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

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### Running command:
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###   /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
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* 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.

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

name	user	system	elapsed
af	2.175	0.040	2.215
center	0.505	0.224	0.729
centerscale	0.548	0.212	0.759
lfa	0.683	0.008	0.692
model.gof	26.033	0.044	26.255
pca_af	2.100	0.024	2.123
read.bed	0	0	0
read.tped.recode	0	0	0
sHWE	22.105	0.036	22.147