Package: mgsa

Version: 1.30.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mgsa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mgsa_1.30.0.tar.gz

StartedAt: 2019-04-16 01:15:34 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:16:27 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 52.5 seconds

RetCode: 0

Status:  OK

CheckDir: mgsa.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mgsa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mgsa_1.30.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/mgsa.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mgsa/DESCRIPTION’ ... OK
* this is package ‘mgsa’ version ‘1.30.0’
* 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 ‘mgsa’ 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘mgsa’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘gplots’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘DBI’ ‘GO.db’ ‘RSQLite’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘gplots’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
createMgsaGoSets: no visible global function definition for ‘new’
mcmcSummary: no visible binding for global variable ‘sd’
mgsa.wrapper: no visible global function definition for ‘str’
mgsa.wrapper: no visible global function definition for ‘new’
readGAF: no visible global function definition for ‘read.delim’
readGAF: no visible global function definition for ‘na.omit’
readGAF: no visible global function definition for ‘new’
initialize,MgsaSets: no visible global function definition for
  ‘callNextMethod’
initialize,MgsaSets: no visible global function definition for ‘relist’
mgsa,character-MgsaSets: no visible global function definition for
  ‘na.omit’
plot,MgsaResults: no visible global function definition for
  ‘split.screen’
plot,MgsaResults: no visible global function definition for ‘screen’
plot,MgsaResults: no visible global function definition for ‘par’
plot,MgsaResults: no visible global function definition for ‘barplot2’
plot,MgsaResults: no visible global function definition for
  ‘close.screen’
Undefined global functions or variables:
  barplot2 callNextMethod close.screen na.omit new par read.delim
  relist screen sd split.screen str
Consider adding
  importFrom("graphics", "close.screen", "par", "screen", "split.screen")
  importFrom("methods", "callNextMethod", "new")
  importFrom("stats", "na.omit", "sd")
  importFrom("utils", "read.delim", "relist", "str")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 shell scripts ... 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
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/mgsa/libs/mgsa.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)

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
Examples with CPU or elapsed time > 5s
              user system elapsed
mgsa-methods 5.572  1.634   1.281
readGAF      6.026  0.637   6.737
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/mgsa.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL mgsa
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘mgsa’ ...
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c mgsa-core.c -o mgsa-core.o
mgsa-core.c:796:13: warning: unused function 'print_context' [-Wunused-function]
static void print_context(struct context *cn)
            ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c mgsa.c -o mgsa.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I. -fopenmp -fPIC  -Wall -g -O2  -c mt.c -o mt.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 mgsa.so mgsa-core.o mgsa.o mt.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/mgsa/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mgsa)

R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("testthat")
> library("mgsa")
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

> 
> 
> test_check("mgsa")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 25 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 13.894   4.984  10.590 

name	user	system	elapsed
MgsaSets-class	0.008	0.000	0.008
mgsa-methods	5.572	1.634	1.281
readGAF	6.026	0.637	6.737