Back to Multiple platform build/check report for BioC 3.16:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2023-04-12 11:05:27 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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

CHECK results for BUScorrect on palomino4


To the developers/maintainers of the BUScorrect package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BUScorrect.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 239/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BUScorrect 1.16.0  (landing page)
Xiangyu Luo
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/BUScorrect
git_branch: RELEASE_3_16
git_last_commit: e1645d7
git_last_commit_date: 2022-11-01 11:18:17 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BUScorrect
Version: 1.16.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BUScorrect.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings BUScorrect_1.16.0.tar.gz
StartedAt: 2023-04-10 23:34:44 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 23:37:30 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 166.3 seconds
RetCode: 0
Status:   OK  
CheckDir: BUScorrect.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BUScorrect.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings BUScorrect_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/BUScorrect.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BUScorrect/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BUScorrect' version '1.16.0'
* 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 'BUScorrect' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 x64 is not available
File 'F:/biocbuild/bbs-3.16-bioc/R/library/BUScorrect/libs/x64/BUScorrect.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
BUScorrect-package 13.31   0.74   14.04
BUSgibbs           12.42   0.16   12.58
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.16-bioc/meat/BUScorrect.Rcheck/00check.log'
for details.



Installation output

BUScorrect.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL BUScorrect
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'BUScorrect' ...
** using staged installation
** libs
gcc  -I"F:/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG     -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c BUS_Cfunctions.c -o BUS_Cfunctions.o
gcc -shared -s -static-libgcc -o BUScorrect.dll tmp.def BUS_Cfunctions.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.16-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.16-bioc/R/library/00LOCK-BUScorrect/00new/BUScorrect/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BUScorrect)

Tests output

BUScorrect.Rcheck/tests/runTests.Rout


R version 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("BUScorrect")
  running the Gibbs sampler ...

  The Gibbs sampler takes: 0.001 mins

  calculating posterior means and posterior modes...

  calculating BIC...



RUNIT TEST PROTOCOL -- Mon Apr 10 23:37:16 2023 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BUScorrect RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   5.17    0.35    5.45 

Example timings

BUScorrect.Rcheck/BUScorrect-Ex.timings

nameusersystemelapsed
BIC_BUS0.530.010.55
BUScorrect-package13.31 0.7414.04
BUSexample_data000
BUSgibbs12.42 0.1612.58
IG_index0.060.000.07
Subtypes0.090.010.11
adjusted_values0.100.030.12
baseline_expression_values0.120.000.13
calculate_EPSR_gamma000
calculate_EPSR_mu0.000.020.01
calculate_EPSR_sigma_sq000
estimate_IG_indicators0.060.000.06
location_batch_effects0.050.000.05
postprob_DE0.060.000.06
postprob_DE_thr_fun0.060.000.07
print.BUSfits0.050.010.06
scale_batch_effects0.050.000.05
subtype_effects0.050.000.04
summary.BUSfits0.070.000.08
visualize_data0.020.000.02