Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-11-26 11:05:47 -0500 (Sat, 26 Nov 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4503
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4277
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4309
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for oppar on nebbiolo2


To the developers/maintainers of the oppar package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/oppar.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1407/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oppar 1.26.0  (landing page)
Soroor Hediyeh zadeh
Snapshot Date: 2022-11-25 14:00:04 -0500 (Fri, 25 Nov 2022)
git_url: https://git.bioconductor.org/packages/oppar
git_branch: RELEASE_3_16
git_last_commit: 1d125d9
git_last_commit_date: 2022-11-01 11:13:31 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: oppar
Version: 1.26.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:oppar.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings oppar_1.26.0.tar.gz
StartedAt: 2022-11-25 22:27:00 -0500 (Fri, 25 Nov 2022)
EndedAt: 2022-11-25 22:35:53 -0500 (Fri, 25 Nov 2022)
EllapsedTime: 533.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: oppar.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:oppar.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/library --timings oppar_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/oppar.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘oppar/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘oppar’ version ‘1.26.0’
* 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 LazyData ... WARNING
  LazyData DB of 5.1 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* 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
getSampleOutlier 23.087  0.376  23.880
getSubtypeProbes 21.795  0.196  22.723
opa              21.788  0.124  22.196
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘oppar.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/oppar.Rcheck/00check.log’
for details.



Installation output

oppar.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL oppar
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/library’
* installing *source* package ‘oppar’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.16-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-3.16-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-3.16-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]
   22 |  double mx_value = 0.0;
      |         ^~~~~~~~
gcc -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o oppar.so R_init_oppar.o kernel_estimation.o ks_test.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-bioc/R/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
getSampleOutlier23.087 0.37623.880
getSubtypeProbes21.795 0.19622.723
gsva0.4170.0090.451
opa21.788 0.12422.196