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CHECK report for MEIGOR on tokay2

This page was generated on 2020-10-17 11:57:02 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE MEIGOR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1021/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MEIGOR 1.22.0
Jose A. Egea
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/MEIGOR
Branch: RELEASE_3_11
Last Commit: fd6dc85
Last Changed Date: 2020-07-07 04:54:35 -0400 (Tue, 07 Jul 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: MEIGOR
Version: 1.22.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MEIGOR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MEIGOR_1.22.0.tar.gz
StartedAt: 2020-10-17 05:46:20 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:49:15 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 175.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: MEIGOR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MEIGOR.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings MEIGOR_1.22.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/MEIGOR.Rcheck'
* using R version 4.0.3 (2020-10-10)
* 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 '1.22.0'
* 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-3.11-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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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_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 prior_mean prior_var rnorm runif
  sd var
Consider adding
  importFrom("graphics", "hist")
  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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following files look like leftovers/mistakes:
  'MEIGOR-vignette.bbl'
Please remove them from your package.
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
cur_params  12.15   0.08   12.29
runBayesFit 10.52   0.09   10.61
essR         9.36   0.03    9.41
CeSSR        0.13   0.02    6.16
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
cur_params  12.88   0.08   13.25
essR         9.86   0.00    9.91
runBayesFit  8.89   0.09    8.98
CeSSR        0.06   0.01    5.72
* 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, 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/MEIGOR.Rcheck/00check.log'
for details.



Installation output

MEIGOR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/MEIGOR_1.22.0.tar.gz && rm -rf MEIGOR.buildbin-libdir && mkdir MEIGOR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MEIGOR.buildbin-libdir MEIGOR_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL MEIGOR_1.22.0.zip && rm MEIGOR_1.22.0.tar.gz MEIGOR_1.22.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2375k  100 2375k    0     0  25.4M      0 --:--:-- --:--:-- --:--:-- 27.6M

install for i386

* installing *source* package 'MEIGOR' ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'MEIGOR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MEIGOR' as MEIGOR_1.22.0.zip
* DONE (MEIGOR)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'MEIGOR' successfully unpacked and MD5 sums checked

Tests output


Example timings

MEIGOR.Rcheck/examples_i386/MEIGOR-Ex.timings

nameusersystemelapsed
CeSSR0.130.026.16
MEIGO0.060.010.09
cur_params12.15 0.0812.29
essR9.360.039.41
runBayesFit10.52 0.0910.61
rvnds_hamming0.140.000.14

MEIGOR.Rcheck/examples_x64/MEIGOR-Ex.timings

nameusersystemelapsed
CeSSR0.060.015.72
MEIGO0.090.000.09
cur_params12.88 0.0813.25
essR9.860.009.91
runBayesFit8.890.098.98
rvnds_hamming0.110.000.11