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This page was generated on 2024-03-29 11:35:55 -0400 (Fri, 29 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4669
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4404
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4427
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

Package 617/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
EBcoexpress 1.46.0  (landing page)
John A. Dawson
Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/EBcoexpress
git_branch: RELEASE_3_18
git_last_commit: 85b8c64
git_last_commit_date: 2023-10-24 09:49:57 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 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
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for EBcoexpress on nebbiolo2


To the developers/maintainers of the EBcoexpress package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EBcoexpress.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: EBcoexpress
Version: 1.46.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:EBcoexpress.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings EBcoexpress_1.46.0.tar.gz
StartedAt: 2024-03-27 22:08:41 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 22:09:32 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 51.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: EBcoexpress.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:EBcoexpress.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings EBcoexpress_1.46.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/EBcoexpress.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘EBcoexpress/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EBcoexpress’ version ‘1.46.0’
* 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-3.18-bioc/meat/EBcoexpress.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 loading without being on the library search path ... 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 ‘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 ‘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’
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 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 segments
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "box", "lines", "par", "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 ...
  ‘EBcoexpressVignette.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/EBcoexpress.Rcheck/00check.log’
for details.



Installation output

EBcoexpress.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL EBcoexpress
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘EBcoexpress’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-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]
   74 |       if(temp < -1 | temp > 1)
      |          ~~~~~^~~~
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o EBcoexpress.so EBcoexpress.o -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-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
ebCoexpressMeta0.6360.0000.635
ebCoexpressSeries0.3540.0040.358
fiftyGenes0.0020.0000.001
initializeHP0.2790.0000.279
makeMyD0.0210.0000.021
priorDiagnostic0.5130.0000.514
rankMyGenes0.3650.0000.365
showNetwork0.6890.0030.694
showPair0.1280.0010.127
utilities0.0030.0000.003