Package: PSEA

Version: 1.17.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PSEA_1.17.0.tar.gz

StartedAt: 2019-04-09 05:07:03 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 05:08:05 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 61.5 seconds

RetCode: 0

Status:  OK

CheckDir: PSEA.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:PSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings PSEA_1.17.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/PSEA.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 'PSEA/DESCRIPTION' ... OK
* this is package 'PSEA' version '1.17.0'
* 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 'PSEA' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
crplot: no visible global function definition for 'residuals'
crplot: no visible global function definition for 'dev.new'
crplot: no visible global function definition for 'plot'
crplot: no visible global function definition for 'abline'
crplot: no visible global function definition for 'points'
lmfitst : <anonymous>: no visible global function definition for
  'lm.fit'
swlm: no visible global function definition for 'formula'
swlm: no visible global function definition for 'lm'
Undefined global functions or variables:
  abline dev.new formula lm lm.fit plot points residuals
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "plot", "points")
  importFrom("stats", "formula", "lm", "lm.fit", "residuals")
to your NAMESPACE file.
* 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
** running examples for arch 'x64' ... OK
* 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-3.9-bioc/meat/PSEA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/PSEA_1.17.0.tar.gz && rm -rf PSEA.buildbin-libdir && mkdir PSEA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PSEA.buildbin-libdir PSEA_1.17.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL PSEA_1.17.0.zip && rm PSEA_1.17.0.tar.gz PSEA_1.17.0.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
 74 5847k   74 4336k    0     0  5980k      0 --:--:-- --:--:-- --:--:-- 6030k
100 5847k  100 5847k    0     0  7923k      0 --:--:-- --:--:-- --:--:-- 7988k

install for i386

* installing *source* package 'PSEA' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PSEA'
    finding HTML links ... done
    coefmat                                 html  
    crplot                                  html  
    em_quantvg                              html  
    expression                              html  
    expression_GSE19380                     html  
    fmm                                     html  
    groups                                  html  
    information                             html  
    lmfitst                                 html  
    marker                                  html  
    pvalmat                                 html  
    slt                                     html  
    swlm                                    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 'PSEA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PSEA' as PSEA_1.17.0.zip
* DONE (PSEA)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'PSEA' successfully unpacked and MD5 sums checked