Package: MEIGOR

Version: 1.14.0

Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MEIGOR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings MEIGOR_1.14.0.tar.gz

StartedAt: 2018-10-17 03:09:17 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 03:11:50 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 153.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MEIGOR.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MEIGOR.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings MEIGOR_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/MEIGOR.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MEIGOR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MEIGOR' version '1.14.0'
* 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 'MEIGOR' can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'runif(seed = options$seed)': unused argument (seed = options$seed) 
See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/MEIGOR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* 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.
* 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
CeSSR: no visible global function definition for 'sd'
CeSSR: no visible binding for global variable 'sd'
between_chain_variances: no visible global function definition for
  'var'
essR: no visible global function definition for 'combn'
essR: no visible global function definition for 'runif'
essR_multistart: no visible global function definition for 'runif'
essR_multistart: no visible global function definition for 'hist'
estimate: no visible global function definition for 'runif'
generate_new_position: no visible global function definition for
  'rnorm'
initialize: no visible global function definition for 'runif'
initialize_and_pool: no visible binding for global variable 'mulichain'
nls_fobj: no visible binding for global variable 'fobj_global'
nls_fobj: no visible binding for '<<-' assignment to 'n_fun_eval'
nls_fobj: no visible binding for global variable 'n_fun_eval'
optim_fobj: no visible binding for global variable 'fobj_global'
optim_fobj: no visible binding for '<<-' assignment to 'n_fun_eval'
optim_fobj: no visible binding for global variable 'n_fun_eval'
runBayesFit : prior: no visible binding for global variable
  'prior_mean'
runBayesFit : prior: no visible binding for global variable 'prior_var'
rvnds_hamming: no visible global function definition for 'runif'
solnp_eq: no visible binding for global variable 'fobj_global'
solnp_eq: no visible binding for '<<-' assignment to 'n_fun_eval'
solnp_eq: no visible binding for global variable 'n_fun_eval'
solnp_eq: no visible binding for global variable 'neq_global'
solnp_fobj: no visible binding for global variable 'fobj_global'
solnp_fobj: no visible binding for '<<-' assignment to 'n_fun_eval'
solnp_fobj: no visible binding for global variable 'n_fun_eval'
solnp_ineq: no visible binding for global variable 'fobj_global'
solnp_ineq: no visible binding for '<<-' assignment to 'n_fun_eval'
solnp_ineq: no visible binding for global variable 'n_fun_eval'
solnp_ineq: no visible binding for global variable 'neq_global'
solnp_ineq: no visible binding for global variable 'nconst_global'
ssm_beyond: no visible global function definition for 'runif'
ssm_defaults: no visible binding for global variable 'plot'
ssm_localsolver: no visible binding for '<<-' assignment to
  'n_fun_eval'
ssm_localsolver: no visible binding for '<<-' assignment to
  'fobj_global'
ssm_localsolver: no visible binding for '<<-' assignment to
  'neq_global'
ssm_localsolver: no visible binding for '<<-' assignment to
  'nconst_global'
ssm_localsolver: no visible binding for '<<-' assignment to
  'extra_args'
ssm_localsolver: no visible global function definition for 'optim'
ssm_localsolver: no visible binding for global variable 'n_fun_eval'
ssm_localsolver: no visible global function definition for 'nls'
ssm_localsolver: no visible binding for global variable 'extra_args'
ssm_localsolver: no visible global function definition for 'coef'
within_chain_variances: no visible global function definition for 'var'
Undefined global functions or variables:
  coef combn extra_args fobj_global hist mulichain n_fun_eval
  nconst_global neq_global nls optim plot prior_mean prior_var rnorm
  runif sd var
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "coef", "nls", "optim", "rnorm", "runif", "sd",
             "var")
  importFrom("utils", "combn")
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
essR        9.30   0.05    9.35
runBayesFit 8.62   0.03    8.65
cur_params  7.64   0.03    7.67
CeVNSR      0.42   0.01    8.22
CeSSR       0.11   0.06    5.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
runBayesFit 9.69   0.00    9.68
essR        9.55   0.03    9.58
cur_params  9.41   0.02    9.44
CeVNSR      0.41   0.02    8.88
CeSSR       0.14   0.01    5.51
* 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
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/MEIGOR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/MEIGOR_1.14.0.tar.gz && rm -rf MEIGOR.buildbin-libdir && mkdir MEIGOR.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MEIGOR.buildbin-libdir MEIGOR_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL MEIGOR_1.14.0.zip && rm MEIGOR_1.14.0.tar.gz MEIGOR_1.14.0.zip
###
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install for i386

* installing *source* package 'MEIGOR' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'runif(seed = options$seed)': unused argument (seed = options$seed) 
** help
*** installing help indices
  converting help for package 'MEIGOR'
    finding HTML links ... done
    BayesFit                                html  
    CeSSR                                   html  
    CeVNSR                                  html  
    MEIGO                                   html  
    MEIGOR-package                          html  
    cnolist                                 html  
    cur_params                              html  
    dhc                                     html  
    essR-MEIGOR                             html  
    essR                                    html  
    essR_multistart                         html  
    eucl_dist                               html  
    ith_VNSR                                html  
    ith_essR                                html  
    model                                   html  
    nls_fobj                                html  
    optim_fobj                              html  
    paramsOpt                               html  
    runBayesFit                             html  
    rvnds_hamming                           html  
    rvnds_local                             html  
    solnp_eq                                html  
    solnp_fobj                              html  
    solnp_ineq                              html  
    ssm_beyond                              html  
    ssm_defaults                            html  
    ssm_evalfc                              html  
    ssm_isdif2                              html  
    ssm_localsolver                         html  
    ssm_optset                              html  
    ssm_penalty_function                    html  
    ssm_round_int                           html  
    vns_defaults                            html  
    vns_optset                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'MEIGOR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MEIGOR' as MEIGOR_1.14.0.zip
* DONE (MEIGOR)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'MEIGOR' successfully unpacked and MD5 sums checked
In R CMD INSTALL