| Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:45:55 -0400 (Wed, 17 Oct 2018).
| Package 564/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| genefilter 1.62.0 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: genefilter |
| Version: 1.62.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:genefilter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings genefilter_1.62.0.tar.gz |
| StartedAt: 2018-10-16 21:33:47 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 21:35:50 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 122.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genefilter.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:genefilter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings genefilter_1.62.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/genefilter.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 ‘genefilter/DESCRIPTION’ ... OK
* this is package ‘genefilter’ version ‘1.62.0’
* 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 ... 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’
filter_volcano: no visible global function definition for ‘segments’
filter_volcano: no visible global function definition for ‘legend’
filtered_p: no visible global function definition for ‘p.adjust’
isESet: no visible global function definition for ‘tkmessageBox’
kappa_p: no visible global function definition for ‘qt’
rejection_plot: no visible global function definition for ‘rainbow’
rejection_plot : <anonymous>: no visible global function definition for
‘na.omit’
rejection_plot : <anonymous>: no visible global function definition for
‘stepfun’
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’
Undefined global functions or variables:
END dbmeta legend makeViewer na.omit p.adjust qt rainbow segments
stepfun tclVar tclvalue tkbind tkbutton tkconfigure tkcurselection
tkdestroy tkentry tkframe tkget tkgrid tkgrid.configure tklabel
tkmessageBox tkpack tktext tktitle<- tktoplevel tkwait.window
writeList writeText
Consider adding
importFrom("grDevices", "rainbow")
importFrom("graphics", "legend", "segments")
importFrom("stats", "na.omit", "p.adjust", "qt", "stepfun")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'rowROC,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
rowFtests 5.159 0.096 5.278
* 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: 1 WARNING, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.7-bioc/meat/genefilter.Rcheck/00check.log’
for details.
genefilter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL genefilter ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘genefilter’ ... ** libs clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c half_range_mode.cpp -o half_range_mode.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c nd.c -o nd.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c pAUC.c -o pAUC.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c rowPAUCs.c -o rowPAUCs.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c rowttests.c -o rowttests.o gfortran -fPIC -g -O2 -c ttest.f -o ttest.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 genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/genefilter/libs ** R ** data *** moving datasets to lazyload DB ** inst ** 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 (genefilter)
genefilter.Rcheck/genefilter-Ex.timings
| name | user | system | elapsed | |
| Anova | 0.018 | 0.001 | 0.019 | |
| coxfilter | 0.064 | 0.003 | 0.068 | |
| cv | 0.003 | 0.001 | 0.003 | |
| dist2 | 0.011 | 0.001 | 0.012 | |
| eSetFilter | 0.002 | 0.000 | 0.001 | |
| filter_volcano | 0.001 | 0.001 | 0.001 | |
| filtered_p | 0.002 | 0.000 | 0.001 | |
| filterfun | 0.020 | 0.001 | 0.021 | |
| findLargest | 0.473 | 0.017 | 0.494 | |
| gapFilter | 0.004 | 0.000 | 0.003 | |
| genefilter | 0.004 | 0.000 | 0.004 | |
| genefinder | 0.070 | 0.022 | 0.094 | |
| genescale | 0.002 | 0.001 | 0.003 | |
| half.range.mode | 3.906 | 0.088 | 4.006 | |
| kOverA | 0.001 | 0.001 | 0.002 | |
| kappa_p | 0.001 | 0.000 | 0.001 | |
| maxA | 0.002 | 0.000 | 0.002 | |
| nsFilter | 0.437 | 0.010 | 0.448 | |
| pOverA | 0.002 | 0.000 | 0.002 | |
| rejection_plot | 0.001 | 0.000 | 0.001 | |
| rowFtests | 5.159 | 0.096 | 5.278 | |
| rowROC-class | 0.071 | 0.005 | 0.076 | |
| rowSds | 0.003 | 0.000 | 0.002 | |
| rowpAUCs | 1.793 | 0.051 | 1.850 | |
| shorth | 0.005 | 0.000 | 0.005 | |
| tdata | 0.003 | 0.001 | 0.003 | |
| ttest | 0.008 | 0.001 | 0.008 | |