genefilter 1.52.0
Bioconductor Package Maintainer
| Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/genefilter | | Last Changed Rev: 109589 / Revision: 110496 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genefilter_1.52.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/genefilter.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genefilter/DESCRIPTION’ ... OK
* this is package ‘genefilter’ version ‘1.52.0’
* 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 ‘genefilter’ can be installed ... [10s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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' call to ‘tkWidgets’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': ‘tkWidgets:::formatArg’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.findDBMeta: no visible global function definition for ‘dbmeta’
eSetFilter : buildGUI: no visible binding for '<<-' assignment to ‘END’
eSetFilter : buildGUI : setFilter: no visible global function
definition for ‘tkget’
eSetFilter : buildGUI : setFilter: no visible global function
definition for ‘tkcurselection’
eSetFilter : buildGUI : setFilter: no visible global function
definition for ‘writeList’
eSetFilter : buildGUI : setFilter: no visible global function
definition for ‘tkconfigure’
eSetFilter : buildGUI : cancel: no visible global function definition
for ‘tkdestroy’
eSetFilter : buildGUI : finish: no visible binding for '<<-' assignment
to ‘END’
eSetFilter : buildGUI : finish: no visible global function definition
for ‘tkdestroy’
eSetFilter : buildGUI : viewFilter: no visible global function
definition for ‘tkget’
eSetFilter : buildGUI : viewFilter: no visible global function
definition for ‘tkcurselection’
eSetFilter : buildGUI : viewFilter: no visible global function
definition for ‘tkconfigure’
eSetFilter : buildGUI : viewFilter: no visible global function
definition for ‘writeText’
eSetFilter : buildGUI : pickedSel: no visible global function
definition for ‘tkconfigure’
eSetFilter : buildGUI : remove: no visible global function definition
for ‘tkget’
eSetFilter : buildGUI : remove: no visible global function definition
for ‘tkcurselection’
eSetFilter : buildGUI : remove: no visible global function definition
for ‘writeList’
eSetFilter : buildGUI : remove: no visible global function definition
for ‘tkconfigure’
eSetFilter : buildGUI: no visible global function definition for
‘tktoplevel’
eSetFilter : buildGUI: no visible global function definition for
‘tktitle<-’
eSetFilter : buildGUI: no visible global function definition for
‘tktext’
eSetFilter : buildGUI: no visible global function definition for
‘writeText’
eSetFilter : buildGUI: no visible global function definition for
‘tkconfigure’
eSetFilter : buildGUI: no visible global function definition for
‘tkpack’
eSetFilter : buildGUI: no visible global function definition for
‘tkframe’
eSetFilter : buildGUI: no visible global function definition for
‘tklabel’
eSetFilter : buildGUI: no visible global function definition for
‘makeViewer’
eSetFilter : buildGUI: no visible global function definition for
‘tkbind’
eSetFilter : buildGUI: no visible global function definition for
‘writeList’
eSetFilter : buildGUI: no visible global function definition for
‘tkbutton’
eSetFilter : buildGUI: no visible global function definition for
‘tkwait.window’
eSetFilter : buildGUI: no visible binding for global variable ‘END’
isESet: no visible global function definition for ‘tkmessageBox’
setESetArgs: no visible global function definition for ‘tkdestroy’
setESetArgs : cancel: no visible global function definition for
‘tkdestroy’
setESetArgs : end: no visible global function definition for
‘tkdestroy’
setESetArgs: no visible global function definition for ‘tktoplevel’
setESetArgs: no visible global function definition for ‘tktitle<-’
setESetArgs: no visible global function definition for ‘tkgrid’
setESetArgs: no visible global function definition for ‘tklabel’
setESetArgs: no visible global function definition for ‘tclVar’
setESetArgs: no visible global function definition for ‘tkframe’
setESetArgs: no visible global function definition for ‘makeViewer’
setESetArgs: no visible global function definition for ‘writeText’
setESetArgs: no visible global function definition for ‘tkconfigure’
setESetArgs: no visible global function definition for ‘tkentry’
setESetArgs: no visible global function definition for ‘tkbind’
setESetArgs: no visible global function definition for
‘tkgrid.configure’
setESetArgs: no visible global function definition for ‘tkbutton’
setESetArgs: no visible global function definition for ‘tkpack’
setESetArgs: no visible global function definition for ‘tkwait.window’
setESetArgs: no visible global function definition for ‘tclvalue’
showESet : end: no visible global function definition for ‘tkdestroy’
showESet: no visible global function definition for ‘tktoplevel’
showESet: no visible global function definition for ‘tktitle<-’
showESet: no visible global function definition for ‘tkframe’
showESet: no visible global function definition for ‘makeViewer’
showESet: no visible global function definition for ‘writeList’
showESet: no visible global function definition for ‘tkpack’
showESet: no visible global function definition for ‘tkbutton’
* 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 ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [19s/19s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
rowFtests 6.596 0.106 6.702
* 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
‘/Users/biocbuild/bbs-3.2-bioc/meat/genefilter.Rcheck/00check.log’
for details.
* installing *source* package ‘genefilter’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c half_range_mode.cpp -o half_range_mode.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c init.c -o init.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c nd.c -o nd.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c pAUC.c -o pAUC.o
pAUC.c: In function ‘pAUC’:
pAUC.c:140: warning: suggest parentheses around comparison in operand of |
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c rowPAUCs.c -o rowPAUCs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c rowttests.c -o rowttests.o
gfortran-4.2 -arch x86_64 -fPIC -g -O2 -Wall -c ttest.f -o ttest.o
llvm-g++-4.2 -arch x86_64 -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 -L/usr/local/lib -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3/x86_64 -L/usr/local/lib/x86_64 -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/genefilter.Rcheck/genefilter/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘genefilter’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genefilter)