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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netresponse.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netresponse_1.64.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/netresponse.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netresponse/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netresponse’ version ‘1.64.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocStyle', 'Rgraphviz', 'rmarkdown', 'minet', 'mclust', 'reshape2'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘netresponse’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... 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 ... OK
* checking Rd files ... NOTE
checkRd: (-1) vdp.mixt.Rd:88: Lost braces; missing escapes or markup?
    88 |    'Nc' = \\sum_{n=1}^N q_{z_n} (z_n = c) (larger is better).
       |                 ^
checkRd: (-1) vdp.mixt.Rd:88: Lost braces; missing escapes or markup?
    88 |    'Nc' = \\sum_{n=1}^N q_{z_n} (z_n = c) (larger is better).
       |                           ^
checkRd: (-1) vdp.mixt.Rd:92: Lost braces; missing escapes or markup?
    92 |         q_{z_n}(z_n = c_1) and q_{z_n}(z_n = c_2). 
       |           ^
checkRd: (-1) vdp.mixt.Rd:92: Lost braces; missing escapes or markup?
    92 |         q_{z_n}(z_n = c_1) and q_{z_n}(z_n = c_2). 
       |                                  ^
checkRd: (-1) vdp.mixt.Rd:94: Lost braces
    94 |         belonged to c, and determine the new value for the free energy, F{T+1}.
       |                                                                          ^
checkRd: (-1) vdp.mixt.Rd:97: Lost braces
    97 | 4. Select the split that lead to the maximal reduction of free energy, F{T+1}.
       |                                                                         ^
checkRd: (-1) vdp.mixt.Rd:99: Lost braces
    99 | 6. If FT - F{T+1} < \\epsilon then halt, else set T := T +1 and go to step 2.
       |             ^
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'generate.toydata.Rd':
  ‘Dim’ ‘Nc’ ‘Ns’ ‘sd0’ ‘rgam.shape’ ‘rgam.scale’
Assignments in \usage in Rd file 'generate.toydata.Rd':
  D <- generate.toydata()

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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘bicmixture.R’
  Running ‘mixture.model.test.R’
  Running ‘mixture.model.test.multimodal.R’
  Running ‘mixture.model.test.singlemode.R’
  Running ‘timing.R’
  Running ‘toydata2.R’
  Running ‘validate.netresponse.R’
  Running ‘vdpmixture.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/netresponse.Rcheck/00check.log’
for details.