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CHECK report for lfa on tokay1

This page was generated on 2018-04-12 13:26:56 -0400 (Thu, 12 Apr 2018).

Package 744/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lfa 1.8.0
Wei Hao , John D. Storey
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/lfa
Branch: RELEASE_3_6
Last Commit: 6863217
Last Changed Date: 2017-10-30 12:41:05 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: lfa
Version: 1.8.0
Command: rm -rf lfa.buildbin-libdir lfa.Rcheck && mkdir lfa.buildbin-libdir lfa.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lfa.buildbin-libdir lfa_1.8.0.tar.gz >lfa.Rcheck\00install.out 2>&1 && cp lfa.Rcheck\00install.out lfa-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=lfa.buildbin-libdir --install="check:lfa-install.out" --force-multiarch --no-vignettes --timings lfa_1.8.0.tar.gz
StartedAt: 2018-04-12 01:01:01 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 01:02:41 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 99.2 seconds
RetCode: 0
Status:  OK  
CheckDir: lfa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf lfa.buildbin-libdir lfa.Rcheck && mkdir lfa.buildbin-libdir lfa.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=lfa.buildbin-libdir lfa_1.8.0.tar.gz >lfa.Rcheck\00install.out 2>&1 && cp lfa.Rcheck\00install.out lfa-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=lfa.buildbin-libdir --install="check:lfa-install.out" --force-multiarch --no-vignettes --timings lfa_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/lfa.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'lfa/DESCRIPTION' ... OK
* this is package 'lfa' version '1.8.0'
* 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 whether package 'lfa' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
compute.nulls: no visible global function definition for 'rbinom'
lfa: no visible global function definition for 'complete.cases'
lfa: no visible global function definition for 'residuals'
lfa: no visible global function definition for 'lm'
lreg: no visible global function definition for 'glm'
read.bed: no visible global function definition for 'read.table'
trunc.svd: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  complete.cases glm lm rbinom read.table residuals rnorm
Consider adding
  importFrom("stats", "complete.cases", "glm", "lm", "rbinom",
             "residuals", "rnorm")
  importFrom("utils", "read.table")
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 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/lfa.buildbin-libdir/lfa/libs/i386/lfa.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
model.gof 29.11   0.32   29.44
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
model.gof 27.73   0.11   27.85
* 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/lfa.Rcheck/00check.log'
for details.



Installation output

lfa.Rcheck/00install.out


install for i386

* installing *source* package 'lfa' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c fastmat.c -o fastmat.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c lfa-init.c -o lfa-init.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c lfa.c -o lfa.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c lreg.c -o lreg.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o lfa.dll tmp.def fastmat.o lfa-init.o lfa.o lreg.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/lfa.buildbin-libdir/lfa/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'lfa'
    finding HTML links ... done
    af                                      html  
    af_snp                                  html  
    center                                  html  
    centerscale                             html  
    hgdp_subset                             html  
    lfa                                     html  
    model.gof                               html  
    pca_af                                  html  
    read.bed                                html  
    read.tped.recode                        html  
    trunc.svd                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'lfa' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c fastmat.c -o fastmat.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c lfa-init.c -o lfa-init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c lfa.c -o lfa.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c lreg.c -o lreg.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o lfa.dll tmp.def fastmat.o lfa-init.o lfa.o lreg.o -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/lfa.buildbin-libdir/lfa/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'lfa' as lfa_1.8.0.zip
* DONE (lfa)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

lfa.Rcheck/examples_i386/lfa-Ex.timings

nameusersystemelapsed
af2.200.062.27
center0.500.110.61
centerscale0.480.100.58
lfa0.640.000.64
model.gof29.11 0.3229.44
pca_af2.640.072.70
read.bed000
read.tped.recode000

lfa.Rcheck/examples_x64/lfa-Ex.timings

nameusersystemelapsed
af2.200.072.29
center0.540.180.72
centerscale0.350.150.50
lfa0.550.020.56
model.gof27.73 0.1127.85
pca_af3.140.093.23
read.bed000
read.tped.recode000