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This page was generated on 2022-03-16 11:07:53 -0400 (Wed, 16 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4060
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4081
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4133
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for MEIGOR on riesling1


To the developers/maintainers of the MEIGOR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MEIGOR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1084/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MEIGOR 1.29.0  (landing page)
Jose A. Egea
Snapshot Date: 2022-03-15 13:55:23 -0400 (Tue, 15 Mar 2022)
git_url: https://git.bioconductor.org/packages/MEIGOR
git_branch: master
git_last_commit: 49fbd50
git_last_commit_date: 2021-10-26 12:14:40 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'CNORode' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MEIGOR
Version: 1.29.0
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MEIGOR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MEIGOR_1.29.0.tar.gz
StartedAt: 2022-03-15 19:22:31 -0400 (Tue, 15 Mar 2022)
EndedAt: 2022-03-15 19:24:04 -0400 (Tue, 15 Mar 2022)
EllapsedTime: 92.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MEIGOR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MEIGOR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MEIGOR_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MEIGOR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.29.0'
* 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 'D:/biocbuild/bbs-3.15-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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
essR        9.70   0.03    9.85
runBayesFit 6.45   0.06    6.78
cur_params  5.88   0.07    5.93
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/MEIGOR.Rcheck/00check.log'
for details.



Installation output

MEIGOR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MEIGOR
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (MEIGOR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'PAIRADISE' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'universalmotif' is missing or broken
 done

Tests output


Example timings

MEIGOR.Rcheck/MEIGOR-Ex.timings

nameusersystemelapsed
CeSSR0.080.014.49
MEIGO0.030.000.03
cur_params5.880.075.93
essR9.700.039.85
runBayesFit6.450.066.78
rvnds_hamming0.050.000.05