Package: pathprint

Version: 1.6.0

Command: rm -rf pathprint.buildbin-libdir pathprint.Rcheck && mkdir pathprint.buildbin-libdir pathprint.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pathprint.buildbin-libdir pathprint_1.6.0.tar.gz >pathprint.Rcheck\00install.out 2>&1 && cp pathprint.Rcheck\00install.out pathprint-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=pathprint.buildbin-libdir --install="check:pathprint-install.out" --force-multiarch --no-vignettes --timings pathprint_1.6.0.tar.gz

StartedAt: 2018-04-12 02:01:37 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:09:01 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 444.9 seconds

RetCode: 0

Status:  OK

CheckDir: pathprint.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf pathprint.buildbin-libdir pathprint.Rcheck && mkdir pathprint.buildbin-libdir pathprint.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=pathprint.buildbin-libdir pathprint_1.6.0.tar.gz >pathprint.Rcheck\00install.out 2>&1 && cp pathprint.Rcheck\00install.out pathprint-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=pathprint.buildbin-libdir --install="check:pathprint-install.out" --force-multiarch --no-vignettes --timings pathprint_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/pathprint.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pathprint/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'pathprint' 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'pathprint' 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 ... NOTE
exprs2fingerprint: no visible binding for global variable 'chipframe'
exprs2fingerprint: no visible binding for global variable 'genesets'
thresholdFingerprint: no visible binding for global variable
  'platform.thresholds'
Undefined global functions or variables:
  chipframe genesets platform.thresholds
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
single.chip.enrichment 44.53   5.23   49.79
diffPathways           40.00   2.57   43.50
pathprint-package      17.80   0.85   18.64
consensusDistance      16.61   1.36   18.45
consensusFingerprint   14.80   1.31   16.18
thresholdFingerprint   14.28   0.48   14.77
pluripotents.frame     11.67   0.69   12.36
exprs2fingerprint      10.06   0.60   10.67
customCDFAnn            9.37   0.95   10.33
platform.thresholds     6.16   0.67    6.83
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
single.chip.enrichment 60.11   1.27   61.38
diffPathways           32.78   0.88   33.66
consensusDistance      20.20   0.94   21.14
pathprint-package      16.50   0.77   17.27
thresholdFingerprint   14.80   0.52   15.31
consensusFingerprint   13.81   0.84   14.65
pluripotents.frame     11.62   0.71   12.35
exprs2fingerprint       9.73   0.61   10.34
customCDFAnn            9.22   0.73    9.97
platform.thresholds     5.28   0.75    6.03
* 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-3.6-bioc/meat/pathprint.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'pathprint' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'pathprint'
    finding HTML links ... done
    chipframe                               html  
    consensusDistance                       html  
    consensusFingerprint                    html  
    customCDFAnn                            html  
    diffPathways                            html  
    exprs2fingerprint                       html  
    genesets                                html  
    pathprint-package                       html  
    pathprint.Ce.gs                         html  
    pathprint.Dm.gs                         html  
    pathprint.Dr.gs                         html  
    pathprint.Hs.gs                         html  
    pathprint.Mm.gs                         html  
    pathprint.Rn.gs                         html  
    platform.thresholds                     html  
    pluripotents.frame                      html  
    single.chip.enrichment                  html  
    thresholdFingerprint                    html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'pathprint' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'pathprint' as pathprint_1.6.0.zip
* DONE (pathprint)
In R CMD INSTALL
In R CMD INSTALL