Multiple platform build/check report for BioC 3.20 - CHECK results for BAGS on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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 BAGS on merida1

To the developers/maintainers of the BAGS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BAGS.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: BAGS

Version: 2.46.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BAGS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BAGS_2.46.0.tar.gz

StartedAt: 2024-12-19 23:54:29 -0500 (Thu, 19 Dec 2024)

EndedAt: 2024-12-19 23:56:31 -0500 (Thu, 19 Dec 2024)

EllapsedTime: 121.9 seconds

RetCode: 0

Status: OK

CheckDir: BAGS.Rcheck

Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BAGS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BAGS_2.46.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BAGS.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BAGS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BAGS’ version ‘2.46.0’
* 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 ‘BAGS’ can be installed ... OK
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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 ... NOTE
Package in Depends field not imported from: ‘Biobase’
  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 ... 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 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
Gibbs2       31.622  1.274  34.221
MCMCDataSet  20.197  1.386  22.401
DataGeneSets 18.340  1.025  19.600
* 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/meat/BAGS.Rcheck/00check.log’
for details.

Installation output

BAGS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BAGS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘BAGS’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c BAGS.c -o BAGS.o
In file included from BAGS.c:8:
./FuncionesFast-Final.h:145:70: warning: unused variable 'YMu1' [-Wunused-variable]
    double media1,media,varianza1,varianza,resultado,varaux0,varaux1,YMu1;
                                                                     ^
./FuncionesFast-Final.h:166:92: warning: unused variable 'C' [-Wunused-variable]
    double CSiDiff,CNoDiff,Cest,Mu,aux1,aux4,suma,zuma,cons,rznLog,rzn,prob,alea,resultado,C,A,varianza,MediaDiff;
                                                                                           ^
./FuncionesFast-Final.h:166:94: warning: unused variable 'A' [-Wunused-variable]
    double CSiDiff,CNoDiff,Cest,Mu,aux1,aux4,suma,zuma,cons,rznLog,rzn,prob,alea,resultado,C,A,varianza,MediaDiff;
                                                                                             ^
./FuncionesFast-Final.h:166:105: warning: unused variable 'MediaDiff' [-Wunused-variable]
    double CSiDiff,CNoDiff,Cest,Mu,aux1,aux4,suma,zuma,cons,rznLog,rzn,prob,alea,resultado,C,A,varianza,MediaDiff;
                                                                                                        ^
BAGS.c:25:43: warning: unused variable 'rate' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;
                                          ^
BAGS.c:18:80: warning: variable 'ResSgmA' set but not used [-Wunused-but-set-variable]
    double ResRho1,ResRho2,ResRho3,ResRho4,ResSgmA1,ResSgmA2,ResSgmA3,ResSgmA4,ResSgmA;
                                                                               ^
BAGS.c:25:48: warning: unused variable 'resI' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;
                                               ^
BAGS.c:25:28: warning: unused variable 'escala3' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;
                           ^
BAGS.c:25:36: warning: unused variable 'escala' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;
                                   ^
BAGS.c:25:12: warning: unused variable 'escala1' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;
           ^
BAGS.c:25:20: warning: unused variable 'escala2' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;
                   ^
BAGS.c:24:12: warning: unused variable 'formaAux' [-Wunused-variable]
    double formaAux;
           ^
BAGS.c:15:15: warning: variable 'AaPi' set but not used [-Wunused-but-set-variable]
    double Mm,AaPi,Ade,Ss,Rr,c0,prob,alea,forma1,forma2,shape1,shape2;
              ^
BAGS.c:335:63: warning: variable 'ResSgmA' set but not used [-Wunused-but-set-variable]
    double ResRho1,ResRho2,ResRho3,ResSgmA1,ResSgmA2,ResSgmA3,ResSgmA;
                                                              ^
BAGS.c:342:36: warning: unused variable 'escala' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                   ^
BAGS.c:342:28: warning: unused variable 'escala3' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                           ^
BAGS.c:332:15: warning: variable 'AaPi' set but not used [-Wunused-but-set-variable]
    double Mm,AaPi,Ade,Ss,Rr,c0,prob,alea,forma1,forma2,shape1,shape2;
              ^
BAGS.c:342:48: warning: unused variable 'resI' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                               ^
BAGS.c:342:43: warning: unused variable 'rate' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                          ^
BAGS.c:341:12: warning: unused variable 'formaAux' [-Wunused-variable]
    double formaAux;
           ^
BAGS.c:342:20: warning: unused variable 'escala2' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                   ^
BAGS.c:342:12: warning: unused variable 'escala1' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
           ^
BAGS.c:592:12: warning: unused variable 'formaAux' [-Wunused-variable]
    double formaAux;
           ^
BAGS.c:586:46: warning: variable 'ResSgmA' set but not used [-Wunused-but-set-variable]
    double ResRho1,ResRho2,ResSgmA1,ResSgmA2,ResSgmA;
                                             ^
BAGS.c:593:43: warning: unused variable 'rate' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                          ^
BAGS.c:593:48: warning: unused variable 'resI' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                               ^
BAGS.c:583:15: warning: variable 'AaPi' set but not used [-Wunused-but-set-variable]
    double Mm,AaPi,Ade,Ss,Rr,c0,prob,alea,forma1,forma2,shape1,shape2;
              ^
BAGS.c:593:12: warning: unused variable 'escala1' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
           ^
BAGS.c:593:20: warning: unused variable 'escala2' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                   ^
BAGS.c:593:28: warning: unused variable 'escala3' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                           ^
BAGS.c:593:36: warning: unused variable 'escala' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                   ^
BAGS.c:786:36: warning: unused variable 'escala' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                   ^
BAGS.c:779:29: warning: variable 'ResSgmA' set but not used [-Wunused-but-set-variable]
    double ResRho1,ResSgmA1,ResSgmA;
                            ^
BAGS.c:786:28: warning: unused variable 'escala3' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                           ^
BAGS.c:786:48: warning: unused variable 'resI' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                               ^
BAGS.c:786:43: warning: unused variable 'rate' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                                          ^
BAGS.c:785:12: warning: unused variable 'formaAux' [-Wunused-variable]
    double formaAux;
           ^
BAGS.c:776:15: warning: variable 'AaPi' set but not used [-Wunused-but-set-variable]
    double Mm,AaPi,Ade,Ss,Rr,c0,prob,alea,forma1,forma2,shape1,shape2;
              ^
BAGS.c:786:20: warning: unused variable 'escala2' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
                   ^
BAGS.c:786:12: warning: unused variable 'escala1' [-Wunused-variable]
    double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
           ^
40 warnings generated.
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o BAGS.so BAGS.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-BAGS/00new/BAGS/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 (BAGS)

Tests output

Example timings

BAGS.Rcheck/BAGS-Ex.timings

name	user	system	elapsed
AnnotationMFGO	0.050	0.012	0.062
BAGS-package	0.000	0.000	0.001
DataGeneSets	18.340	1.025	19.600
Gibbs2	31.622	1.274	34.221
Gibbs3	0.000	0.000	0.001
Gibbs4	0.000	0.000	0.001
Gibbs5	0.000	0.000	0.001
MCMCDataSet	20.197	1.386	22.401
ReadGMT	0.000	0.000	0.001