| Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:20:55 -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: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:genefilter.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings genefilter_1.62.0.tar.gz |
| StartedAt: 2018-10-16 00:39:05 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 00:40:32 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 87.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genefilter.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:genefilter.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings genefilter_1.62.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/genefilter.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ... WARNING
Found the following significant warnings:
pAUC.c:140:13: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/biocbuild/bbs-3.7-bioc/meat/genefilter.Rcheck/00install.out’ for details.
* 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 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: 2 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.7-bioc/meat/genefilter.Rcheck/00check.log’
for details.
genefilter.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL genefilter
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘genefilter’ ...
** libs
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c half_range_mode.cpp -o half_range_mode.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nd.c -o nd.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c pAUC.c -o pAUC.o
pAUC.c: In function ‘pAUC’:
pAUC.c:140:13: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
if(rows != INTEGER(dimSens)[1] | columns != INTEGER(dimSens)[0])
^
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rowPAUCs.c -o rowPAUCs.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rowttests.c -o rowttests.o
f95 -fpic -g -O2 -Wall -c ttest.f -o ttest.o
ttest.f:47:12:
dm=dm1-dm2
1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
ttest.f:50:12:
dm=dm1/dm2
1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
ttest.f:59:13:
tst=(dm1-dm2)/sqrt((1.d0/ng1+1.d0/ng2)*(dss1+dss2)/(ng1+ng2-2))
1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
ttest.f:62:10:
tst=(dm1-dm2)/sqrt(dss1/((ng1-1)*ng1)+dss2/((ng2-1)*ng2))
1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
g++ -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/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 | 0.012 | 0.000 | 0.011 | |
| coxfilter | 0.044 | 0.000 | 0.045 | |
| cv | 0.000 | 0.004 | 0.001 | |
| dist2 | 0.028 | 0.000 | 0.026 | |
| eSetFilter | 0.000 | 0.000 | 0.001 | |
| filter_volcano | 0.000 | 0.000 | 0.001 | |
| filtered_p | 0 | 0 | 0 | |
| filterfun | 0.000 | 0.000 | 0.002 | |
| findLargest | 0.348 | 0.000 | 0.352 | |
| gapFilter | 0.004 | 0.000 | 0.002 | |
| genefilter | 0.000 | 0.000 | 0.001 | |
| genefinder | 0.044 | 0.004 | 0.051 | |
| genescale | 0.004 | 0.000 | 0.001 | |
| half.range.mode | 3.212 | 0.004 | 3.217 | |
| kOverA | 0.000 | 0.000 | 0.001 | |
| kappa_p | 0.000 | 0.004 | 0.001 | |
| maxA | 0.000 | 0.000 | 0.001 | |
| nsFilter | 0.324 | 0.004 | 0.329 | |
| pOverA | 0.000 | 0.000 | 0.001 | |
| rejection_plot | 0 | 0 | 0 | |
| rowFtests | 3.964 | 0.024 | 3.993 | |
| rowROC-class | 0.052 | 0.000 | 0.054 | |
| rowSds | 0.000 | 0.000 | 0.002 | |
| rowpAUCs | 1.440 | 0.008 | 1.446 | |
| shorth | 0.004 | 0.000 | 0.005 | |
| tdata | 0.004 | 0.000 | 0.001 | |
| ttest | 0.004 | 0.000 | 0.005 | |