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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:genefu.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings genefu_2.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/genefu.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘genefu/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genefu’ version ‘2.38.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘genefu’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’
See ‘/Users/biocbuild/bbs-3.20-bioc/meat/genefu.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
* 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
Packages in Depends field not imported from:
  ‘AIMS’ ‘biomaRt’ ‘iC10’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘mclust:::grid1’ ‘mclust:::grid2’
  See the note in ?`:::` about the use of this operator.
* 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) fuzzy.ttest.Rd:41: Lost braces; missing escapes or markup?
    41 | in w1 and w2 should lay in [0,1] and \verb{0 <= (w1[i] + w2[i]) <= 1} for i in {0,1,...,n} where
       |                                                                                ^
* 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 ... ERROR
Running examples in ‘genefu-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: molecular.subtyping
> ### Title: Function to identify breast cancer molecular subtypes using the
> ###   Subtype Clustering Model
> ### Aliases: molecular.subtyping
> 
> ### ** Examples
> 
> ##### without mapping (affy hgu133a or plus2 only)
> # load VDX data
> data(vdxs)
> data(AIMSmodel)
> data(scmgene.robust)
> 
> # Subtype Clustering Model fitted on EXPO and applied on VDX
> sbt.vdx.SCMGENE <- molecular.subtyping(sbt.model="scmgene",
+   data=data.vdxs, annot=annot.vdxs, do.mapping=FALSE)
> table(sbt.vdx.SCMGENE$subtype)

ER+/HER2- High Prolif  ER+/HER2- Low Prolif             ER-/HER2- 
                   42                    27                    56 
                HER2+ 
                   25 
> 
> # Using the AIMS molecular subtyping algorithm
> sbt.vdxs.AIMS <- molecular.subtyping(sbt.model="AIMS", data=data.vdxs,
+                                      annot=annot.vdxs, do.mapping=FALSE)
You are missing the pair or have more than one 3872<79624 in 
You are missing the pair or have more than one 3852<51514 in 
You are missing the pair or have more than one 3861<7802 in 
You are missing the pair or have more than one 4316<7153 in 
You are missing the pair or have more than one 3400<6787 in 
You are missing the pair or have more than one 10055<2950 in 
You are missing the pair or have more than one 2099<2934 in 
You are missing the pair or have more than one 4781<9070 in 
You are missing the pair or have more than one 2674<57447 in 
You are missing the pair or have more than one 10477<9897 in 
You are missing the pair or have more than one 306<55165 in 
You are missing the pair or have more than one 12<2064 in 
You are missing the pair or have more than one 5932<6241 in 
You are missing the pair or have more than one 10948<3861 in 
You are missing the pair or have more than one 6422<8942 in 
You are missing the pair or have more than one 4886<79152 in 
You are missing the pair or have more than one 29842<55765 in 
You are missing the pair or have more than one 4651<57447 in 
You are missing the pair or have more than one 2317<25803 in 
You are missing the pair or have more than one 3909<9914 in 
You are missing the pair or have more than one 54463<55040 in 
You are missing the pair or have more than one 1728<2099 in 
You are missing the pair or have more than one 2264<3815 in 
You are missing the pair or have more than one 3872<6279 in 
You are missing the pair or have more than one 1153<6382 in 
You are missing the pair or have more than one 6416<9133 in 
You are missing the pair or have more than one 11004<25759 in 
You are missing the pair or have more than one 54970<55165 in 
You are missing the pair or have more than one 3476<9232 in 
You are missing the pair or have more than one 83464<9833 in 
You are missing the pair or have more than one 2053<259266 in 
You are missing the pair or have more than one 2330<7272 in 
You are missing the pair or have more than one 51295<991 in 
You are missing the pair or have more than one 1033<4331 in 
You are missing the pair or have more than one 2617<79083 in 
You are missing the pair or have more than one 4067<54843 in 
You are missing the pair or have more than one 25803<27242 in 
You are missing the pair or have more than one 3202<9833 in 
You are missing the pair or have more than one 1063<1264 in 
You are missing the pair or have more than one 3861<51571 in 
You are missing the pair or have more than one 1308<55165 in 
You are missing the pair or have more than one 1164<9452 in 
You are missing the pair or have more than one 1058<55084 in 
You are missing the pair or have more than one 1033<7102 in 
You are missing the pair or have more than one 1028<4171 in 
You are missing the pair or have more than one 1036<4085 in 
You are missing the pair or have more than one 142<7450 in 
You are missing the pair or have more than one 11065<5764 in 
You are missing the pair or have more than one 128553<51182 in 
You are missing the pair or have more than one 7083<72 in 
You are missing the pair or have more than one 3489<5984 in 
Current k = 20
> table(sbt.vdxs.AIMS$subtype)

 Basal   Her2   LumA   LumB Normal 
    53     31     24     33      9 
> 
> # Using the IntClust molecular subtyping algorithm
> colnames(annot.vdxs)[3]<-"Gene.Symbol"
> sbt.vdxs.intClust <- molecular.subtyping(sbt.model="intClust", data=data.vdxs,
+   annot=annot.vdxs, do.mapping=FALSE)
Warning in data(Map.CN, envir = environment()) :
  data set ‘Map.CN’ not found
Warning in data(Map.Exp, envir = environment()) :
  data set ‘Map.Exp’ not found
Warning in data(train.CN, envir = environment()) :
  data set ‘train.CN’ not found
Warning in data(train.Exp, envir = environment()) :
  data set ‘train.Exp’ not found
Warning in data(IntClustMemb, envir = environment()) :
  data set ‘IntClustMemb’ not found
Warning in data(Map.All, envir = environment()) :
  data set ‘Map.All’ not found
Error in iC10::matchFeatures(Exp = dd, Exp.by.feat = "Gene.Symbol") : 
  object 'Map.All' not found
Calls: molecular.subtyping -> <Anonymous>
Execution halted
* 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 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/genefu.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL genefu
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘genefu’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘limma::logsumexp’ by ‘mclust::logsumexp’ when loading ‘genefu’
** testing if installed package keeps a record of temporary installation path
* DONE (genefu)