Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:30 -0400 (Fri, 15 Oct 2021).

CHECK results for BUS on machv2

To the developers/maintainers of the BUS package:
- Please 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 How and When does the builder pull? When will my changes propagate? here 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 225/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BUS 1.48.0  (landing page)
Yuanhua Liu
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/BUS
git_branch: RELEASE_3_13
git_last_commit: 4069c62
git_last_commit_date: 2021-05-19 11:43:31 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BUS
Version: 1.48.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BUS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BUS_1.48.0.tar.gz
StartedAt: 2021-10-14 16:59:22 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 16:59:54 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 32.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BUS.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BUS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BUS_1.48.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/BUS.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BUS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BUS’ version ‘1.48.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BUS’ can be installed ... OK
* 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 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
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 ... 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/BUS.Rcheck/00check.log’
for details.



Installation output

BUS.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BUS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘BUS’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c BUS.cpp -o BUS.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BUS.so BUS.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/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
BUS0.0500.0060.057
gene.pvalue1.1450.0661.212
gene.similarity0.0030.0010.005
gene.trait.pvalue1.1420.0111.154
gene.trait.similarity0.0190.0040.022
pred.network1.2270.0541.282
tumors.mRNA0.0130.0020.016
tumors.miRNA0.0010.0020.003