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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Pigengene.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings Pigengene_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/Pigengene.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 'Pigengene/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Pigengene' version '1.16.0'
* 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 'Pigengene' 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 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 ... NOTE
'library' or 'require' calls in package code:
  'AnnotationDbi' 'biomaRt' 'energy' 'org.Hs.eg.db' 'org.Mm.eg.db'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Found the following possibly unsafe calls:
File 'Pigengene/R/bn.calculation.R':
  assignInNamespace("supported.clusters", fixArgs, "bnlearn")

combine.networks: no visible binding for global variable 'netwok'
Undefined global functions or variables:
  netwok
* 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 contents of 'data' directory ... NOTE
Output for data("pigengene", package = "Pigengene"):
  
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
one.step.pigengene 72.88   3.56   77.36
Pigengene-package  60.39   3.70   65.05
module.heatmap     51.05   5.09   56.17
gene.mapping       32.61   0.55   41.37
make.decision.tree 16.55   0.22   16.78
compact.tree       15.50   0.30   15.81
learn.bn           13.34   0.10   14.34
pigengene           8.53   0.44    9.90
plot.pigengene      8.14   0.61    8.75
compute.pigengene   8.04   0.48    8.53
combine.networks    8.35   0.03    8.66
wgcna.one.step      7.72   0.06    7.78
project.eigen       7.04   0.39    7.42
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
Pigengene-package  66.69   2.52   70.33
one.step.pigengene 60.24   2.56   65.05
module.heatmap     38.23   3.86   43.06
gene.mapping       16.95   0.46   23.28
make.decision.tree 14.44   0.06   14.98
compact.tree       13.75   0.15   14.01
learn.bn           12.91   0.06   13.69
combine.networks    9.08   0.04    9.16
wgcna.one.step      8.49   0.02    8.50
compute.pigengene   6.41   0.38    6.78
plot.pigengene      5.96   0.48    6.44
pigengene           5.96   0.32    6.30
project.eigen       5.40   0.41    5.82
* 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/Pigengene.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/Pigengene_1.16.0.tar.gz && rm -rf Pigengene.buildbin-libdir && mkdir Pigengene.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Pigengene.buildbin-libdir Pigengene_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL Pigengene_1.16.0.zip && rm Pigengene_1.16.0.tar.gz Pigengene_1.16.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

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100 2465k  100 2465k    0     0  6283k      0 --:--:-- --:--:-- --:--:-- 6305k

install for i386

* installing *source* package 'Pigengene' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Pigengene'
    finding HTML links ... done
    Pigengene-package                       html  
    aml                                     html  
    balance                                 html  
    calculate.beta                          html  
    check.nas                               html  
    check.pigengene.input                   html  
    combine.networks                        html  
    compact.tree                            html  
    compute.pigengene                       html  
    dcor.matrix                             html  
    draw.bn                                 html  
    eigengenes33                            html  
    gene.mapping                            html  
    get.fitted.leaf                         html  
    get.genes                               html  
    get.used.features                       html  
    learn.bn                                html  
    make.decision.tree                      html  
    mds                                     html  
    message.if                              html  
    module.heatmap                          html  
    one.step.pigengene                      html  
    pheatmap.type                           html  
    pigengene-class                         html  
    pigengene                               html  
    plot.pigengene                          html  
    preds.at                                html  
    project.eigen                           html  
    pvalues.manova                          html  
    save.if                                 html  
    wgcna.one.step                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'Pigengene' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Pigengene' as Pigengene_1.16.0.zip
* DONE (Pigengene)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'Pigengene' successfully unpacked and MD5 sums checked