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This page was generated on 2024-04-17 11:37:41 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 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 merida1


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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EBcoexpress.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EBcoexpress_1.46.0.tar.gz
StartedAt: 2024-04-16 02:19:13 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 02:20:18 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 65.4 seconds
RetCode: 0
Status:   OK  
CheckDir: EBcoexpress.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EBcoexpress.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EBcoexpress_1.46.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/EBcoexpress.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EBcoexpress/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EBcoexpress’ version ‘1.46.0’
* 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 ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ‘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 sizes of PDF files under ‘inst/doc’ ... OK
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/EBcoexpress.Rcheck/00check.log’
for details.



Installation output

EBcoexpress.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL EBcoexpress
###
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##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘EBcoexpress’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c EBcoexpress.c -o EBcoexpress.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o EBcoexpress.so EBcoexpress.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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
ebCoexpressMeta1.6350.0331.806
ebCoexpressSeries0.8200.0120.877
fiftyGenes0.0030.0030.005
initializeHP0.5740.0090.635
makeMyD0.0580.0050.069
priorDiagnostic1.1700.0141.290
rankMyGenes0.8230.0130.916
showNetwork1.5430.0501.737
showPair0.0480.0070.061
utilities0.1360.0050.149