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) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:32:37 -0400 (Wed, 17 Oct 2018).
| Package 621/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| GlobalAncova 3.48.0 Manuela Hummel
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: GlobalAncova |
| Version: 3.48.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GlobalAncova.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GlobalAncova_3.48.0.tar.gz |
| StartedAt: 2018-10-17 02:26:08 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 02:30:47 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 278.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GlobalAncova.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:GlobalAncova.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings GlobalAncova_3.48.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/GlobalAncova.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '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 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
* 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
'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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-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)
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
** running examples for arch 'x64' ... 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
'C:/Users/biocbuild/bbs-3.7-bioc/meat/GlobalAncova.Rcheck/00check.log'
for details.
GlobalAncova.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/GlobalAncova_3.48.0.tar.gz && rm -rf GlobalAncova.buildbin-libdir && mkdir GlobalAncova.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GlobalAncova.buildbin-libdir GlobalAncova_3.48.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL GlobalAncova_3.48.0.zip && rm GlobalAncova_3.48.0.tar.gz GlobalAncova_3.48.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 589k 100 589k 0 0 8551k 0 --:--:-- --:--:-- --:--:-- 9512k
install for i386
* installing *source* package 'GlobalAncova' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-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˜1.7-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˜1.7-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˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/GlobalAncova.buildbin-libdir/GlobalAncova/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'GlobalAncova'
finding HTML links ... done
GlobalAncova-methods html
GlobalAncova html
GlobalAncova.closed-methods html
GlobalAncova.closed html
GlobalAncova.decomp html
Plot.all html
Plot.genes-methods html
Plot.genes html
Plot.sequential html
Plot.subjects-methods html
Plot.subjects html
colon.normal html
colon.pheno html
colon.tumour html
genesettesting html
pair.compare html
pathways html
phenodata html
vantVeer html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'GlobalAncova' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-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˜1.7-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˜1.7-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˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/GlobalAncova.buildbin-libdir/GlobalAncova/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GlobalAncova' as GlobalAncova_3.48.0.zip
* DONE (GlobalAncova)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'GlobalAncova' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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GlobalAncova.Rcheck/examples_i386/GlobalAncova-Ex.timings
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GlobalAncova.Rcheck/examples_x64/GlobalAncova-Ex.timings
|