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This page was generated on 2022-04-13 12:08:17 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 machv2


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? 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 1080/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MEIGOR 1.28.0  (landing page)
Jose A. Egea
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/MEIGOR
git_branch: RELEASE_3_14
git_last_commit: 2debaf5
git_last_commit_date: 2021-10-26 12:14:40 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: MEIGOR
Version: 1.28.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MEIGOR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MEIGOR_1.28.0.tar.gz
StartedAt: 2022-04-12 15:07:16 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 15:09:51 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 155.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MEIGOR.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MEIGOR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MEIGOR_1.28.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/MEIGOR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEIGOR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MEIGOR’ version ‘1.28.0’
* 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 ‘MEIGOR’ can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'runif(seed = options$seed)': unused argument (seed = options$seed) 
See ‘/Users/biocbuild/bbs-3.14-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 sizes of PDF files under ‘inst/doc’ ... 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
runBayesFit 18.023  0.755  18.833
cur_params  18.018  0.741  18.780
essR         9.530  0.113   9.706
CeSSR        0.138  0.024   7.789
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/MEIGOR.Rcheck/00check.log’
for details.



Installation output

MEIGOR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MEIGOR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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
** 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)

Tests output


Example timings

MEIGOR.Rcheck/MEIGOR-Ex.timings

nameusersystemelapsed
CeSSR0.1380.0247.789
MEIGO0.1000.0090.109
cur_params18.018 0.74118.780
essR9.5300.1139.706
runBayesFit18.023 0.75518.833
rvnds_hamming0.1730.0070.180