Package: sagenhaft

Version: 1.56.0

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sagenhaft.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings sagenhaft_1.56.0.tar.gz

StartedAt: 2020-04-15 06:22:13 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 06:24:38 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 144.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: sagenhaft.Rcheck

Warnings: 1

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### Running command:
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###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sagenhaft.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings sagenhaft_1.56.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/sagenhaft.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'sagenhaft/DESCRIPTION' ... OK
* this is package 'sagenhaft' version '1.56.0'
* 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 'sagenhaft' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    extdata   7.0Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'methods' 'SparseM'
A package should be listed in only one of these fields.
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.sage.library plot.sage.library.comparison print.sage.library
  print.sage.library.comparison summary.sage.library
  summary.sage.library.comparison
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
sage.test: warning in dbinom(0:isize, p = (prob[i])[1], size = isize):
  partial argument match of 'p' to 'prob'
extract.lib.from.zip: no visible global function definition for
  'zip.unpack'
Undefined global functions or variables:
  zip.unpack
Consider adding
  importFrom("utils", "zip.unpack")
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 ... WARNING
Documented arguments not in \usage in documentation object 'sage.utilities':
  '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
error.correction     45.99   0.74   47.14
sagelibrary.simulate 13.45   0.25   13.75
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
error.correction     37.64   0.52   38.16
sagelibrary.simulate 10.54   0.11   10.69
* 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-3.10-bioc/meat/sagenhaft.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/sagenhaft_1.56.0.tar.gz && rm -rf sagenhaft.buildbin-libdir && mkdir sagenhaft.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sagenhaft.buildbin-libdir sagenhaft_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL sagenhaft_1.56.0.zip && rm sagenhaft_1.56.0.tar.gz sagenhaft_1.56.0.zip
###
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100 2484k  100 2484k    0     0  42.1M      0 --:--:-- --:--:-- --:--:-- 44.9M

install for i386

* installing *source* package 'sagenhaft' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sagenhaft'
    finding HTML links ... done
    error.correction                        html  
    extract.lib                             html  
    sage.library                            html  
    sage.library.comparison                 html  
    sage.test                               html  
    sage.utilities                          html  
    sagelibrary.simulate                    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 'sagenhaft' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sagenhaft' as sagenhaft_1.56.0.zip
* DONE (sagenhaft)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'sagenhaft' successfully unpacked and MD5 sums checked