| Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:54:49 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE genefilter PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 679/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| genefilter 1.70.0 Bioconductor Package Maintainer
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] |  | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: genefilter |
| Version: 1.70.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:genefilter.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings genefilter_1.70.0.tar.gz |
| StartedAt: 2020-10-17 01:35:26 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 01:37:29 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 122.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genefilter.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:genefilter.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings genefilter_1.70.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/genefilter.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genefilter/DESCRIPTION’ ... OK
* this is package ‘genefilter’ version ‘1.70.0’
* 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 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-3.11-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
.findDBMeta: no visible global function definition for ‘dbmeta’
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 dbmeta 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 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
half.range.mode 5.596 0.004 5.600
rowFtests 5.416 0.016 5.433
* 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
‘/home/biocbuild/bbs-3.11-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-3.11-bioc/R/bin/R CMD INSTALL genefilter
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘genefilter’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-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-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c nd.c -o nd.o
gcc -I"/home/biocbuild/bbs-3.11-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]
if(rows != INTEGER(dimSens)[1] | columns != INTEGER(dimSens)[0])
~~~~~^~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c rowPAUCs.c -o rowPAUCs.o
gcc -I"/home/biocbuild/bbs-3.11-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:
dm=dm1-dm2
1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
ttest.f:50:12:
dm=dm1/dm2
1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
ttest.f:59:13:
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:
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++11 -shared -L/home/biocbuild/bbs-3.11-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-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/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 | 0.01 | 0.00 | 0.01 | |
| coxfilter | 0.049 | 0.000 | 0.049 | |
| cv | 0.001 | 0.000 | 0.001 | |
| dist2 | 0.007 | 0.000 | 0.007 | |
| eSetFilter | 0.001 | 0.000 | 0.001 | |
| filter_volcano | 0 | 0 | 0 | |
| filtered_p | 0 | 0 | 0 | |
| filterfun | 0.001 | 0.000 | 0.001 | |
| findLargest | 0.604 | 0.016 | 0.620 | |
| gapFilter | 0.001 | 0.000 | 0.001 | |
| genefilter | 0.001 | 0.000 | 0.002 | |
| genefinder | 0.054 | 0.004 | 0.058 | |
| genescale | 0.001 | 0.000 | 0.001 | |
| half.range.mode | 5.596 | 0.004 | 5.600 | |
| kOverA | 0 | 0 | 0 | |
| kappa_p | 0 | 0 | 0 | |
| maxA | 0 | 0 | 0 | |
| nsFilter | 0.550 | 0.008 | 0.558 | |
| pOverA | 0 | 0 | 0 | |
| rejection_plot | 0 | 0 | 0 | |
| rowFtests | 5.416 | 0.016 | 5.433 | |
| rowROC-class | 0.408 | 0.000 | 0.408 | |
| rowSds | 0.002 | 0.000 | 0.002 | |
| rowpAUCs | 1.672 | 0.008 | 1.710 | |
| shorth | 0.003 | 0.000 | 0.003 | |
| tdata | 0.001 | 0.000 | 0.001 | |
| ttest | 0.004 | 0.000 | 0.004 | |