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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:KnowSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings KnowSeq_1.4.5.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/KnowSeq.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'KnowSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'KnowSeq' version '1.4.5'
* 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 whether package 'KnowSeq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   5.1Mb
* 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DEGsExtraction: warning in topTable(fit, number = number, coef = 2,
  sort.by = "logFC", p.value = pvalue, adjust = "fdr", lfc = lfc):
  partial argument match of 'adjust' to 'adjust.method'
DEGsEvidences: no visible binding for global variable 'evidence'
RNAseqQA : outlierBarPlot: no visible binding for global variable 'x'
RNAseqQA : outlierBarPlot: no visible binding for global variable 'y'
RNAseqQA: no visible binding for global variable 'Var1'
RNAseqQA: no visible binding for global variable 'Var2'
RNAseqQA: no visible binding for global variable 'value'
RNAseqQA: no visible binding for global variable 'Expression'
RNAseqQA: no visible binding for global variable 'Samples'
dataPlot: no visible binding for global variable 'Var1'
dataPlot: no visible binding for global variable 'Var2'
dataPlot: no visible binding for global variable 'value'
dataPlot: no visible binding for global variable 'Classes'
dataPlot: no visible binding for global variable 'Value'
featureSelection: no visible binding for global variable 'target'
featureSelection: no visible binding for global variable
  'association_score'
knowseqReport: no visible binding for global variable 'target'
Undefined global functions or variables:
  Classes Expression Samples Value Var1 Var2 association_score evidence
  target value x y
* checking Rd files ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
svm_test             51.64   0.12   51.87
svm_trn              44.61   0.15   45.37
rf_trn               42.83   0.05   42.88
dataPlot             33.57   0.28   34.07
rf_test              13.64   0.04   13.68
downloadPublicSeries  2.93   0.14   20.21
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
svm_test             53.16   0.11   53.30
rf_trn               45.08   0.15   45.40
svm_trn              36.70   0.08   36.80
dataPlot             30.45   0.25   30.76
rf_test              14.41   0.10   14.50
downloadPublicSeries  2.39   0.01   17.24
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/KnowSeq.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/KnowSeq_1.4.5.tar.gz && rm -rf KnowSeq.buildbin-libdir && mkdir KnowSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=KnowSeq.buildbin-libdir KnowSeq_1.4.5.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL KnowSeq_1.4.5.zip && rm KnowSeq_1.4.5.tar.gz KnowSeq_1.4.5.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3924k  100 3924k    0     0  54.8M      0 --:--:-- --:--:-- --:--:-- 55.5M

install for i386

* installing *source* package 'KnowSeq' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
In .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** help
*** installing help indices
  converting help for package 'KnowSeq'
    finding HTML links ... done
    DEGsEvidences                           html  
    DEGsExtraction                          html  
    DEGsToDiseases                          html  
    DEGsToPathways                          html  
    RNAseqQA                                html  
    batchEffectRemoval                      html  
    calculateGeneExpressionValues           html  
    countsToMatrix                          html  
    dataPlot                                html  
    downloadPublicSeries                    html  
    featureSelection                        html  
    fileMove                                html  
    gdcClientDownload                       html  
    geneOntologyEnrichment                  html  
    getGenesAnnotation                      html  
    hisatAlignment                          html  
    knn_test                                html  
    knn_trn                                 html  
    knowseqReport                           html  
    plotConfMatrix                          html  
    rawAlignment                            html  
    rf_test                                 html  
    rf_trn                                  html  
    sraToFastq                              html  
    svm_test                                html  
    svm_trn                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** testing if installed package can be loaded from final location
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'KnowSeq' ...
** testing if installed package can be loaded
Warning in .recacheSubclasses(def@className, def, env) :
  undefined subclass "numericVector" of class "Mnumeric"; definition not updated
* MD5 sums
packaged installation of 'KnowSeq' as KnowSeq_1.4.5.zip
* DONE (KnowSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'KnowSeq' successfully unpacked and MD5 sums checked