Back to Multiple platform build/check report for BioC 3.9
ABCDEFGHIJK[L]MNOPQRSTUVWXYZ

CHECK report for lfa on malbec2

This page was generated on 2019-04-09 11:43:51 -0400 (Tue, 09 Apr 2019).

Package 855/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
lfa 1.13.0
Wei Hao , John D. Storey
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/lfa
Branch: master
Last Commit: adae5ff
Last Changed Date: 2018-10-30 11:54:35 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: lfa
Version: 1.13.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:lfa.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings lfa_1.13.0.tar.gz
StartedAt: 2019-04-09 01:34:34 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:35:48 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 73.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: lfa.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:lfa.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings lfa_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/lfa.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘lfa/DESCRIPTION’ ... OK
* this is package ‘lfa’ version ‘1.13.0’
* 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 ‘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
* 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 ... WARNING
Codoc mismatches from documentation object 'lfa':
lfa
  Code: function(X, d, adjustments = NULL, override = FALSE, safety =
                 FALSE, ploidy = 2)
  Docs: function(X, d, adjustments = NULL, override = FALSE, safety =
                 FALSE)
  Argument names in code not in docs:
    ploidy

* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
model.gof 26.033  0.044  26.255
sHWE      22.105  0.036  22.147
* 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, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/lfa.Rcheck/00check.log’
for details.



Installation output

lfa.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL lfa
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘lfa’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c fastmat.c -o fastmat.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c lfa-init.c -o lfa-init.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c lfa.c -o lfa.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c lreg.c -o lreg.o
gcc -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o lfa.so fastmat.o lfa-init.o lfa.o lreg.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-lfa/00new/lfa/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (lfa)

Tests output


Example timings

lfa.Rcheck/lfa-Ex.timings

nameusersystemelapsed
af2.1750.0402.215
center0.5050.2240.729
centerscale0.5480.2120.759
lfa0.6830.0080.692
model.gof26.033 0.04426.255
pca_af2.1000.0242.123
read.bed000
read.tped.recode000
sHWE22.105 0.03622.147