Multiple platform build/check report for BioC 3.20 - CHECK results for BAGS on nebbiolo2

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 nebbiolo2

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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BAGS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BAGS_2.46.0.tar.gz

StartedAt: 2024-12-19 20:09:18 -0500 (Thu, 19 Dec 2024)

EndedAt: 2024-12-19 20:14:03 -0500 (Thu, 19 Dec 2024)

EllapsedTime: 285.1 seconds

RetCode: 0

Status: OK

CheckDir: BAGS.Rcheck

Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:BAGS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings BAGS_2.46.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/BAGS.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
Gibbs2       12.913  0.174  13.088
MCMCDataSet   8.200  0.139   8.340
DataGeneSets  7.525  0.118   7.642
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/BAGS.Rcheck/00check.log’
for details.

Installation output

BAGS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL BAGS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘BAGS’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c BAGS.c -o BAGS.o
In file included from BAGS.c:8:
FuncionesFast-Final.h: In function ‘BetaFunCSDiff2’:
FuncionesFast-Final.h:145:70: warning: unused variable ‘YMu1’ [-Wunused-variable]
  145 |     double media1,media,varianza1,varianza,resultado,varaux0,varaux1,YMu1;
      |                                                                      ^~~~
FuncionesFast-Final.h: In function ‘AlfaFunCS’:
FuncionesFast-Final.h:166:105: warning: unused variable ‘MediaDiff’ [-Wunused-variable]
  166 |     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]
  166 |     double CSiDiff,CNoDiff,Cest,Mu,aux1,aux4,suma,zuma,cons,rznLog,rzn,prob,alea,resultado,C,A,varianza,MediaDiff;
      |                                                                                              ^
FuncionesFast-Final.h:166:92: warning: unused variable ‘C’ [-Wunused-variable]
  166 |     double CSiDiff,CNoDiff,Cest,Mu,aux1,aux4,suma,zuma,cons,rznLog,rzn,prob,alea,resultado,C,A,varianza,MediaDiff;
      |                                                                                            ^
BAGS.c: In function ‘Gibbs5’:
BAGS.c:25:48: warning: unused variable ‘resI’ [-Wunused-variable]
   25 |     double escala1,escala2,escala3,escala,rate,resI;
      |                                                ^~~~
BAGS.c:25:43: warning: unused variable ‘rate’ [-Wunused-variable]
   25 |     double escala1,escala2,escala3,escala,rate,resI;
      |                                           ^~~~
BAGS.c:25:36: warning: unused variable ‘escala’ [-Wunused-variable]
   25 |     double escala1,escala2,escala3,escala,rate,resI;
      |                                    ^~~~~~
BAGS.c:25:28: warning: unused variable ‘escala3’ [-Wunused-variable]
   25 |     double escala1,escala2,escala3,escala,rate,resI;
      |                            ^~~~~~~
BAGS.c:25:20: warning: unused variable ‘escala2’ [-Wunused-variable]
   25 |     double escala1,escala2,escala3,escala,rate,resI;
      |                    ^~~~~~~
BAGS.c:25:12: warning: unused variable ‘escala1’ [-Wunused-variable]
   25 |     double escala1,escala2,escala3,escala,rate,resI;
      |            ^~~~~~~
BAGS.c:24:12: warning: unused variable ‘formaAux’ [-Wunused-variable]
   24 |     double formaAux;
      |            ^~~~~~~~
BAGS.c:18:80: warning: variable ‘ResSgmA’ set but not used [-Wunused-but-set-variable]
   18 |     double ResRho1,ResRho2,ResRho3,ResRho4,ResSgmA1,ResSgmA2,ResSgmA3,ResSgmA4,ResSgmA;
      |                                                                                ^~~~~~~
BAGS.c:15:15: warning: variable ‘AaPi’ set but not used [-Wunused-but-set-variable]
   15 |     double Mm,AaPi,Ade,Ss,Rr,c0,prob,alea,forma1,forma2,shape1,shape2;
      |               ^~~~
BAGS.c: In function ‘Gibbs4’:
BAGS.c:342:48: warning: unused variable ‘resI’ [-Wunused-variable]
  342 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |                                                ^~~~
BAGS.c:342:43: warning: unused variable ‘rate’ [-Wunused-variable]
  342 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |                                           ^~~~
BAGS.c:342:36: warning: unused variable ‘escala’ [-Wunused-variable]
  342 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |                                    ^~~~~~
