Back to Multiple platform build/check report for BioC 3.7
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

CHECK report for GlobalAncova on merida2

This page was generated on 2018-10-17 08:46:44 -0400 (Wed, 17 Oct 2018).

Package 621/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GlobalAncova 3.48.0
Manuela Hummel
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/GlobalAncova
Branch: RELEASE_3_7
Last Commit: bb788b4
Last Changed Date: 2018-04-30 10:35:03 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GlobalAncova
Version: 3.48.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GlobalAncova.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GlobalAncova_3.48.0.tar.gz
StartedAt: 2018-10-16 21:44:56 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 21:46:54 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 117.8 seconds
RetCode: 0
Status:  OK 
CheckDir: GlobalAncova.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GlobalAncova.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GlobalAncova_3.48.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/GlobalAncova.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GlobalAncova/DESCRIPTION’ ... OK
* this is package ‘GlobalAncova’ version ‘3.48.0’
* 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 ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘annotate’
A package should be listed in only one of these fields.
* 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
'library' or 'require' calls to packages already attached by Depends:
  ‘corpcor’ ‘methods’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘GO.db’ ‘GSEABase’ ‘KEGG.db’ ‘annotate’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘corpcor’ ‘globaltest’ ‘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
File ‘GlobalAncova/R/zzz.r’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

.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’
.pGAapprox : <anonymous>: no visible global function definition for
  ‘cov.shrink’
GABroad: no visible binding for global variable ‘collectionType’
GABroad: no visible binding for global variable ‘bcCategory’
GABroad: no visible global function definition for ‘mapIdentifiers’
GABroad: no visible global function definition for
  ‘AnnotationIdentifier’
GABroad: no visible binding for global variable ‘geneIds’
GABroad: no visible global function definition for ‘p.adjust’
GAGO: no visible global function definition for ‘mappedkeys’
GAGO: no visible binding for global variable ‘Ontology’
GAGO : <anonymous>: no visible global function definition for ‘keys’
GAGO: no visible global function definition for ‘findFocus’
GAGO: no visible global function definition for ‘focusLevel’
GAGO: no visible global function definition for ‘p.adjust’
GAKEGG: no visible global function definition for ‘mappedkeys’
GAKEGG: no visible global function definition for ‘p.adjust’
Plot.all: no visible global function definition for ‘par’
Plot.all: no visible global function definition for ‘layout’
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’
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’
expr.test: no visible global function definition for ‘terms’
expr.test: no visible global function definition for ‘model.matrix’
expr.test : <anonymous>: no visible global function definition for
  ‘cov.shrink’
group2formula: no visible global function definition for ‘as.formula’
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.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:
  AnnotationIdentifier Ontology addVigs2WinMenu anova as.formula axis
  barplot bcCategory box collectionType cov.shrink findFocus focusLevel
  geneIds keys layout legend lines lm mapIdentifiers mappedkeys
  model.matrix p.adjust palette par pchisq pf plot plot.new 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("stats", "anova", "as.formula", "lm", "model.matrix",
             "p.adjust", "pchisq", "pf", "qnorm", "terms")
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
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/GlobalAncova.Rcheck/00check.log’
for details.



Installation output

GlobalAncova.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GlobalAncova
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘GlobalAncova’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c GlobalAncova.c -o GlobalAncova.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ludcmp.c -o ludcmp.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c matrix.c -o matrix.o
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 GlobalAncova.so GlobalAncova.o ludcmp.o matrix.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/GlobalAncova/libs
** R
** data
** 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)

Tests output


Example timings

GlobalAncova.Rcheck/GlobalAncova-Ex.timings

nameusersystemelapsed
GlobalAncova1.710.041.76
GlobalAncova.decomp0.2010.0210.222
Plot.all0.0580.0040.063
Plot.genes1.0800.0301.119
Plot.sequential0.0330.0050.038
Plot.subjects0.6130.0180.634
colon.normal0.0060.0020.008
colon.pheno0.0020.0010.004
colon.tumour0.0060.0020.006
genesettesting0.0010.0000.001
pair.compare3.0450.2373.298
pathways0.0020.0000.004
phenodata0.0020.0000.002
vantVeer0.0090.0010.011