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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:RTopper.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings RTopper_1.53.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RTopper.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘RTopper/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RTopper’ version ‘1.53.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RTopper’ 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 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) adjustPvalGSE.Rd:25: Lost braces
    25 |       \code{"SidakSS"}, code{"SidakSD"}, \code{"BH"} (the default),
       |                             ^
checkRd: (-1) computeDrStat.Rd:39: Lost braces
    39 |   \code{"dev"}{: this approach computes the score as the difference of deviances;}
       |               ^
checkRd: (-1) computeDrStat.Rd:41-42: Lost braces
    41 |   \code{"aic"}{: this approach computes the score as the Akaike
       |               ^
checkRd: (-1) computeDrStat.Rd:44: Lost braces
    44 |   \code{"bic"}{: this approach computes the score as the penalized likelihood ratio;}
       |               ^
checkRd: (-1) dat.Rd:31: Lost braces
    31 |   \code{"dat.affy"}{: DGE obtained using Affymetrix microarrays;}
       |                    ^
checkRd: (-1) dat.Rd:33: Lost braces
    33 |   \code{"dat.agilent"}{: DGE obtained using Agilent microarrays;}
       |                       ^
checkRd: (-1) dat.Rd:35: Lost braces
    35 |   \code{"dat.cnvHarvard"}{: CNV data obtained at Harvard;}
       |                          ^
checkRd: (-1) dat.Rd:37: Lost braces
    37 |   \code{"dat.cnvMskcc"}{: CNV data obtained at Memorial Sloan Ketterng Cancer Center;}
       |                        ^
checkRd: (-1) fgsList.Rd:25-27: Lost braces
    25 |   \code{"go"}{: this is a \code{list} of 5 \code{character} vectors,
       |              ^
checkRd: (-1) fgsList.Rd:29-31: Lost braces
    29 |   \code{"kegg"}{: this is a \code{list} of 5 \code{character} vectors,
       |                ^
checkRd: (-1) gseResultsSep.Rd:30-36: Lost braces
    30 |   \code{"dat.affy"}{: a \code{list} of legnth two:
       |                    ^
checkRd: (-1) gseResultsSep.Rd:38-44: Lost braces
    38 |   \code{"dat.agilent"}{: a \code{list} of legnth two:
       |                       ^
checkRd: (-1) gseResultsSep.Rd:46-52: Lost braces
    46 |   \code{"dat.cnvHarvard"}{: a \code{list} of legnth two:
       |                          ^
checkRd: (-1) gseResultsSep.Rd:54-60: Lost braces
    54 |   \code{"dat.cnvMskcc"}{: a \code{list} of legnth two:
       |                        ^
checkRd: (-1) intScores.Rd:27-29: Lost braces
    27 |   \code{"integrated"}{: a \code{numeric} vector of length 500,
       |                      ^
checkRd: (-1) pheno.Rd:24: Lost braces
    24 |   \code{"Sample"}{: the first column contains the patients identifiers;}
       |                  ^
checkRd: (-1) pheno.Rd:26-27: Lost braces
    26 |   \code{"Class"}{: the second columns contain a numeric indicator
       |                 ^
checkRd: (-1) runBatchGSE.Rd:43-45: Lost braces
    43 |   \code{absolute}{  logical, this specifies whether the absolute values of
       |                  ^
checkRd: (-1) runBatchGSE.Rd:47-54: Lost braces
    47 |   \code{gseFunc}{  a function to perform GSE analysis. If not specified
       |                 ^
checkRd: (-1) runBatchGSE.Rd:58-61: Lost braces
    58 |   \code{type}{  character, specifies the type of statistics used to rank
       |              ^
checkRd: (-1) runBatchGSE.Rd:63-66: Lost braces
    63 |   \code{alternative}{  character, defines the alternative with the
       |                     ^
checkRd: (-1) runBatchGSE.Rd:68-69: Lost braces
    68 |   \code{ranks.only}{  logical, if \code{TRUE} (default) only ranks will be
       |                    ^
checkRd: (-1) runBatchGSE.Rd:71-72: Lost braces
    71 |   \code{nsim}{  numeric, the number of randomly selected sets of genes to
       |              ^
checkRd: (-1) sepScores.Rd:28-30: Lost braces
    28 |   \code{"dat.affy"}{: a \code{numeric} vector of length 500,
       |                    ^
checkRd: (-1) sepScores.Rd:32-34: Lost braces
    32 |   \code{"dat.agilent"}{: a \code{numeric} vector of length 500,
       |                       ^
checkRd: (-1) sepScores.Rd:36-38: Lost braces
    36 |   \code{"dat.cnvHarvard"}{: a \code{numeric} vector of length 500,
       |                          ^
checkRd: (-1) sepScores.Rd:40-42: Lost braces
    40 |   \code{"dat.cnvMskcc"}{: a \code{numeric} vector of length 500,
       |                        ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  adjustPvalGSE.Rd: mt.rawp2adjp
  runBatchGSE.Rd: geneSetTest
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
computeDrStat 10.074  0.012  10.087
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/RTopper.Rcheck/00check.log’
for details.