Package: LOBSTAHS

Version: 1.4.0

Command: rm -rf LOBSTAHS.buildbin-libdir LOBSTAHS.Rcheck && mkdir LOBSTAHS.buildbin-libdir LOBSTAHS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LOBSTAHS.buildbin-libdir LOBSTAHS_1.4.0.tar.gz >LOBSTAHS.Rcheck\00install.out 2>&1 && cp LOBSTAHS.Rcheck\00install.out LOBSTAHS-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=LOBSTAHS.buildbin-libdir --install="check:LOBSTAHS-install.out" --force-multiarch --no-vignettes --timings LOBSTAHS_1.4.0.tar.gz

StartedAt: 2018-04-12 01:02:43 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:07:19 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 276.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: LOBSTAHS.Rcheck

Warnings: 2

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### Running command:
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###   rm -rf LOBSTAHS.buildbin-libdir LOBSTAHS.Rcheck && mkdir LOBSTAHS.buildbin-libdir LOBSTAHS.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=LOBSTAHS.buildbin-libdir LOBSTAHS_1.4.0.tar.gz >LOBSTAHS.Rcheck\00install.out 2>&1 && cp LOBSTAHS.Rcheck\00install.out LOBSTAHS-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=LOBSTAHS.buildbin-libdir --install="check:LOBSTAHS-install.out" --force-multiarch --no-vignettes --timings LOBSTAHS_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/LOBSTAHS.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 'LOBSTAHS/DESCRIPTION' ... OK
* this is package 'LOBSTAHS' version '1.4.0'
* 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 ... 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 'LOBSTAHS' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMprCeY/R.INSTALL282c3b5f3689/LOBSTAHS/man/doLOBscreen.Rd:20: missing file link 'findIsotopes'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMprCeY/R.INSTALL282c3b5f3689/LOBSTAHS/man/doLOBscreen.Rd:41: missing file link 'findIsotopes'
  Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMprCeY/R.INSTALL282c3b5f3689/LOBSTAHS/man/doLOBscreen.Rd:125: missing file link 'findIsotopes'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/LOBSTAHS.Rcheck/00install.out' for details.
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                         old_size new_size compress
  default.LOBdbase.RData    1.9Mb    612Kb       xz
* 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
loadLOBdbase 13.47   0.18   13.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
loadLOBdbase 8.91   0.05    8.95
* 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 WARNINGs, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/LOBSTAHS.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'LOBSTAHS' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'LOBSTAHS'
    finding HTML links ... done
    LOBSet-class                            html  
    finding level-2 HTML links ... done

    LOBSet                                  html  
    LOBdbase-class                          html  
    LOBdbase                                html  
    LOBdefaults                             html  
    doLOBscreen                             html  
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMprCeY/R.INSTALL282c3b5f3689/LOBSTAHS/man/doLOBscreen.Rd:20: missing file link 'findIsotopes'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMprCeY/R.INSTALL282c3b5f3689/LOBSTAHS/man/doLOBscreen.Rd:41: missing file link 'findIsotopes'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpMprCeY/R.INSTALL282c3b5f3689/LOBSTAHS/man/doLOBscreen.Rd:125: missing file link 'findIsotopes'
    exportDBtoCSV                           html  
    extractLOBdbasedata                     html  
    generateLOBdbase                        html  
    getLOBpeaklist                          html  
    loadLOBdbase                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'LOBSTAHS' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'LOBSTAHS' as LOBSTAHS_1.4.0.zip
* DONE (LOBSTAHS)
In R CMD INSTALL
In R CMD INSTALL