| Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 793/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| genefilter 1.88.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
|
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: 1.88.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genefilter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genefilter_1.88.0.tar.gz |
| StartedAt: 2024-12-20 03:46:14 -0500 (Fri, 20 Dec 2024) |
| EndedAt: 2024-12-20 03:50:50 -0500 (Fri, 20 Dec 2024) |
| EllapsedTime: 275.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: genefilter.Rcheck |
| Warnings: 3 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genefilter.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genefilter_1.88.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/genefilter.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genefilter/DESCRIPTION’ ... OK
* this is package ‘genefilter’ version ‘1.88.0’
* 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:
half_range_mode.cpp:100:88: warning: format specifies type 'int' but the argument has type 'std::vector<int>::size_type' (aka 'unsigned long') [-Wformat]
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/genefilter.Rcheck/00install.out’ for details.
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... WARNING
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/genefilter/libs/genefilter.so’:
Found ‘___sprintf_chk’, possibly from ‘sprintf’ (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 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
half.range.mode 6.052 0.145 6.241
* 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: 3 WARNINGs, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/genefilter.Rcheck/00check.log’
for details.
genefilter.Rcheck/00install.out
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL genefilter
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘genefilter’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using Fortran compiler: ‘GNU Fortran (GCC) 12.2.0’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c half_range_mode.cpp -o half_range_mode.o
half_range_mode.cpp:100:88: warning: format specifies type 'int' but the argument has type 'std::vector<int>::size_type' (aka 'unsigned long') [-Wformat]
if (diag) Rprintf( "N = %i, N'' = %i, w = %.4f, |J| = %i\n", N, N_double_prime, w, J.size() );
~~ ^~~~~~~~
%lu
1 warning generated.
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nd.c -o nd.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pAUC.c -o pAUC.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rowPAUCs.c -o rowPAUCs.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rowttests.c -o rowttests.o
/opt/gfortran/bin/gfortran -arch x86_64 -fPIC -Wall -g -O2 -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]
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 | 0.017 | 0.001 | 0.019 | |
| coxfilter | 0.672 | 0.058 | 0.734 | |
| cv | 0.001 | 0.001 | 0.002 | |
| dist2 | 0.014 | 0.003 | 0.018 | |
| eSetFilter | 0.000 | 0.001 | 0.001 | |
| filter_volcano | 0.001 | 0.001 | 0.001 | |
| filtered_p | 0.000 | 0.001 | 0.000 | |
| filterfun | 0.001 | 0.000 | 0.002 | |
| findLargest | 0.922 | 0.057 | 0.999 | |
| gapFilter | 0.002 | 0.001 | 0.002 | |
| genefilter | 0.003 | 0.001 | 0.003 | |
| genefinder | 0.118 | 0.090 | 0.209 | |
| genescale | 0.001 | 0.001 | 0.002 | |
| half.range.mode | 6.052 | 0.145 | 6.241 | |
| kOverA | 0.000 | 0.000 | 0.001 | |
| kappa_p | 0.000 | 0.000 | 0.001 | |
| maxA | 0.000 | 0.000 | 0.001 | |
| nsFilter | 0.588 | 0.020 | 0.609 | |
| pOverA | 0.000 | 0.000 | 0.001 | |
| rejection_plot | 0 | 0 | 0 | |
| rowFtests | 1.502 | 0.106 | 1.613 | |
| rowROC-class | 0.105 | 0.007 | 0.112 | |
| rowSds | 0.003 | 0.001 | 0.003 | |
| rowpAUCs | 2.294 | 0.048 | 2.353 | |
| shorth | 0.006 | 0.001 | 0.007 | |
| tdata | 0.001 | 0.002 | 0.003 | |
| ttest | 0.007 | 0.001 | 0.008 | |