BAGS.c:342:28: warning: unused variable ‘escala3’ [-Wunused-variable]
  342 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |                            ^~~~~~~
BAGS.c:342:20: warning: unused variable ‘escala2’ [-Wunused-variable]
  342 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |                    ^~~~~~~
BAGS.c:342:12: warning: unused variable ‘escala1’ [-Wunused-variable]
  342 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |            ^~~~~~~
BAGS.c:341:12: warning: unused variable ‘formaAux’ [-Wunused-variable]
  341 |     double formaAux;
      |            ^~~~~~~~
BAGS.c:335:63: warning: variable ‘ResSgmA’ set but not used [-Wunused-but-set-variable]
  335 |     double ResRho1,ResRho2,ResRho3,ResSgmA1,ResSgmA2,ResSgmA3,ResSgmA;
      |                                                               ^~~~~~~
BAGS.c:332:15: warning: variable ‘AaPi’ set but not used [-Wunused-but-set-variable]
  332 |     double Mm,AaPi,Ade,Ss,Rr,c0,prob,alea,forma1,forma2,shape1,shape2;
      |               ^~~~
BAGS.c: In function ‘Gibbs3’:
BAGS.c:593:48: warning: unused variable ‘resI’ [-Wunused-variable]
  593 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |                                                ^~~~
BAGS.c:593:43: warning: unused variable ‘rate’ [-Wunused-variable]
  593 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |                                           ^~~~
BAGS.c:593:36: warning: unused variable ‘escala’ [-Wunused-variable]
  593 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |                                    ^~~~~~
BAGS.c:593:28: warning: unused variable ‘escala3’ [-Wunused-variable]
  593 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |                            ^~~~~~~
BAGS.c:593:20: warning: unused variable ‘escala2’ [-Wunused-variable]
  593 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |                    ^~~~~~~
BAGS.c:593:12: warning: unused variable ‘escala1’ [-Wunused-variable]
  593 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |            ^~~~~~~
BAGS.c:592:12: warning: unused variable ‘formaAux’ [-Wunused-variable]
  592 |     double formaAux;
      |            ^~~~~~~~
BAGS.c:586:46: warning: variable ‘ResSgmA’ set but not used [-Wunused-but-set-variable]
  586 |     double ResRho1,ResRho2,ResSgmA1,ResSgmA2,ResSgmA;
      |                                              ^~~~~~~
BAGS.c:583:15: warning: variable ‘AaPi’ set but not used [-Wunused-but-set-variable]
  583 |     double Mm,AaPi,Ade,Ss,Rr,c0,prob,alea,forma1,forma2,shape1,shape2;
      |               ^~~~
BAGS.c: In function ‘Gibbs2’:
BAGS.c:786:48: warning: unused variable ‘resI’ [-Wunused-variable]
  786 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |                                                ^~~~
BAGS.c:786:43: warning: unused variable ‘rate’ [-Wunused-variable]
  786 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |                                           ^~~~
BAGS.c:786:36: warning: unused variable ‘escala’ [-Wunused-variable]
  786 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |                                    ^~~~~~
BAGS.c:786:28: warning: unused variable ‘escala3’ [-Wunused-variable]
  786 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |                            ^~~~~~~
BAGS.c:786:20: warning: unused variable ‘escala2’ [-Wunused-variable]
  786 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |                    ^~~~~~~
BAGS.c:786:12: warning: unused variable ‘escala1’ [-Wunused-variable]
  786 |     double escala1,escala2,escala3,escala,rate,resI;    // Aqui tengo duda
      |            ^~~~~~~
BAGS.c:785:12: warning: unused variable ‘formaAux’ [-Wunused-variable]
  785 |     double formaAux;
      |            ^~~~~~~~
BAGS.c:779:29: warning: variable ‘ResSgmA’ set but not used [-Wunused-but-set-variable]
  779 |     double ResRho1,ResSgmA1,ResSgmA;
      |                             ^~~~~~~
BAGS.c:776:15: warning: variable ‘AaPi’ set but not used [-Wunused-but-set-variable]
  776 |     double Mm,AaPi,Ade,Ss,Rr,c0,prob,alea,forma1,forma2,shape1,shape2;
      |               ^~~~
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o BAGS.so BAGS.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-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	0.020	0.003	0.023
BAGS-package	0	0	0
DataGeneSets	7.525	0.118	7.642
Gibbs2	12.913	0.174	13.088
Gibbs3	0	0	0
Gibbs4	0.001	0.000	0.000
Gibbs5	0	0	0
MCMCDataSet	8.200	0.139	8.340
ReadGMT	0	0	0