Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-11 14:42 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4522
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4468
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 255/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BUS 1.60.0  (landing page)
Yuanhua Liu
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/BUS
git_branch: RELEASE_3_19
git_last_commit: dccc1a9
git_last_commit_date: 2024-04-30 10:20:13 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for BUS on lconway

To the developers/maintainers of the BUS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BUS.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: BUS
Version: 1.60.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BUS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BUS_1.60.0.tar.gz
StartedAt: 2024-06-09 19:11:26 -0400 (Sun, 09 Jun 2024)
EndedAt: 2024-06-09 19:11:56 -0400 (Sun, 09 Jun 2024)
EllapsedTime: 30.7 seconds
RetCode: 0
Status:   OK  
CheckDir: BUS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BUS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BUS_1.60.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/BUS.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* 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 ‘BUS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BUS’ version ‘1.60.0’
* 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 ‘BUS’ 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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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
Package in Depends field not imported from: ‘minet’
  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 ... NOTE
Call with DUP:
   .Call("MINempirical", mat, nat, N, n1, n2, DUP = FALSE)
DUP is no longer supported and will be ignored.
* checking R code for possible problems ... NOTE
gene.pvalue : fi: warning in matrix(1:nrow(EXP), nc = 1): partial
  argument match of 'nc' to 'ncol'
gene.pvalue: warning in matrix(1:nrow(EXP), nc = 1): partial argument
  match of 'nc' to 'ncol'
gene.pvalue : fi: warning in matrix(1:ncol(real), nc = 1): partial
  argument match of 'nc' to 'ncol'
gene.pvalue: warning in matrix(1:nrow(real), nc = 1): partial argument
  match of 'nc' to 'ncol'
gene.pvalue : fi1: warning in matrix(1:ncol(real), nc = 1): partial
  argument match of 'nc' to 'ncol'
gene.trait.pvalue: warning in matrix(0, nr = nrow(EXP), nc =
  nrow(trait)): partial argument match of 'nr' to 'nrow'
gene.trait.pvalue: warning in matrix(0, nr = nrow(EXP), nc =
  nrow(trait)): partial argument match of 'nc' to 'ncol'
gene.trait.pvalue : fi: warning in matrix(1:nrow(trait), nc = 1):
  partial argument match of 'nc' to 'ncol'
gene.trait.pvalue: warning in matrix(1:nrow(EXP), nc = 1): partial
  argument match of 'nc' to 'ncol'
gene.trait.pvalue : fi: warning in matrix(1:ncol(real), nc = 1):
  partial argument match of 'nc' to 'ncol'
gene.trait.pvalue: warning in matrix(1:nrow(real), nc = 1): partial
  argument match of 'nc' to 'ncol'
gene.trait.pvalue : fj: warning in matrix(1:nrow(real), nc = 1):
  partial argument match of 'nc' to 'ncol'
gene.trait.pvalue: warning in matrix(1:ncol(real), nc = 1): partial
  argument match of 'nc' to 'ncol'
gene.pvalue: multiple local function definitions for ‘fi’ with
  different formal arguments
gene.similarity : s.similarity: no visible global function definition
  for ‘build.mim’
gene.similarity : s.similarity: no visible global function definition
  for ‘mrnet’
gene.similarity : s.similarity: no visible global function definition
  for ‘aracne’
gene.similarity : s.similarity: no visible global function definition
  for ‘clr’
gene.trait.pvalue: multiple local function definitions for ‘fi’ with
  different formal arguments
Undefined global functions or variables:
  aracne build.mim clr mrnet
* checking Rd files ... NOTE
checkRd: (-1) pred.network.Rd:15: Lost braces
    15 |   A MxM matrix of the predicted network, where cell emph{ij} infers a link between gene i and j and set 0 when the p-value is not significant (no link).
       |                                                         ^
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/BUS.Rcheck/00check.log’
for details.


Installation output

BUS.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘BUS’ ...
** 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 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c BUS.cpp -o BUS.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o BUS.so BUS.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-BUS/00new/BUS/libs
** R
** data
** 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 (BUS)

Tests output


Example timings

BUS.Rcheck/BUS-Ex.timings

nameusersystemelapsed
BUS0.0420.0090.052
gene.pvalue0.8340.0481.029
gene.similarity0.0030.0010.004
gene.trait.pvalue0.6700.0070.678
gene.trait.similarity0.0140.0040.018
pred.network0.9020.0380.944
tumors.mRNA0.0090.0020.011
tumors.miRNA0.0020.0020.003