| Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:05:05 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 756/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| genefilter 1.80.3 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: genefilter |
| Version: 1.80.3 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:genefilter.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings genefilter_1.80.3.tar.gz |
| StartedAt: 2023-04-10 20:52:04 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 20:54:54 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 169.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genefilter.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:genefilter.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings genefilter_1.80.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/genefilter.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘genefilter/DESCRIPTION’ ... OK * this is package ‘genefilter’ version ‘1.80.3’ * 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-3.16-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 loading without being on the library search path ... 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 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 ... ‘independent_filtering_plots.Rnw’... OK ‘howtogenefilter.Rnw’... OK ‘howtogenefinder.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/home/biocbuild/bbs-3.16-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-3.16-bioc/R/bin/R CMD INSTALL genefilter
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘genefilter’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nd.c -o nd.o
gcc -I"/home/biocbuild/bbs-3.16-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]
140 | if(rows != INTEGER(dimSens)[1] | columns != INTEGER(dimSens)[0])
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rowPAUCs.c -o rowPAUCs.o
gcc -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rowttests.c -o rowttests.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -Wall -c ttest.f -o ttest.o
ttest.f:47:12:
47 | dm=dm1-dm2
| 1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
ttest.f:50:12:
50 | dm=dm1/dm2
| 1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
ttest.f:59:13:
59 | 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:
62 | 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++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.16-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-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-genefilter/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** 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 | 0.009 | 0.000 | 0.009 | |
| coxfilter | 0.037 | 0.000 | 0.038 | |
| cv | 0.000 | 0.000 | 0.001 | |
| dist2 | 0.005 | 0.000 | 0.005 | |
| eSetFilter | 0.000 | 0.000 | 0.001 | |
| filter_volcano | 0 | 0 | 0 | |
| filtered_p | 0.001 | 0.000 | 0.000 | |
| filterfun | 0 | 0 | 0 | |
| findLargest | 0.349 | 0.004 | 0.353 | |
| gapFilter | 0 | 0 | 0 | |
| genefilter | 0.001 | 0.000 | 0.000 | |
| genefinder | 0.039 | 0.004 | 0.043 | |
| genescale | 0.001 | 0.000 | 0.001 | |
| half.range.mode | 3.774 | 0.056 | 3.830 | |
| kOverA | 0 | 0 | 0 | |
| kappa_p | 0 | 0 | 0 | |
| maxA | 0 | 0 | 0 | |
| nsFilter | 0.285 | 0.016 | 0.301 | |
| pOverA | 0.000 | 0.000 | 0.001 | |
| rejection_plot | 0 | 0 | 0 | |
| rowFtests | 1.508 | 0.088 | 1.596 | |
| rowROC-class | 0.062 | 0.003 | 0.065 | |
| rowSds | 0.001 | 0.000 | 0.002 | |
| rowpAUCs | 1.414 | 0.008 | 1.422 | |
| shorth | 0.003 | 0.000 | 0.002 | |
| tdata | 0.000 | 0.000 | 0.001 | |
| ttest | 0.003 | 0.000 | 0.004 | |