CGEN 3.12.1
William Wheeler
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/CGEN | | Last Changed Rev: 129423 / Revision: 131943 | | Last Changed Date: 2017-05-05 15:32:27 -0400 (Fri, 05 May 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings CGEN_3.12.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/CGEN.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CGEN/DESCRIPTION’ ... OK
* this is package ‘CGEN’ version ‘3.12.1’
* 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 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
snp.matched 14.980 0.000 14.987
getMatchedSets 13.288 0.536 13.855
* 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
‘/home/biocbuild/bbs-3.5-bioc/meat/CGEN.Rcheck/00check.log’
for details.
* installing *source* package ‘CGEN’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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;
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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)
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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)
^
f95 -fpic -g -O2 -Wall -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]
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f951: Warning: Nonconforming tab character in column 1 of line 317 [-Wtabs]
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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
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c fsclust.c -o fsclust.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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)
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pmatch.c -o pmatch.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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;
^
gcc -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o CGEN.so Additive.o CML.o ccl.o csclust.o fsclust.o hcl.o pmatch.o score.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-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)