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This page was generated on 2021-10-22 12:03:55 -0400 (Fri, 22 Oct 2021).

CHECK results for BAGS on nebbiolo2

To the developers/maintainers of the BAGS package:
- Please 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 How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 108/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BAGS 2.33.0  (landing page)
Alejandro Quiroz-Zarate
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/BAGS
git_branch: master
git_last_commit: 817b625
git_last_commit_date: 2021-05-19 11:51:16 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BAGS
Version: 2.33.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BAGS.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BAGS_2.33.0.tar.gz
StartedAt: 2021-10-21 19:10:17 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 19:11:40 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 82.7 seconds
RetCode: 0
Status:   OK  
CheckDir: BAGS.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:BAGS.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings BAGS_2.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/BAGS.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BAGS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BAGS’ version ‘2.33.0’
* 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
* 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 R 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
Gibbs2       44.979  0.403  45.383
MCMCDataSet   7.860  0.087   7.949
DataGeneSets  7.522  0.143   7.667
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/BAGS.Rcheck/00check.log’
for details.



Installation output

BAGS.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL BAGS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘BAGS’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.14-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-3.14-bioc/R/lib -L/usr/local/lib -o BAGS.so BAGS.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/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

nameusersystemelapsed
AnnotationMFGO0.0770.0000.078
BAGS-package000
DataGeneSets7.5220.1437.667
Gibbs244.979 0.40345.383
Gibbs3000
Gibbs40.0000.0000.001
Gibbs5000
MCMCDataSet7.8600.0877.949
ReadGMT000