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CHECK report for EBcoexpress on malbec1

This page was generated on 2020-04-15 12:06:55 -0400 (Wed, 15 Apr 2020).

Package 499/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBcoexpress 1.30.0
John A. Dawson
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/EBcoexpress
Branch: RELEASE_3_10
Last Commit: 658c76c
Last Changed Date: 2019-10-29 13:08:31 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: EBcoexpress
Version: 1.30.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:EBcoexpress.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings EBcoexpress_1.30.0.tar.gz
StartedAt: 2020-04-15 01:18:44 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:19:22 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 38.9 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: EBcoexpress.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:EBcoexpress.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings EBcoexpress_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/EBcoexpress.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBcoexpress/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EBcoexpress’ version ‘1.30.0’
* 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 ‘EBcoexpress’ can be installed ... WARNING
Found the following significant warnings:
  EBcoexpress.c:74:15: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/biocbuild/bbs-3.10-bioc/meat/EBcoexpress.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' calls in package code:
  ‘colorspace’ ‘graph’ ‘igraph’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘EBarrays’ ‘mclust’ ‘minqa’
  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
rankMyGenes: warning in sort(table(allNames), decr = TRUE): partial
  argument match of 'decr' to 'decreasing'
bwmc: no visible binding for global variable ‘median’
bwmc: no visible binding for global variable ‘mad’
ebCoexpressFullTCAECM: no visible global function definition for
  ‘bobyqa’
ebCoexpressOneStep: no visible global function definition for ‘bobyqa’
initializeHP : getMclustHPests : devHelper: no visible global function
  definition for ‘density’
initializeHP : getMclustHPests : devHelper : fundDev: no visible global
  function definition for ‘dnorm’
initializeHP : getMclustHPests: no visible global function definition
  for ‘Mclust’
initializeHP : getMclustHPests : checkMyData : funa: no visible global
  function definition for ‘dnorm’
initializeHP : getMclustHPests : checkMyData: no visible global
  function definition for ‘density’
initializeHP : getMclustHPests : checkMyData: no visible global
  function definition for ‘plot’
initializeHP : getMclustHPests : checkMyData: no visible global
  function definition for ‘lines’
initializeHP: no visible global function definition for ‘par’
makeMyD: no visible global function definition for ‘cor’
priorDiagnostic : funa: no visible global function definition for
  ‘dnorm’
priorDiagnostic: no visible global function definition for ‘density’
priorDiagnostic: no visible global function definition for ‘plot’
priorDiagnostic: no visible global function definition for ‘lines’
showNetwork: no visible global function definition for ‘graph.full’
showNetwork: no visible global function definition for ‘hex’
showNetwork: no visible global function definition for ‘RGB’
showNetwork: no visible global function definition for ‘layout.circle’
showNetwork: no visible global function definition for ‘plot’
showPair: no visible global function definition for ‘palette’
showPair : getUsed: no visible global function definition for ‘median’
showPair : getUsed: no visible global function definition for ‘mad’
showPair: no visible binding for global variable ‘plot’
showPair: no visible global function definition for ‘box’
showPair: no visible global function definition for ‘lm’
showPair: no visible binding for global variable ‘segments’
Undefined global functions or variables:
  Mclust RGB bobyqa box cor density dnorm graph.full hex layout.circle
  lines lm mad median palette par plot segments
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "box", "lines", "par", "plot", "segments")
  importFrom("stats", "cor", "density", "dnorm", "lm", "mad", "median")
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
* 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: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/EBcoexpress.Rcheck/00check.log’
for details.



Installation output

EBcoexpress.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL EBcoexpress
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘EBcoexpress’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c EBcoexpress.c -o EBcoexpress.o
EBcoexpress.c: In function ‘bwmcCworker’:
EBcoexpress.c:74:15: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
       if(temp < -1 | temp > 1)
          ~~~~~^~~~
gcc -shared -L/home/biocbuild/bbs-3.10-bioc/R/lib -L/usr/local/lib -o EBcoexpress.so EBcoexpress.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-EBcoexpress/00new/EBcoexpress/libs
** R
** data
** demo
** 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 (EBcoexpress)

Tests output


Example timings

EBcoexpress.Rcheck/EBcoexpress-Ex.timings

nameusersystemelapsed
ebCoexpressMeta1.5080.0041.514
ebCoexpressSeries0.5480.0000.549
fiftyGenes0.0000.0000.001
initializeHP0.4520.0000.454
makeMyD0.0280.0000.027
priorDiagnostic0.9200.0000.921
rankMyGenes0.8560.0000.858
showNetwork0.5600.0080.565
showPair0.0240.0000.025
utilities0.0040.0000.004