Package: FoldGO

Version: 1.1.1

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FoldGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings FoldGO_1.1.1.tar.gz

StartedAt: 2019-04-09 02:49:14 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:52:10 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 175.6 seconds

RetCode: 0

Status:  OK

CheckDir: FoldGO.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FoldGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings FoldGO_1.1.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/FoldGO.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'FoldGO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'FoldGO' version '1.1.1'
* 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 'FoldGO' 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 ... 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 or elapsed time > 5s
                             user system elapsed
plot-FoldSpecTest-ANY-method 6.36   0.00    6.36
fagroupstopgo_class          4.69   0.27    5.05
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
plot-FoldSpecTest-ANY-method 6.67   0.00    6.67
fagroupstopgo_class          4.92   0.19    5.11
* 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: OK

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/FoldGO_1.1.1.tar.gz && rm -rf FoldGO.buildbin-libdir && mkdir FoldGO.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FoldGO.buildbin-libdir FoldGO_1.1.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL FoldGO_1.1.1.zip && rm FoldGO_1.1.1.tar.gz FoldGO_1.1.1.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1748k  100 1748k    0     0  16.9M      0 --:--:-- --:--:-- --:--:-- 18.1M

install for i386

* installing *source* package 'FoldGO' ...
** R
** data
*** moving datasets to lazyload DB

** inst
** byte-compile and prepare package for lazy loading
in method for 'getAnnotation' with signature '"MgsaSets"': no definition for class "MgsaSets"
** help
*** installing help indices
  converting help for package 'FoldGO'
    finding HTML links ... done
    examdata_bg                             html  
    examdata_degs                           html  
    examdata_objs                           html  
    fagroupstopgo_class                     html  
    foldspectest_class                      html  
    gafreader_class                         html  
    genegroups_class                        html  
    getAnnotation                           html  
    getWholeIntName                         html  
    plot-FoldSpecTest-ANY-method            html  
    rna_seq_data                            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 'FoldGO' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FoldGO' as FoldGO_1.1.1.zip
* DONE (FoldGO)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'FoldGO' successfully unpacked and MD5 sums checked