GlobalAncova 3.41.0
Manuela Hummel
| Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GlobalAncova | | Last Changed Rev: 117081 / Revision: 121152 | | Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016) |
| zin1 | Linux (Ubuntu 16.04 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GlobalAncova_3.41.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GlobalAncova.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘3.41.0’
* 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 loading without being on the library search path ... 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
File ‘GlobalAncova/libs/GlobalAncova.so’:
Found ‘putchar’, possibly from ‘putchar’ (C)
Object: ‘matrix.o’
Found ‘rand’, possibly from ‘rand’ (C)
Object: ‘matrix.o’
Found ‘srand’, possibly from ‘srand’ (C)
Object: ‘matrix.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘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
‘/home/biocbuild/bbs-3.4-bioc/meat/GlobalAncova.Rcheck/00check.log’
for details.
* installing *source* package ‘GlobalAncova’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-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-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c ludcmp.c -o ludcmp.o
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c matrix.c -o matrix.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o GlobalAncova.so GlobalAncova.o ludcmp.o matrix.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/GlobalAncova.Rcheck/GlobalAncova/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 (GlobalAncova)