Mac ARM64 build report for BioC 3.20 - CHECK results for BUScorrect on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4381
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: BUScorrect

Version: 1.23.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BUScorrect.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BUScorrect_1.23.0.tar.gz

StartedAt: 2024-05-19 07:15:21 -0400 (Sun, 19 May 2024)

EndedAt: 2024-05-19 07:19:00 -0400 (Sun, 19 May 2024)

EllapsedTime: 218.7 seconds

RetCode: 0

Status: OK

CheckDir: BUScorrect.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BUScorrect.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BUScorrect_1.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/BUScorrect.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: aarch64-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 Ventura 13.6.6
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘BUScorrect’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* 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 ... 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 is not available
* 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 20.138  2.426  22.620
BUSgibbs           18.530  2.578  21.155
* 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
  ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/BUScorrect.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BUScorrect
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘BUScorrect’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c BUS_Cfunctions.c -o BUS_Cfunctions.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o BUScorrect.so BUS_Cfunctions.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-BUScorrect/00new/BUScorrect/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 (BUScorrect)


R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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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
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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 -- Sun May 19 07:18:49 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 
  7.592   0.357   7.965

name	user	system	elapsed
BIC_BUS	0.069	0.005	0.074
BUScorrect-package	20.138	2.426	22.620
BUSexample_data	0.000	0.001	0.001
BUSgibbs	18.530	2.578	21.155
IG_index	0.071	0.002	0.073
Subtypes	0.067	0.003	0.070
adjusted_values	0.069	0.004	0.072
baseline_expression_values	0.068	0.010	0.078
calculate_EPSR_gamma	0.003	0.001	0.003
calculate_EPSR_mu	0.003	0.001	0.003
calculate_EPSR_sigma_sq	0.004	0.001	0.004
estimate_IG_indicators	0.071	0.010	0.081
location_batch_effects	0.082	0.015	0.097
postprob_DE	0.064	0.003	0.067
postprob_DE_thr_fun	0.067	0.003	0.069
print.BUSfits	0.063	0.003	0.066
scale_batch_effects	0.063	0.002	0.066
subtype_effects	0.063	0.004	0.068
summary.BUSfits	0.081	0.017	0.099
visualize_data	0.034	0.002	0.036

CHECK results for BUScorrect on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings