| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:36:10 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 777/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| genefilter 1.82.1 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: genefilter |
| Version: 1.82.1 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:genefilter.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings genefilter_1.82.1.tar.gz |
| StartedAt: 2023-10-16 02:25:41 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 02:27:58 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 137.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genefilter.Rcheck |
| Warnings: 2 |
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### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:genefilter.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings genefilter_1.82.1.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/genefilter.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.2.0
GNU Fortran (GCC) 12.2.0
* 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 '1.82.1'
* 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:
pAUC.c:140:13: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'F:/biocbuild/bbs-3.17-bioc/meat/genefilter.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 12.2.0'
* used Fortran compiler: 'GNU Fortran (GCC) 12.2.0'
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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 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 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-3.17-bioc/R/library/genefilter/libs/x64/genefilter.dll':
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 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 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, 3 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc/meat/genefilter.Rcheck/00check.log'
for details.
genefilter.Rcheck/00install.out
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL genefilter
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'genefilter' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using Fortran compiler: 'GNU Fortran (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c half_range_mode.cpp -o half_range_mode.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init.c -o init.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c nd.c -o nd.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/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-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rowPAUCs.c -o rowPAUCs.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"C:/rtools43/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:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -lgfortran -lm -lquadmath -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-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)
genefilter.Rcheck/genefilter-Ex.timings
| name | user | system | elapsed | |
| Anova | 0 | 0 | 0 | |
| coxfilter | 0.05 | 0.00 | 0.04 | |
| cv | 0 | 0 | 0 | |
| dist2 | 0 | 0 | 0 | |
| eSetFilter | 0 | 0 | 0 | |
| filter_volcano | 0 | 0 | 0 | |
| filtered_p | 0 | 0 | 0 | |
| filterfun | 0 | 0 | 0 | |
| findLargest | 0.46 | 0.08 | 0.86 | |
| gapFilter | 0 | 0 | 0 | |
| genefilter | 0.02 | 0.00 | 0.01 | |
| genefinder | 0.02 | 0.05 | 0.07 | |
| genescale | 0 | 0 | 0 | |
| half.range.mode | 3.19 | 0.05 | 3.23 | |
| kOverA | 0.01 | 0.00 | 0.02 | |
| kappa_p | 0 | 0 | 0 | |
| maxA | 0 | 0 | 0 | |
| nsFilter | 0.33 | 0.01 | 0.47 | |
| pOverA | 0 | 0 | 0 | |
| rejection_plot | 0 | 0 | 0 | |
| rowFtests | 1.07 | 0.00 | 1.06 | |
| rowROC-class | 0.04 | 0.02 | 0.07 | |
| rowSds | 0 | 0 | 0 | |
| rowpAUCs | 1.39 | 0.04 | 1.50 | |
| shorth | 0 | 0 | 0 | |
| tdata | 0 | 0 | 0 | |
| ttest | 0 | 0 | 0 | |