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CHECK report for oppar on tokay1

This page was generated on 2018-04-12 13:27:57 -0400 (Thu, 12 Apr 2018).

Package 981/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oppar 1.6.0
Soroor Hediyeh zadeh
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/oppar
Branch: RELEASE_3_6
Last Commit: 45482b0
Last Changed Date: 2017-10-30 12:41:15 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: oppar
Version: 1.6.0
Command: rm -rf oppar.buildbin-libdir oppar.Rcheck && mkdir oppar.buildbin-libdir oppar.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oppar.buildbin-libdir oppar_1.6.0.tar.gz >oppar.Rcheck\00install.out 2>&1 && cp oppar.Rcheck\00install.out oppar-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=oppar.buildbin-libdir --install="check:oppar-install.out" --force-multiarch --no-vignettes --timings oppar_1.6.0.tar.gz
StartedAt: 2018-04-12 01:56:07 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 02:00:08 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 241.5 seconds
RetCode: 0
Status:  OK  
CheckDir: oppar.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf oppar.buildbin-libdir oppar.Rcheck && mkdir oppar.buildbin-libdir oppar.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=oppar.buildbin-libdir oppar_1.6.0.tar.gz >oppar.Rcheck\00install.out 2>&1 && cp oppar.Rcheck\00install.out oppar-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=oppar.buildbin-libdir --install="check:oppar-install.out" --force-multiarch --no-vignettes --timings oppar_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/oppar.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 'oppar/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'oppar' version '1.6.0'
* 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 'oppar' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
compute.gene.density : <anonymous>: no visible global function
  definition for 'ecdf'
compute.geneset.es: no visible global function definition for
  'txtProgressBar'
compute.geneset.es: no visible global function definition for
  'setTxtProgressBar'
ks_test_Rcode: no visible global function definition for 'plot'
ks_test_m: no visible global function definition for
  'setTxtProgressBar'
plage: no visible global function definition for 'txtProgressBar'
plage : <anonymous>: no visible global function definition for 'sd'
plage : <anonymous>: no visible global function definition for
  'setTxtProgressBar'
plage: no visible global function definition for 'setTxtProgressBar'
ssgsea: no visible global function definition for 'txtProgressBar'
ssgsea : <anonymous>: no visible global function definition for
  'setTxtProgressBar'
ssgsea: no visible global function definition for 'setTxtProgressBar'
zscore: no visible global function definition for 'txtProgressBar'
zscore : <anonymous>: no visible global function definition for 'sd'
zscore : <anonymous>: no visible global function definition for
  'setTxtProgressBar'
zscore: no visible global function definition for 'setTxtProgressBar'
computeGeneSetsOverlap,list-ExpressionSet : <anonymous>: no visible
  global function definition for 'na.omit'
computeGeneSetsOverlap,list-character : <anonymous>: no visible global
  function definition for 'na.omit'
gsva,ExpressionSet-GeneSetCollection: no visible binding for global
  variable 'sd'
gsva,ExpressionSet-GeneSetCollection : <anonymous>: no visible global
  function definition for 'na.omit'
gsva,ExpressionSet-list: no visible binding for global variable 'sd'
gsva,ExpressionSet-list : <anonymous>: no visible global function
  definition for 'na.omit'
gsva,matrix-GeneSetCollection: no visible binding for global variable
  'sd'
gsva,matrix-GeneSetCollection : <anonymous>: no visible global function
  definition for 'na.omit'
gsva,matrix-list: no visible binding for global variable 'sd'
gsva,matrix-list : <anonymous>: no visible global function definition
  for 'na.omit'
opa,matrix: no visible global function definition for 'relevel'
opa,matrix : <anonymous>: no visible global function definition for
  'mad'
opa,matrix : <anonymous>: no visible global function definition for
  'median'
opa,matrix : <anonymous>: no visible binding for global variable
  'quantile'
opa,matrix : <anonymous>: no visible global function definition for
  'IQR'
show,OPPARList: no visible global function definition for 'head'
Undefined global functions or variables:
  IQR ecdf head mad median na.omit plot quantile relevel sd
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "IQR", "ecdf", "mad", "median", "na.omit",
             "quantile", "relevel", "sd")
  importFrom("utils", "head", "setTxtProgressBar", "txtProgressBar")
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 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/oppar.buildbin-libdir/oppar/libs/i386/oppar.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
getSampleOutlier 15.53   0.02   15.54
opa              15.11   0.02   15.13
getSubtypeProbes 13.63   0.04   13.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
getSampleOutlier 16.83   0.10   16.92
getSubtypeProbes 16.65   0.05   16.71
opa              16.08   0.00   16.08
* 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-3.6-bioc/meat/oppar.Rcheck/00check.log'
for details.



Installation output

oppar.Rcheck/00install.out


install for i386

* installing *source* package 'oppar' ...
** 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 R_init_oppar.c -o R_init_oppar.o
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 kernel_estimation.c -o kernel_estimation.o
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 ks_test.c -o ks_test.o
ks_test.c: In function 'ks_sample':
ks_test.c:22:9: warning: unused variable 'mx_value' [-Wunused-variable]
  double mx_value = 0.0;
         ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o oppar.dll tmp.def R_init_oppar.o kernel_estimation.o ks_test.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/oppar.buildbin-libdir/oppar/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'oppar'
    finding HTML links ... done
    OPPARList-class                         html  
    bcm                                     html  
    eset                                    html  
    getSampleOutlier                        html  
    getSubtypeProbes                        html  
    gsva                                    html  
    maupin                                  html  
    opa                                     html  
    oppar                                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'oppar' ...
** 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 R_init_oppar.c -o R_init_oppar.o
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 kernel_estimation.c -o kernel_estimation.o
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 ks_test.c -o ks_test.o
ks_test.c: In function 'ks_sample':
ks_test.c:22:9: warning: unused variable 'mx_value' [-Wunused-variable]
  double mx_value = 0.0;
         ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o oppar.dll tmp.def R_init_oppar.o kernel_estimation.o ks_test.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/oppar.buildbin-libdir/oppar/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'oppar' as oppar_1.6.0.zip
* DONE (oppar)
In R CMD INSTALL
In R CMD INSTALL

Tests output


Example timings

oppar.Rcheck/examples_i386/oppar-Ex.timings

nameusersystemelapsed
getSampleOutlier15.53 0.0215.54
getSubtypeProbes13.63 0.0413.68
gsva0.350.000.34
opa15.11 0.0215.13

oppar.Rcheck/examples_x64/oppar-Ex.timings

nameusersystemelapsed
getSampleOutlier16.83 0.1016.92
getSubtypeProbes16.65 0.0516.71
gsva0.400.000.41
opa16.08 0.0016.08