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This page was generated on 2024-11-25 11:38 -0500 (Mon, 25 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4748
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4459
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4349
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 123/2272HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BAGS 2.47.0  (landing page)
Alejandro Quiroz-Zarate
Snapshot Date: 2024-11-24 13:40 -0500 (Sun, 24 Nov 2024)
git_url: https://git.bioconductor.org/packages/BAGS
git_branch: devel
git_last_commit: 323f3fe
git_last_commit_date: 2024-10-29 09:39:57 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for BAGS on palomino7

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: 2.47.0
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BAGS.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BAGS_2.47.0.tar.gz
StartedAt: 2024-11-24 22:22:46 -0500 (Sun, 24 Nov 2024)
EndedAt: 2024-11-24 22:24:10 -0500 (Sun, 24 Nov 2024)
EllapsedTime: 83.6 seconds
RetCode: 0
Status:   OK  
CheckDir: BAGS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BAGS.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings BAGS_2.47.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/BAGS.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 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 'BAGS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BAGS' version '2.47.0'
* 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 'BAGS' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 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 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 for x64 is not available
File 'E:/biocbuild/bbs-3.21-bioc/R/library/BAGS/libs/x64/BAGS.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
Gibbs2       20.91   1.26   22.17
DataGeneSets 12.61   1.27   14.26
MCMCDataSet  12.25   1.27   13.52
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/BAGS.Rcheck/00check.log'
for details.

Installation output

BAGS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL BAGS
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'BAGS' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc  -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 -s -static-libgcc -o BAGS.dll tmp.def BAGS.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-BAGS/00new/BAGS/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 (BAGS)

Tests output


Example timings

BAGS.Rcheck/BAGS-Ex.timings

nameusersystemelapsed
AnnotationMFGO0.020.010.03
BAGS-package000
DataGeneSets12.61 1.2714.26
Gibbs220.91 1.2622.17
Gibbs3000
Gibbs4000
Gibbs5000
MCMCDataSet12.25 1.2713.52
ReadGMT000