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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:netSmooth.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings netSmooth_1.27.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/netSmooth.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘netSmooth/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘netSmooth’ version ‘1.27.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘netSmooth’ can be installed ... OK
* 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 dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
* 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) human.ppi.Rd:7: Lost braces; missing escapes or markup?
     7 | \format{A square matrix where A_{ij}=1 if gene i interacts with gene j}
       |                                 ^
checkRd: (-1) mouse.ppi.Rd:7: Lost braces; missing escapes or markup?
     7 | \format{A square matrix where A_{ij}=1 if gene i interacts with gene j}
       |                                 ^
checkRd: (-1) randomWalkByMatrixInv-matrix-method.Rd:29: Lost braces; missing escapes or markup?
    29 |   f_{ss} = (1 - alpha) * (I - alpha * A)^{-1} * f_0
       |     ^
checkRd: (-1) randomWalkByMatrixInv-matrix-method.Rd:29: Lost braces; missing escapes or markup?
    29 |   f_{ss} = (1 - alpha) * (I - alpha * A)^{-1} * f_0
       |                                          ^
* 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 'projectFromNetworkRecombine-matrix-method.Rd':
  ‘filepath’

Documented arguments not in \usage in Rd file 'smoothAndRecombine-matrix-method.Rd':
  ‘filepath’

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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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-3.21-bioc/meat/netSmooth.Rcheck/00check.log’
for details.