| Back to Multiple platform build/check report for BioC 3.15 |
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This page was generated on 2022-03-18 11:07:35 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
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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. |
| Package 724/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| genefilter 1.77.1 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: genefilter |
| Version: 1.77.1 |
| 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_1.77.1.tar.gz |
| StartedAt: 2022-03-17 19:09:35 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:11:34 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 118.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genefilter.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_1.77.1.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 '1.77.1' * 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 '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 * 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.
genefilter.Rcheck/00install.out
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###
### 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' ... done
genefilter.Rcheck/genefilter-Ex.timings
| name | user | system | elapsed | |
| Anova | 0 | 0 | 0 | |
| coxfilter | 0.01 | 0.02 | 0.03 | |
| cv | 0 | 0 | 0 | |
| dist2 | 0.01 | 0.00 | 0.01 | |
| eSetFilter | 0 | 0 | 0 | |
| filter_volcano | 0 | 0 | 0 | |
| filtered_p | 0 | 0 | 0 | |
| filterfun | 0 | 0 | 0 | |
| findLargest | 0.28 | 0.01 | 0.30 | |
| gapFilter | 0 | 0 | 0 | |
| genefilter | 0 | 0 | 0 | |
| genefinder | 0.04 | 0.02 | 0.05 | |
| genescale | 0 | 0 | 0 | |
| half.range.mode | 2.98 | 0.04 | 3.03 | |
| kOverA | 0 | 0 | 0 | |
| kappa_p | 0 | 0 | 0 | |
| maxA | 0 | 0 | 0 | |
| nsFilter | 0.22 | 0.02 | 0.23 | |
| pOverA | 0 | 0 | 0 | |
| rejection_plot | 0 | 0 | 0 | |
| rowFtests | 3.95 | 0.14 | 4.10 | |
| rowROC-class | 0.05 | 0.00 | 0.04 | |
| rowSds | 0 | 0 | 0 | |
| rowpAUCs | 1.15 | 0.02 | 1.15 | |
| shorth | 0 | 0 | 0 | |
| tdata | 0 | 0 | 0 | |
| ttest | 0 | 0 | 0 | |