Package: GlobalAncova

Version: 4.0.0

Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:GlobalAncova.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings GlobalAncova_4.0.0.tar.gz

StartedAt: 2019-04-16 00:19:07 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:23:50 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 283.5 seconds

RetCode: 0

Status:  OK

CheckDir: GlobalAncova.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:GlobalAncova.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings GlobalAncova_4.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/GlobalAncova.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GlobalAncova/DESCRIPTION’ ... OK
* this is package ‘GlobalAncova’ version ‘4.0.0’
* 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 ‘GlobalAncova’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... NOTE
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.nPerms: no visible global function definition for ‘terms’
.onAttach: no visible global function definition for ‘addVigs2WinMenu’
.pAsymptotic: no visible global function definition for ‘qnorm’
.pAsymptotic: no visible global function definition for ‘pchisq’
.pGAapprox: no visible global function definition for ‘model.matrix’
GABroad: no visible global function definition for ‘is’
GABroad: no visible binding for global variable ‘collectionType’
GABroad: no visible binding for global variable ‘geneIds’
GABroad: no visible global function definition for ‘p.adjust’
GAGO: no visible binding for global variable ‘Ontology’
GAGO: no visible global function definition for ‘is’
GAGO: no visible global function definition for ‘p.adjust’
GAGO : <anonymous>: no visible global function definition for ‘is’
GAKEGG: no visible global function definition for ‘is’
GAKEGG: no visible global function definition for ‘p.adjust’
Gsquared: no visible global function definition for ‘glm’
Gsquared: no visible binding for global variable ‘multinomial’
Gsquared: no visible global function definition for ‘pchisq’
Gsquared: no visible global function definition for ‘qchisq’
Plot.all: no visible global function definition for ‘par’
Plot.all: no visible global function definition for ‘layout’
Plot.features: no visible global function definition for ‘barplot’
Plot.sequential: no visible global function definition for ‘par’
Plot.sequential: no visible global function definition for ‘barplot’
Plot.sequential: no visible global function definition for ‘legend’
Plot.sequential: no visible global function definition for ‘axis’
Tperm.catcat: no visible global function definition for ‘pchisq’
Tperm.catcat: no visible global function definition for ‘qchisq’
coldend: no visible global function definition for ‘is.leaf’
decomp.ssq: no visible global function definition for ‘model.matrix’
decomp.ssq: no visible global function definition for ‘as.formula’
decomp.ssq: no visible global function definition for ‘anova’
decomp.ssq: no visible global function definition for ‘lm’
decomp.ssq: no visible global function definition for ‘pf’
decomp.ssq.genewise: no visible global function definition for
  ‘model.matrix’
decomp.ssq.genewise: no visible global function definition for
  ‘as.formula’
decomp.ssq.genewise: no visible global function definition for ‘anova’
decomp.ssq.genewise: no visible global function definition for ‘lm’
decomp.ssq.genewise: no visible global function definition for ‘pf’
devtest: no visible global function definition for ‘formula’
devtest: no visible global function definition for ‘na.omit’
devtest: no visible global function definition for ‘pchisq’
devtest: no visible global function definition for ‘qchisq’
expr.test: no visible global function definition for ‘terms’
expr.test: no visible global function definition for ‘model.matrix’
gGAteststats: no visible global function definition for ‘terms’
gGAteststats: no visible global function definition for
  ‘complete.cases’
gGAteststats : <anonymous>: no visible global function definition for
  ‘na.omit’
gGAteststats: no visible global function definition for ‘model.matrix’
gGlobalAncova.hierarchical: no visible global function definition for
  ‘new’
getdev: no visible binding for global variable ‘nobs’
getdev: no visible global function definition for ‘glm.fit’
getdev: no visible global function definition for ‘binomial’
group2formula: no visible global function definition for ‘as.formula’
hiertest: no visible global function definition for ‘na.omit’
horizontal.bars: no visible global function definition for ‘plot.new’
horizontal.bars: no visible global function definition for ‘strwidth’
horizontal.bars: no visible global function definition for ‘par’
horizontal.bars: no visible global function definition for ‘plot’
horizontal.bars: no visible global function definition for ‘rect’
horizontal.bars: no visible global function definition for ‘box’
horizontal.bars: no visible global function definition for ‘axis’
my.colors: no visible global function definition for ‘rainbow’
my.colors: no visible global function definition for ‘rgb’
pair.compare: no visible global function definition for ‘model.matrix’
plot.ssq.all: no visible global function definition for ‘par’
plot.ssq.all: no visible global function definition for ‘barplot’
plot.ssq.all: no visible global function definition for ‘axis’
plot.ssq.genewise2: no visible global function definition for ‘par’
plot.ssq.genewise2: no visible global function definition for ‘barplot’
plot.ssq.genewise2: no visible global function definition for ‘legend’
plot.ssq.genewise2: no visible global function definition for ‘axis’
plotallgenes: no visible global function definition for ‘par’
plotallgenes: no visible global function definition for ‘barplot’
plotallgenes: no visible global function definition for ‘lines’
plotgenes: no visible global function definition for ‘palette’
plotgenes: no visible global function definition for ‘rgb’
plotgenes: no visible global function definition for ‘lines’
plotgenes: no visible global function definition for ‘legend’
plotgenes2: no visible global function definition for ‘par’
plotgenes2: no visible global function definition for ‘barplot’
plotgenes2: no visible global function definition for ‘axis’
plotgenes2: no visible global function definition for ‘lines’
plotgenes2: no visible global function definition for ‘rect’
plotsubjects: no visible global function definition for ‘palette’
plotsubjects: no visible global function definition for ‘rgb’
plotsubjects: no visible global function definition for ‘legend’
reduSQ: no visible global function definition for ‘model.matrix’
GlobalAncova.closed,matrix-list-formula-missing-ANY-missing-missing-character:
  no visible global function definition for ‘model.matrix’
GlobalAncova,matrix-formula-missing-ANY-missing-missing-character: no
  visible global function definition for ‘model.matrix’
Plot.genes,matrix-formula-missing-ANY-missing-missing-character: no
  visible global function definition for ‘model.matrix’
Plot.hierarchy,GAhier: no visible global function definition for ‘plot’
Plot.subjects,matrix-formula-missing-ANY-missing-missing-character: no
  visible global function definition for ‘model.matrix’
pGAapprox,matrix-formula-missing-ANY-missing-missing-character: no
  visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  Ontology addVigs2WinMenu anova as.formula axis barplot binomial box
  collectionType complete.cases formula geneIds glm glm.fit is is.leaf
  layout legend lines lm model.matrix multinomial na.omit new nobs
  p.adjust palette par pchisq pf plot plot.new qchisq qnorm rainbow
  rect rgb strwidth terms
Consider adding
  importFrom("grDevices", "palette", "rainbow", "rgb")
  importFrom("graphics", "axis", "barplot", "box", "layout", "legend",
             "lines", "par", "plot", "plot.new", "rect", "strwidth")
  importFrom("methods", "is", "new")
  importFrom("stats", "anova", "as.formula", "binomial",
             "complete.cases", "formula", "glm", "glm.fit", "is.leaf",
             "lm", "model.matrix", "na.omit", "nobs", "p.adjust",
             "pchisq", "pf", "qchisq", "qnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
File ‘/home/biocbuild/bbs-3.8-bioc/R/library/GlobalAncova/libs/GlobalAncova.so’:
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘srand’, possibly from ‘srand’ (C)

