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This page was generated on 2022-01-25 11:07:18 -0500 (Tue, 25 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4164
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4059
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4001
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4118
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for genefilter on riesling1


To the developers/maintainers of the genefilter package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/genefilter.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 719/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefilter 1.77.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2022-01-24 13:55:18 -0500 (Mon, 24 Jan 2022)
git_url: https://git.bioconductor.org/packages/genefilter
git_branch: master
git_last_commit: 7911602
git_last_commit_date: 2021-10-26 11:45:31 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'BiocGenerics' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: genefilter
Version: 1.77.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:genefilter.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings genefilter_1.77.0.tar.gz
StartedAt: 2022-01-24 18:57:25 -0500 (Mon, 24 Jan 2022)
EndedAt: 2022-01-24 18:59:25 -0500 (Mon, 24 Jan 2022)
EllapsedTime: 119.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: genefilter.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:genefilter.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings genefilter_1.77.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/genefilter.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'genefilter/DESCRIPTION' ... OK
* this is package 'genefilter' version '1.77.0'
* 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 'genefilter' can be installed ... WARNING
Found the following significant warnings:
  pAUC.c:140:13: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'D:/biocbuild/bbs-3.15-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 ... OK
* 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
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'
getRdAsText: no visible global function definition for '.path.package'
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'
Undefined global functions or variables:
  .path.package END makeViewer tclVar tclvalue tkbind tkbutton
  tkconfigure tkcurselection tkdestroy tkentry tkframe tkget tkgrid
  tkgrid.configure tklabel tkmessageBox tkpack tktext tktitle<-
  tktoplevel tkwait.window writeList writeText
* 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 LazyData ... 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 x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/genefilter/libs/x64/genefilter.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
rowFtests 5.55   0.18    7.06
* 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, 3 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/genefilter.Rcheck/00check.log'
for details.



Installation output

genefilter.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL genefilter
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'genefilter' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c half_range_mode.cpp -o half_range_mode.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c init.c -o init.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c nd.c -o nd.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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])
        ~~~~~^~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c rowPAUCs.c -o rowPAUCs.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c rowttests.c -o rowttests.o
"C:/rtools40/mingw64/bin/"gfortran  -fno-optimize-sibling-calls    -O2  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ttest.f -o ttest.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o genefilter.dll tmp.def half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -lgfortran -lm -lquadmath -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-genefilter/00new/genefilter/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'genefilter'
    finding HTML links ... done
    Anova                                   html  
    coxfilter                               html  
    cv                                      html  
    deprecated                              html  
    dist2                                   html  
    eSetFilter                              html  
    filter_volcano                          html  
    filtered_p                              html  
    filterfun                               html  
    findLargest                             html  
    gapFilter                               html  
    genefilter                              html  
    genefinder                              html  
    genescale                               html  
    half.range.mode                         html  
    kOverA                                  html  
    kappa_p                                 html  
    maxA                                    html  
    nsFilter                                html  
    pOverA                                  html  
    rejection_plot                          html  
    rowFtests                               html  
    rowROC-class                            html  
    rowSds                                  html  
    rowpAUCs                                html  
    shorth                                  html  
    tdata                                   html  
    ttest                                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (genefilter)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'FISHalyseR' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'transite' is missing or broken
 done

Tests output


Example timings

genefilter.Rcheck/genefilter-Ex.timings

nameusersystemelapsed
Anova0.020.000.01
coxfilter0.040.000.05
cv000
dist20.010.000.02
eSetFilter000
filter_volcano000
filtered_p000
filterfun000
findLargest0.300.100.39
gapFilter000
genefilter000
genefinder0.040.010.06
genescale000
half.range.mode3.270.053.31
kOverA000
kappa_p000
maxA000
nsFilter0.250.010.27
pOverA000
rejection_plot000
rowFtests5.550.187.06
rowROC-class0.040.000.08
rowSds0.000.000.02
rowpAUCs1.440.001.84
shorth0.020.000.02
tdata000
ttest0.010.000.01