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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ProteoMM.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings ProteoMM_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/ProteoMM.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ProteoMM/DESCRIPTION' ... OK
* this is package 'ProteoMM' version '1.6.0'
* 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 whether package 'ProteoMM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components which are templates and need '+ file LICENSE':
  MIT
* 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 ... OK
* 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 ... OK
* 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
prot_level_multi_part       27.67   0.02   27.70
prot_level_multiMat_PresAbs  9.93   0.00    9.92
subset_proteins              9.12   0.02    9.16
peptideLevel_PresAbsDE       7.53   0.03    8.17
get_presAbs_prots            6.58   0.00    6.61
plot_volcano                 5.96   0.03    5.99
MBimpute                     5.41   0.05    5.45
plot_volcano_wLab            5.10   0.00    5.11
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
prot_level_multi_part       24.33   0.00   24.33
subset_proteins             11.56   0.01   11.57
prot_level_multiMat_PresAbs  7.39   0.02    7.41
get_presAbs_prots            6.70   0.01    6.72
peptideLevel_PresAbsDE       5.86   0.01    5.87
* 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: 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/ProteoMM.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/ProteoMM_1.6.0.tar.gz && rm -rf ProteoMM.buildbin-libdir && mkdir ProteoMM.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ProteoMM.buildbin-libdir ProteoMM_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL ProteoMM_1.6.0.zip && rm ProteoMM_1.6.0.tar.gz ProteoMM_1.6.0.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  111k  100  111k    0     0  2221k      0 --:--:-- --:--:-- --:--:-- 2538k

install for i386

* installing *source* package 'ProteoMM' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ProteoMM'
    finding HTML links ... done
    MBimpute                                html  
    convert_log2                            html  
    eig_norm1                               html  
    eig_norm2                               html  
    eigen_pi                                html  
    g.test                                  html  
    get_presAbs_prots                       html  
    hs_peptides                             html  
    makeLMFormula                           html  
    make_intencities                        html  
    make_meta                               html  
    mm_peptides                             html  
    peptideLevel_DE                         html  
    peptideLevel_PresAbsDE                  html  
    plot_1prot                              html  
    plot_3_pep_trends_NOfile                html  
    plot_volcano                            html  
    plot_volcano_wLab                       html  
    prot_level_multiMat_PresAbs             html  
    prot_level_multi_part                   html  
    subset_proteins                         html  
    sva.id                                  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 'ProteoMM' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ProteoMM' as ProteoMM_1.6.0.zip
* DONE (ProteoMM)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'ProteoMM' successfully unpacked and MD5 sums checked