Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 12:56:44 -0400 (Tue, 09 Apr 2019).
Package 630/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
GeneSelectMMD 2.27.0 Weiliang Qiu
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
Package: GeneSelectMMD |
Version: 2.27.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneSelectMMD.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneSelectMMD_2.27.0.tar.gz |
StartedAt: 2019-04-09 02:12:30 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 02:13:26 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 55.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: GeneSelectMMD.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneSelectMMD.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneSelectMMD_2.27.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GeneSelectMMD.Rcheck’ * using R Under development (unstable) (2019-03-18 r76245) * using platform: x86_64-apple-darwin15.6.0 (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 ‘2.27.0’ * 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 ... NOTE Malformed Description field: should contain one or more complete sentences. Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘Biobase’ A package should be listed in only one of these fields. * 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 Namespace in Imports field not imported from: ‘survival’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE obtainResi: no visible global function definition for ‘pData’ obtainResi: no visible global function definition for ‘exprs<-’ obtainResi: no visible global function definition for ‘pData<-’ optimalLambda: no visible global function definition for ‘optimize’ Undefined global functions or variables: exprs<- optimize pData pData<- Consider adding importFrom("stats", "optimize") to your NAMESPACE file. * 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/3.6/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, 3 NOTEs See ‘/Users/biocbuild/bbs-3.9-bioc/meat/GeneSelectMMD.Rcheck/00check.log’ for details.
GeneSelectMMD.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneSelectMMD ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘GeneSelectMMD’ ... ** using staged installation ** libs gfortran -fPIC -Wall -g -O2 -c Qfunc.f -o Qfunc.o gfortran -fPIC -Wall -g -O2 -c blas.f -o blas.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c isnan.c -o isnan.o gfortran -fPIC -Wall -g -O2 -c lbfgsb.f -o lbfgsb.o lbfgsb.f:1491:0: t(nbreak) = tu/neggi 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 -fPIC -Wall -g -O2 -c lbfgsbDriver.f -o lbfgsbDriver.o gfortran -fPIC -Wall -g -O2 -c linpack.f -o linpack.o gfortran -fPIC -Wall -g -O2 -c llkhFun.f -o llkhFun.o gfortran -fPIC -Wall -g -O2 -c myTtest.f -o myTtest.o gfortran -fPIC -Wall -g -O2 -c paraEstLoop.f -o paraEstLoop.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c pt.c -o pt.o gfortran -fPIC -Wall -g -O2 -c timer.f -o timer.o gfortran -fPIC -Wall -g -O2 -c wiFun.f -o wiFun.o clang -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 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-darwin15/6.1.0 -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/3.6/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)
GeneSelectMMD.Rcheck/GeneSelectMMD-Ex.timings
name | user | system | elapsed | |
errRates | 0.001 | 0.000 | 0.001 | |
gsMMD | 1.541 | 0.150 | 1.697 | |
gsMMD.default | 0.000 | 0.001 | 0.001 | |
gsMMD2 | 0.001 | 0.001 | 0.001 | |
gsMMD2.default | 0.000 | 0.001 | 0.001 | |
plotHistDensity | 0.001 | 0.001 | 0.001 | |