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CHECK report for oppar on machv2

This page was generated on 2020-10-17 11:59:07 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE oppar PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1241/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oppar 1.16.0
Soroor Hediyeh zadeh
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/oppar
Branch: RELEASE_3_11
Last Commit: 6a96428
Last Changed Date: 2020-04-27 14:56:50 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: oppar
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:oppar.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings oppar_1.16.0.tar.gz
StartedAt: 2020-10-17 03:41:27 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:47:39 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 371.1 seconds
RetCode: 0
Status:  OK 
CheckDir: oppar.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:oppar.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings oppar_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/oppar.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.16.0’
* 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  5.6Mb
  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_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 quantile relevel sd
  setTxtProgressBar txtProgressBar
Consider adding
  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 (user + system) or elapsed time > 5s
                   user system elapsed
getSubtypeProbes 34.029  0.336  58.882
getSampleOutlier 32.984  0.382  42.436
opa              28.704  0.192  28.967
* 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
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/oppar.Rcheck/00check.log’
for details.



Installation output

oppar.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL oppar
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘oppar’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_oppar.c -o R_init_oppar.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c kernel_estimation.c -o kernel_estimation.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c ks_test.c -o ks_test.o
ks_test.c:22:9: warning: unused variable 'mx_value' [-Wunused-variable]
        double mx_value = 0.0;
               ^
1 warning generated.
clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o oppar.so R_init_oppar.o kernel_estimation.o ks_test.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-oppar/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (oppar)

Tests output


Example timings

oppar.Rcheck/oppar-Ex.timings

nameusersystemelapsed
getSampleOutlier32.984 0.38242.436
getSubtypeProbes34.029 0.33658.882
gsva1.1700.0491.225
opa28.704 0.19228.967