Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-03-28 11:37:45 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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

Package 795/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genefilter 1.85.1  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/genefilter
git_branch: devel
git_last_commit: 9f22fda
git_last_commit_date: 2024-01-18 15:47:09 -0400 (Thu, 18 Jan 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for genefilter on palomino3


To the developers/maintainers of the genefilter package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: genefilter
Version: 1.85.1
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:genefilter.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings genefilter_1.85.1.tar.gz
StartedAt: 2024-03-28 02:18:52 -0400 (Thu, 28 Mar 2024)
EndedAt: 2024-03-28 02:21:28 -0400 (Thu, 28 Mar 2024)
EllapsedTime: 156.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: genefilter.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:genefilter.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings genefilter_1.85.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/genefilter.Rcheck'
* using R Under development (unstable) (2024-03-16 r86144 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'genefilter/DESCRIPTION' ... OK
* this is package 'genefilter' version '1.85.1'
* 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:
  half_range_mode.cpp:100:60: warning: format '%i' expects argument of type 'int', but argument 5 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  pAUC.c:140:13: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'F:/biocbuild/bbs-3.19-bioc/meat/genefilter.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* used Fortran compiler: 'GNU Fortran (GCC) 13.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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 ... WARNING
Vignettes with missing or empty \VignetteIndexEntry:
  howtogenefinder.Rmd
See sections 'The INDEX file' and 'Package subdirectories' in the
'Writing R Extensions' manual.
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... 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 'F:/biocbuild/bbs-3.19-bioc/R/library/genefilter/libs/x64/genefilter.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 nor [v]sprintf. 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 usage of KIND in Fortran files ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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, 3 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/genefilter.Rcheck/00check.log'
for details.


Installation output

genefilter.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL genefilter
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'genefilter' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
using Fortran compiler: 'GNU Fortran (GCC) 13.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c half_range_mode.cpp -o half_range_mode.o
half_range_mode.cpp: In function 'double half_range_mode(double*, double*, double, int)':
half_range_mode.cpp:100:60: warning: format '%i' expects argument of type 'int', but argument 5 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
  100 |     if (diag) Rprintf( "N = %i, N'' = %i, w = %.4f, |J| = %i\n", N, N_double_prime, w, J.size() );
      |                                                           ~^                           ~~~~~~~~
      |                                                            |                                 |
      |                                                            int                               std::vector<int>::size_type {aka long long unsigned int}
      |                                                           %lli
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c nd.c -o nd.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pAUC.c -o pAUC.o
pAUC.c: In function 'pAUC':
pAUC.c:140:13: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  140 |     if(rows != INTEGER(dimSens)[1] | columns != INTEGER(dimSens)[0])
      |        ~~~~~^~~~~~~~~~~~~~~~~~~~~~
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rowPAUCs.c -o rowPAUCs.o
gcc  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c rowttests.c -o rowttests.o
gfortran      -O2  -mfpmath=sse -msse2 -mstackrealign  -c ttest.f -o ttest.o
g++ -std=gnu++17 -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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -lgfortran -lm -lquadmath -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-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
** 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)

Tests output


Example timings

genefilter.Rcheck/genefilter-Ex.timings

nameusersystemelapsed
Anova0.020.000.01
coxfilter0.080.000.07
cv000
dist20.000.020.02
eSetFilter000
filter_volcano000
filtered_p000
filterfun000
findLargest0.530.120.70
gapFilter000
genefilter000
genefinder0.530.000.54
genescale000
half.range.mode3.970.034.00
kOverA000
kappa_p000
maxA000
nsFilter0.360.030.42
pOverA000
rejection_plot000
rowFtests1.080.041.12
rowROC-class0.030.020.05
rowSds000
rowpAUCs1.410.091.56
shorth000
tdata000
ttest0.010.000.01