Package: GlobalAncova

Version: 4.2.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GlobalAncova.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GlobalAncova_4.2.0.tar.gz

StartedAt: 2019-10-16 04:06:12 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:10:04 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 231.9 seconds

RetCode: 0

Status:  OK

CheckDir: GlobalAncova.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GlobalAncova.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings GlobalAncova_4.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/GlobalAncova.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GlobalAncova/DESCRIPTION' ... OK
* this is package 'GlobalAncova' version '4.2.0'
* 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 '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
* 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 ... 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 : : 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 : : 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/GlobalAncova/libs/i386/GlobalAncova.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/GlobalAncova/libs/x64/GlobalAncova.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
gGlobalAncova.hierarchical 6.25   0.29    6.67
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                           user system elapsed
gGlobalAncova.hierarchical 5.03   0.08    5.11
* 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/GlobalAncova.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/GlobalAncova_4.2.0.tar.gz && rm -rf GlobalAncova.buildbin-libdir && mkdir GlobalAncova.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GlobalAncova.buildbin-libdir GlobalAncova_4.2.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL GlobalAncova_4.2.0.zip && rm GlobalAncova_4.2.0.tar.gz GlobalAncova_4.2.0.zip
###
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100  605k  100  605k    0     0  1837k      0 --:--:-- --:--:-- --:--:-- 1874k

install for i386

* installing *source* package 'GlobalAncova' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c GlobalAncova.c -o GlobalAncova.o
GlobalAncova.c: In function 'permut_withFperm':
GlobalAncova.c:166:8: warning: 'ord_perm' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int *ord_perm ;
        ^
GlobalAncova.c: In function 'permut':
GlobalAncova.c:268:8: warning: 'ord_perm' may be used uninitialized in this function [-Wmaybe-uninitialized]
   int *ord_perm ;
        ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c ludcmp.c -o ludcmp.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c matrix.c -o matrix.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o GlobalAncova.dll tmp.def GlobalAncova.o ludcmp.o matrix.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/GlobalAncova.buildbin-libdir/00LOCK-GlobalAncova/00new/GlobalAncova/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GlobalAncova'
    finding HTML links ... done
    GAhier-class                            html  
    GlobalAncova-methods                    html  
    GlobalAncova                            html  
    GlobalAncova.closed-methods             html  
    GlobalAncova.closed                     html  
    GlobalAncova.decomp                     html  
    Plot.all                                html  
    Plot.features                           html  
    Plot.genes-methods                      html  
    Plot.genes                              html  
    Plot.sequential                         html  
    Plot.subjects-methods                   html  
    Plot.subjects                           html  
    bindata                                 html  
    colon.normal                            html  
    colon.pheno                             html  
    colon.tumour                            html  
    gGlobalAncova                           html  
    gGlobalAncova.hierarchical              html  
    genesettesting                          html  
    pair.compare                            html  
    pathways                                html  
    phenodata                               html  
    vantVeer                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'GlobalAncova' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -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] ;
                ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ludcmp.c -o ludcmp.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c matrix.c -o matrix.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o GlobalAncova.dll tmp.def GlobalAncova.o ludcmp.o matrix.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/GlobalAncova.buildbin-libdir/GlobalAncova/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GlobalAncova' as GlobalAncova_4.2.0.zip
* DONE (GlobalAncova)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'GlobalAncova' successfully unpacked and MD5 sums checked