *p5, *p6;
               ^
score.c:183:11: warning: unused variable 'p4' [-Wunused-variable]
  double *p4, *p5, *p6;
          ^
score.c:183:21: warning: unused variable 'p6' [-Wunused-variable]
  double *p4, *p5, *p6;
                    ^
4 warnings generated.
clang++ -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-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.6-bioc/meat/CGEN.Rcheck/CGEN/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CGEN)

name	user	system	elapsed
GxE.scan	0.002	0.001	0.002
GxE.scan.combine	0	0	0
GxE.scan.partition	0.003	0.000	0.004
LocusMapData	0.021	0.003	0.024
QQ.plot	0.007	0.001	0.007
Xdata	0.015	0.001	0.017
additive.test	2.818	0.046	2.906
chromosome.plot	0.292	0.002	0.304
getMatchedSets	10.708	0.263	11.146
getSummary	0.015	0.001	0.016
getWaldTest	0.004	0.000	0.006
printEffects	0.252	0.008	0.263
snp.effects	0.213	0.002	0.215
snp.effects.plot	0.775	0.008	0.799
snp.list	0.001	0.000	0.001
snp.logistic	0.318	0.004	0.329
snp.matched	10.400	0.029	10.584
snp.score	0.036	0.004	0.040