Jose A. Egea
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/MEIGOR |
| git_branch: RELEASE_3_13 |
| git_last_commit: c728ace |
| git_last_commit_date: 2021-05-19 12:06:10 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:11 -0400 (Fri, 15 Oct 2021).
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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. |
| Package 1067/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MEIGOR 1.26.0 (landing page) Jose A. Egea
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: MEIGOR |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MEIGOR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MEIGOR_1.26.0.tar.gz |
| StartedAt: 2021-10-15 01:30:30 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 01:33:08 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 158.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MEIGOR.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MEIGOR.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MEIGOR_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MEIGOR.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '1.26.0'
* 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-3.13-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
essR 9.34 0.00 9.34
runBayesFit 8.22 0.06 8.28
cur_params 8.09 0.10 8.19
CeSSR 0.17 0.00 5.31
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
essR 9.36 0.02 9.38
cur_params 8.97 0.03 9.00
runBayesFit 8.12 0.04 8.17
CeSSR 0.11 0.05 5.37
* 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-3.13-bioc/meat/MEIGOR.Rcheck/00check.log'
for details.
MEIGOR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MEIGOR_1.26.0.tar.gz && rm -rf MEIGOR.buildbin-libdir && mkdir MEIGOR.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MEIGOR.buildbin-libdir MEIGOR_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MEIGOR_1.26.0.zip && rm MEIGOR_1.26.0.tar.gz MEIGOR_1.26.0.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
63 2373k 63 1504k 0 0 1857k 0 0:00:01 --:--:-- 0:00:01 1856k
100 2373k 100 2373k 0 0 2126k 0 0:00:01 0:00:01 --:--:-- 2128k
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_1.26.0.zip
* DONE (MEIGOR)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MEIGOR' successfully unpacked and MD5 sums checked
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MEIGOR.Rcheck/examples_i386/MEIGOR-Ex.timings
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MEIGOR.Rcheck/examples_x64/MEIGOR-Ex.timings
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