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 ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
GlobalAncova               46.968  0.788  48.042
Plot.subjects              32.992  0.168  33.708
Plot.genes                 31.640  0.200  32.350
gGlobalAncova.hierarchical 10.720  0.084  10.820
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/GlobalAncova.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL GlobalAncova
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘GlobalAncova’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c GlobalAncova.c -o GlobalAncova.o
GlobalAncova.c: In function ‘permut_withFperm’:
GlobalAncova.c:186:16: warning: ‘ord_perm’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             n1 =  ord_perm[j] ;
                ^
GlobalAncova.c: In function ‘permut’:
GlobalAncova.c:289:16: warning: ‘ord_perm’ may be used uninitialized in this function [-Wmaybe-uninitialized]
             n1 =  ord_perm[j] ;
                ^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c ludcmp.c -o ludcmp.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c matrix.c -o matrix.o
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o GlobalAncova.so GlobalAncova.o ludcmp.o matrix.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/GlobalAncova/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
* DONE (GlobalAncova)

name	user	system	elapsed
GAhier-class	0.004	0.000	0.001
GlobalAncova	46.968	0.788	48.042
GlobalAncova.decomp	2.304	0.024	2.346
Plot.all	0.080	0.000	0.079
Plot.features	0.028	0.000	0.027
Plot.genes	31.64	0.20	32.35
Plot.sequential	0.032	0.000	0.032
Plot.subjects	32.992	0.168	33.708
bindata	0.000	0.000	0.001
colon.normal	0.008	0.000	0.006
colon.pheno	0.000	0.000	0.002
colon.tumour	0.000	0.004	0.005
gGlobalAncova	0.364	0.000	0.364
gGlobalAncova.hierarchical	10.720	0.084	10.820
genesettesting	0	0	0
pair.compare	3.232	0.048	3.284
pathways	0.000	0.000	0.002
phenodata	0.000	0.000	0.003
vantVeer	0.012	0.000	0.009