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CHECK report for BUS on tokay1

This page was generated on 2020-08-09 11:58:37 -0400 (Sun, 09 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BUS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 209/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BUS 1.45.0
Yuanhua Liu
Snapshot Date: 2020-08-08 14:51:01 -0400 (Sat, 08 Aug 2020)
URL: https://git.bioconductor.org/packages/BUS
Branch: master
Last Commit: 91dd3f0
Last Changed Date: 2020-04-27 14:19:39 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BUS
Version: 1.45.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BUS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BUS_1.45.0.tar.gz
StartedAt: 2020-08-09 00:00:02 -0400 (Sun, 09 Aug 2020)
EndedAt: 2020-08-09 00:00:52 -0400 (Sun, 09 Aug 2020)
EllapsedTime: 49.8 seconds
RetCode: 0
Status:  OK  
CheckDir: BUS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BUS.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BUS_1.45.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BUS.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BUS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BUS' version '1.45.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BUS/libs/i386/BUS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BUS/libs/x64/BUS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/BUS.Rcheck/00check.log'
for details.



Installation output

BUS.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BUS_1.45.0.tar.gz && rm -rf BUS.buildbin-libdir && mkdir BUS.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BUS.buildbin-libdir BUS_1.45.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BUS_1.45.0.zip && rm BUS_1.45.0.tar.gz BUS_1.45.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1683k  100 1683k    0     0  43.6M      0 --:--:-- --:--:-- --:--:-- 48.3M

install for i386

* installing *source* package 'BUS' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c BUS.cpp -o BUS.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o BUS.dll tmp.def BUS.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/BUS.buildbin-libdir/00LOCK-BUS/00new/BUS/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BUS'
    finding HTML links ... done
    BUS-package                             html  
    BUS                                     html  
    copasi                                  html  
    gene.pvalue                             html  
    gene.similarity                         html  
    gene.trait.pvalue                       html  
    gene.trait.similarity                   html  
    pred.network                            html  
    tumors.mRNA                             html  
    tumors.miRNA                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'BUS' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c BUS.cpp -o BUS.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o BUS.dll tmp.def BUS.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/BUS.buildbin-libdir/BUS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BUS' as BUS_1.45.0.zip
* DONE (BUS)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BUS' successfully unpacked and MD5 sums checked

Tests output


Example timings

BUS.Rcheck/examples_i386/BUS-Ex.timings

nameusersystemelapsed
BUS0.070.020.07
gene.pvalue0.790.050.85
gene.similarity000
gene.trait.pvalue0.870.030.91
gene.trait.similarity0.040.000.03
pred.network1.150.001.16
tumors.mRNA0.010.000.02
tumors.miRNA0.020.000.01

BUS.Rcheck/examples_x64/BUS-Ex.timings

nameusersystemelapsed
BUS0.100.000.09
gene.pvalue0.940.050.98
gene.similarity000
gene.trait.pvalue1.270.021.28
gene.trait.similarity0.030.000.03
pred.network1.360.001.36
tumors.mRNA0.010.000.02
tumors.miRNA000