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### Running command:
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###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:PERFect.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings PERFect_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/PERFect.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PERFect/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PERFect’ version ‘1.18.0’
* package encoding: UTF-8
* 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 ‘PERFect’ 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 loading without being on the library search path ... 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) DiffFiltLoss.Rd:28: Lost braces; missing escapes or markup?
    28 | for removing the first j taxa as DFL(j+1) = FL(J_{j+1}) - FL(J_j) for taxa j=1, ..., p.
       |                                                  ^
checkRd: (-1) FiltLoss.Rd:38: Lost braces; missing escapes or markup?
    38 | FL_u(j)= 1- (||X^T_{-j} X_{-j}||_F^2/||X^TX||_F^2),
       |                    ^
checkRd: (-1) FiltLoss.Rd:38: Lost braces; missing escapes or markup?
    38 | FL_u(j)= 1- (||X^T_{-j} X_{-j}||_F^2/||X^TX||_F^2),
       |                           ^
checkRd: (-1) FiltLoss.Rd:40: Lost braces; missing escapes or markup?
    40 | where X_{-j} is the matrix X without column corresponding to jth taxon and ||Z||_F is the Frobenious norm of a matrix Z.
       |         ^
checkRd: (-1) FiltLoss.Rd:44: Lost braces; missing escapes or markup?
    44 | FL(J)= 1- (||X^T_{-J}  X_{-J}||_F^2\||X^TX||_F^2),
       |                  ^
checkRd: (-1) FiltLoss.Rd:44: Lost braces; missing escapes or markup?
    44 | FL(J)= 1- (||X^T_{-J}  X_{-J}||_F^2\||X^TX||_F^2),
       |                          ^
checkRd: (-1) FiltLoss.Rd:46: Lost braces; missing escapes or markup?
    46 | where X_{-J} is the n x (p-|J|) dimensional matrix obtained by removing the columns indexed by the set J from the data matrix X.
       |         ^
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/PERFect.Rcheck/00check.log’
for details.