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CHECK report for oppar on malbec2

This page was generated on 2018-10-17 08:28:52 -0400 (Wed, 17 Oct 2018).

Package 1035/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oppar 1.8.0
Soroor Hediyeh zadeh
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/oppar
Branch: RELEASE_3_7
Last Commit: 171fdbe
Last Changed Date: 2018-04-30 10:35:41 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: oppar
Version: 1.8.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:oppar.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings oppar_1.8.0.tar.gz
StartedAt: 2018-10-16 02:29:44 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 02:31:40 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 115.6 seconds
RetCode: 0
Status:  OK 
CheckDir: oppar.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:oppar.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings oppar_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/oppar.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘oppar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘oppar’ version ‘1.8.0’
* 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 for sufficient/correct file permissions ... 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
* 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
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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
getSampleOutlier 14.264  0.036  14.311
getSubtypeProbes 13.416  0.008  13.433
opa              13.328  0.064  13.406
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/oppar.Rcheck/00check.log’
for details.



Installation output

oppar.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL oppar
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘oppar’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_oppar.c -o R_init_oppar.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c kernel_estimation.c -o kernel_estimation.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -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;
         ^
gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o oppar.so R_init_oppar.o kernel_estimation.o ks_test.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/oppar/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (oppar)

Tests output


Example timings

oppar.Rcheck/oppar-Ex.timings

nameusersystemelapsed
getSampleOutlier14.264 0.03614.311
getSubtypeProbes13.416 0.00813.433
gsva0.6280.0200.651
opa13.328 0.06413.406