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This page was generated on 2022-10-19 13:22:59 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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

CHECK results for GeneSelectMMD on merida1


To the developers/maintainers of the GeneSelectMMD package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneSelectMMD.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.

raw results

Package 755/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneSelectMMD 2.40.0  (landing page)
Weiliang Qiu
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/GeneSelectMMD
git_branch: RELEASE_3_15
git_last_commit: 0adb1bb
git_last_commit_date: 2022-04-26 11:02:44 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: GeneSelectMMD
Version: 2.40.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneSelectMMD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneSelectMMD_2.40.0.tar.gz
StartedAt: 2022-10-19 02:45:48 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 02:46:48 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 60.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: GeneSelectMMD.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneSelectMMD.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneSelectMMD_2.40.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/GeneSelectMMD.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneSelectMMD/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneSelectMMD’ version ‘2.40.0’
* 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 ‘GeneSelectMMD’ can be installed ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 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/4.2/Resources/library/GeneSelectMMD/libs/GeneSelectMMD.so’:
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (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. 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/GeneSelectMMD.Rcheck/00check.log’
for details.



Installation output

GeneSelectMMD.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneSelectMMD
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘GeneSelectMMD’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c GeneSelectMMD_init.c -o GeneSelectMMD_init.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c Qfunc.f -o Qfunc.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c blas.f -o blas.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c isnan.c -o isnan.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c lbfgsb.f -o lbfgsb.o
lbfgsb.f:1409:0:

      +                 tu,tl,wmc,wmp,wmw,ddot,tj,tj0,neggi,sbgnrm,
 
Warning: ‘tu’ may be used uninitialized in this function [-Wmaybe-uninitialized]
lbfgsb.f:1482:0:

                t(nbreak) = tl/(-neggi)
 
Warning: ‘tl’ may be used uninitialized in this function [-Wmaybe-uninitialized]
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c lbfgsbDriver.f -o lbfgsbDriver.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c linpack.f -o linpack.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c llkhFun.f -o llkhFun.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c myTtest.f -o myTtest.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c paraEstLoop.f -o paraEstLoop.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c pt.c -o pt.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c timer.f -o timer.o
gfortran -mmacosx-version-min=10.13 -fno-optimize-sibling-calls  -fPIC  -Wall -g -O2  -c wiFun.f -o wiFun.o
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o GeneSelectMMD.so GeneSelectMMD_init.o Qfunc.o blas.o isnan.o lbfgsb.o lbfgsbDriver.o linpack.o llkhFun.o myTtest.o paraEstLoop.o pt.o timer.o wiFun.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: could not create compact unwind for _lbfgsbdriver_: stack subq instruction is too different from dwarf stack size
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-GeneSelectMMD/00new/GeneSelectMMD/libs
** R
** 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 (GeneSelectMMD)

Tests output


Example timings

GeneSelectMMD.Rcheck/GeneSelectMMD-Ex.timings

nameusersystemelapsed
errRates0.0010.0000.000
gsMMD1.8110.0781.902
gsMMD.default0.0010.0000.001
gsMMD20.0000.0010.001
gsMMD2.default0.0000.0000.001
plotHistDensity0.0000.0000.001