Back to Multiple platform build/check report for BioC 3.20:   simplified   long
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-07-16 11:40 -0400 (Tue, 16 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4677
palomino6Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4416
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4444
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4393
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4373
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 253/2243HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BUScorrect 1.23.0  (landing page)
Xiangyu Luo
Snapshot Date: 2024-07-15 14:00 -0400 (Mon, 15 Jul 2024)
git_url: https://git.bioconductor.org/packages/BUScorrect
git_branch: devel
git_last_commit: c3ba6b2
git_last_commit_date: 2024-04-30 11:08:28 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino6Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
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
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  


CHECK results for BUScorrect on palomino6

To the developers/maintainers of the BUScorrect package:
- 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 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: BUScorrect
Version: 1.23.0
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BUScorrect.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BUScorrect_1.23.0.tar.gz
StartedAt: 2024-07-15 22:20:39 -0400 (Mon, 15 Jul 2024)
EndedAt: 2024-07-15 22:23:52 -0400 (Mon, 15 Jul 2024)
EllapsedTime: 192.9 seconds
RetCode: 0
Status:   OK  
CheckDir: BUScorrect.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BUScorrect.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings BUScorrect_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/BUScorrect.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BUScorrect/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BUScorrect' version '1.23.0'
* 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
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* 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 ... 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 ... NOTE
checkRd: (-1) NEWS.Rd:12: Escaped LaTeX specials: \_ \_ \_
checkRd: (-1) BUSgibbs.Rd:34: Lost braces; missing escapes or markup?
    34 |         \code{a_inv_gamma}: the shape of the gamma prior for 1/sigma^2_{bg};
       |                                                                        ^
checkRd: (-1) BUSgibbs.Rd:35: Lost braces; missing escapes or markup?
    35 |         \code{b_inv_gamma}: the rate of the gamma prior for 1/sigma^2_{bg};
       |                                                                       ^
checkRd: (-1) BUSgibbs.Rd:36: Lost braces; missing escapes or markup?
    36 |         \code{a_tau0}: the shape of the gamma prior for 1/tau^2_{mu 0};
       |                                                                 ^
checkRd: (-1) BUSgibbs.Rd:39: Lost braces; missing escapes or markup?
    39 |         \code{tau_{mu1}}: the standard deviation of the normal prior of mu_{gk} (k >= 2) when the gene expression level in subtype k is different from that in subtype one.
       |                                                                            ^
checkRd: (-1) BUSgibbs.Rd:52: Lost braces; missing escapes or markup?
    52 |    \item{tau_mu_zero}{The estimated tau_{mu 0}, which is the prior normal distribution's standard deviation of the subtype effects when there is no differential expression.}
       |                                         ^
checkRd: (-1) BUSgibbs.Rd:57: Lost braces; missing escapes or markup?
    57 |    \item{gamma}{The estimated location batch effects, a G by B matrix, where gamma_{gb} is the ``location'' batch effect on gene g in the batch b. Note that the first column is zero as the first batch is taken as the reference batch without batch effects.}
       |                                                                                    ^
* 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 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/BUScorrect/libs/x64/BUScorrect.dll':
  Found '_exit', possibly from '_exit' (C)
  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 nor [v]sprintf. 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
BUSgibbs           19.28   1.63   20.72
BUScorrect-package 15.33   0.73   16.75
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/BUScorrect.Rcheck/00check.log'
for details.


Installation output

BUScorrect.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL BUScorrect
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'BUScorrect' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 Jul 15 22:23:42 2024 
*********************************************** 
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 
   6.34    0.43    6.76 

Example timings

BUScorrect.Rcheck/BUScorrect-Ex.timings

nameusersystemelapsed
BIC_BUS0.090.000.10
BUScorrect-package15.33 0.7316.75
BUSexample_data000
BUSgibbs19.28 1.6320.72
IG_index0.030.020.06
Subtypes0.060.010.08
adjusted_values0.070.000.06
baseline_expression_values0.060.020.08
calculate_EPSR_gamma000
calculate_EPSR_mu000
calculate_EPSR_sigma_sq0.000.010.02
estimate_IG_indicators0.080.000.08
location_batch_effects0.040.000.04
postprob_DE0.050.020.07
postprob_DE_thr_fun0.060.000.06
print.BUSfits0.050.000.04
scale_batch_effects0.060.000.07
subtype_effects0.070.000.06
summary.BUSfits0.040.000.05
visualize_data0.010.000.02