Package: spliceR

Version: 1.20.0

Command: rm -rf spliceR.buildbin-libdir spliceR.Rcheck && mkdir spliceR.buildbin-libdir spliceR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=spliceR.buildbin-libdir spliceR_1.20.0.tar.gz >spliceR.Rcheck\00install.out 2>&1 && cp spliceR.Rcheck\00install.out spliceR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=spliceR.buildbin-libdir --install="check:spliceR-install.out" --force-multiarch --no-vignettes --timings spliceR_1.20.0.tar.gz

StartedAt: 2018-04-12 03:22:14 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:29:20 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 425.7 seconds

RetCode: 0

Status:  OK

CheckDir: spliceR.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf spliceR.buildbin-libdir spliceR.Rcheck && mkdir spliceR.buildbin-libdir spliceR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=spliceR.buildbin-libdir spliceR_1.20.0.tar.gz >spliceR.Rcheck\00install.out 2>&1 && cp spliceR.Rcheck\00install.out spliceR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=spliceR.buildbin-libdir --install="check:spliceR-install.out" --force-multiarch --no-vignettes --timings spliceR_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/spliceR.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 'spliceR/DESCRIPTION' ... OK
* this is package 'spliceR' version '1.20.0'
* 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 'spliceR' can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
Packages in Depends field not imported from:
  'cummeRbund' 'methods' 'rtracklayer'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.determineAStypeOverlap: no visible global function definition for
  'tail'
.determineNonOverlappingAStype: no visible global function definition
  for 'tail'
.getPreRNA: no visible global function definition for 'IRanges'
.getPreRNA: no visible global function definition for 'end<-'
.getPreRNA: no visible global function definition for 'end'
.getPreRNA: no visible global function definition for 'reduce'
CDSSet: no visible global function definition for 'new'
SpliceRList: no visible global function definition for 'new'
annotatePTC: no visible global function definition for 'seqnames'
annotatePTC: no visible global function definition for 'seqlevels<-'
annotatePTC: no visible global function definition for 'seqlevels'
annotatePTC: no visible global function definition for 'getSeq'
annotatePTC: no visible global function definition for 'txtProgressBar'
annotatePTC: no visible global function definition for
  'setTxtProgressBar'
annotatePTC: no visible binding for global variable 'chrom'
annotatePTC: no visible global function definition for 'DNAString'
annotatePTC: no visible global function definition for 'translate'
conditions: no visible global function definition for 'samples'
conditions: no visible global function definition for 'genes'
exons: no visible global function definition for 'is'
generateGTF: no visible global function definition for 'mcols'
generateGTF: no visible global function definition for 'txtProgressBar'
generateGTF: no visible global function definition for
  'setTxtProgressBar'
generateGTF: no visible global function definition for 'quantile'
generateGTF: no visible global function definition for 'write.table'
getCDS: no visible global function definition for 'browserSession'
getCDS: no visible global function definition for 'genome<-'
getCDS: no visible global function definition for 'ucscTableQuery'
getCDS: no visible global function definition for 'tableName<-'
getCDS: no visible global function definition for 'getTable'
getCDS: no visible global function definition for 'flush.console'
getCDS: no visible global function definition for 'new'
preSpliceRFilter: no visible global function definition for 'mcols'
preSpliceRFilter: no visible global function definition for 'mcols<-'
prepareCuff: no visible global function definition for 'genes'
prepareCuff: no visible global function definition for 'isoforms'
prepareCuff: no visible global function definition for 'annotation'
prepareCuff: no visible global function definition for 'diffData'
prepareCuff: no visible global function definition for 'dbGetQuery'
prepareCuff: no visible global function definition for 'samples'
prepareCuff: no visible global function definition for 'GRanges'
prepareCuff: no visible global function definition for 'IRanges'
prepareCuff: no visible global function definition for 'new'
prepareCuff: no visible global function definition for 'runInfo'
prepareCuffExample: no visible global function definition for
  'readCufflinks'
spliceR: no visible global function definition for 'mcols'
spliceR: no visible global function definition for 'txtProgressBar'
spliceR: no visible global function definition for 'setTxtProgressBar'
spliceR: no visible global function definition for 'mcols<-'
spliceRPlot: no visible global function definition for 'mcols'
spliceRPlot: no visible global function definition for 'grid.newpage'
spliceRPlot: no visible global function definition for 'grid.draw'
topIsoShift: no visible global function definition for 'is'
topIsoShift: no visible global function definition for 'mcols'
totalNumberOfAS: no visible global function definition for 'is'
totalNumberOfAS: no visible global function definition for 'mcols'
transcripts: no visible global function definition for 'is'
Undefined global functions or variables:
  DNAString GRanges IRanges annotation browserSession chrom dbGetQuery
  diffData end end<- flush.console genes genome<- getSeq getTable
  grid.draw grid.newpage is isoforms mcols mcols<- new quantile
  readCufflinks reduce runInfo samples seqlevels seqlevels<- seqnames
  setTxtProgressBar tableName<- tail translate txtProgressBar
  ucscTableQuery write.table
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "end", "quantile")
  importFrom("utils", "flush.console", "setTxtProgressBar", "tail",
             "txtProgressBar", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/spliceR.buildbin-libdir/spliceR/libs/i386/spliceR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* 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
generateGTF     8.97   0.39    9.38
totalNumberOfAS 7.23   0.09    7.32
spliceRPlot     6.99   0.11    7.09
spliceR         5.73   0.15    5.89
topIsoShift     5.05   0.08    5.13
conditions      4.61   0.24    7.26
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
generateGTF     8.50   0.15    8.66
totalNumberOfAS 7.98   0.12    8.11
topIsoShift     6.29   0.13    6.40
spliceR         5.92   0.10    6.02
spliceRPlot     5.46   0.11    5.56
* 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: 4 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/spliceR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'spliceR' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o spliceR.dll tmp.def utils.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/spliceR.buildbin-libdir/spliceR/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'spliceR'
    finding HTML links ... done
    CDSSet                                  html  
    SpliceRList                             html  
    annotatePTC.R                           html  
    conditions                              html  
    dim                                     html  
    generateGTF                             html  
    getCDS                                  html  
    preSpliceRFilter                        html  
    prepareCuff                             html  
    prepareCuffExample                      html  
    spliceR                                 html  
    spliceRPlot                             html  
    tools                                   html  
    topIsoShift                             html  
    totalNumberOfAS                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'spliceR' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o spliceR.dll tmp.def utils.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/spliceR.buildbin-libdir/spliceR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'spliceR' as spliceR_1.20.0.zip
* DONE (spliceR)
In R CMD INSTALL
In R CMD INSTALL